PK 4C09+P * * refs.MYDr? 9 Bohuslavek, J.
Payne, J. W.
Liu, Y.
Bolton, H.
Xun, L. Y. 2001p Cloning, sequencing, and characterization of a gene cluster involved in EDTA degradation from the bacterium BNC1 688-695& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SP STRAIN IGTS8; PHOTOCHEMICAL DEGRADATION;
PRISTINAMYCIN-IIB; BACILLUS-SUBTILIS; ESCHERICHIA-COLI;
PURIFICATION; MONOOXYGENASE; ETHYLENEDIAMINETETRAACETATE;
DESULFURIZATION; OPERON EDTA is a chelating agent, widely used in many industries. Because of its ability to mobilize heavy metals and radionuclides, it can be an environmental pollutant, The EDTA monooxygenases that initiate EDTA degradation have been purified and characterized in bacterial strains BNCl and DSM 9103. However, the genes encoding the enzymes have not been reported. The EDTA monooxygenase gene was cloned by probing a genomic library of strain BNCl with a probe generated from the N-terminal amino acid sequence of the monooxygenase, Sequencing of the cloned DNA fragment revealed a gene cluster containing eight genes. Two of the genes, emoA and emoB, were expressed in Escherichia coli, and the gene products, EmoA and EmoB, were purified and characterized, Both experimental data and sequence analysis showed that EmoA is a reduced flavin mononucleotide-utilizing monooxygenase and that EmoB is an NADH:flavin mononucleotide oxidoreductase, The two-enzyme system oxidized EDTA to ethylenediaminediacetate (EDDA) and nitrilotriacetate (NTA) to iminodiacetate (IDA) with the production of glyoxylate, The emoA and emoB genes were cotranscribed when BNCl cells were grown on EDTA, Other genes in the cluster encoded a hypothetical transport system, a putative regulatory protein, and IDA oxidase that oxidizes IDA and EDDA. We concluded that this gene cluster is responsible for the initial steps of EDTA and NTA degradation. Using Smart Source Parsing ALDER AC, 1990, V24, P733, WATER RES ALTSCHUL SF, 1990, V87, P5509, P NATL ACAD SCI USA AUSUBEL MF, 1993, CURRENT PROTOCOLS MO BELLY RT, 1975, V29, P787, APPL MICROBIOL BERGERS PJM, 1994, V28, P639, WATER RES BLANC V, 1995, V177, P5206, J BACTERIOL BOLTON H, 1993, V22, P125, J ENVIRON QUAL CLEVELAND JM, 1981, V200, P1506, SCIENCE DEJONG J, 1991, V553, P243, J CHROMATOGR DOWER WJ, 1988, V16, P6127, NUCLEIC ACIDS RES DOWNING WL, 1990, V172, P1621, J BACTERIOL GRAY KA, 1996, V14, P1705, NAT BIOTECHNOL JAGOUEIX S, 1994, V44, P379, INT J SYST BACTERIOL JANAKIRAMAN RS, 1997, V179, P5138, J BACTERIOL JORDAN DEC, 1984, V1, BERGEYS MANUAL SYSTE KAHNERT A, 2000, V182, P2869, J BACTERIOL KARI FG, 1995, V29, P1008, ENVIRON SCI TECHNOL KARI FG, 1995, V29, P2814, ENVIRON SCI TECHNOL KLUNER T, 1998, V49, P194, APPL MICROBIOL BIOT KNOBEL HR, 1996, V178, P6123, J BACTERIOL LAEMMLI UK, 1970, V4, P680, NATURE LAUFF JJ, 1990, V56, P3346, APPL ENVIRON MICROB LEI BF, 1996, V178, P5699, J BACTERIOL LOCKHART HB, 1975, V9, P1035, ENVIRON SCI TECHNOL LUDWIG W, 1999, V65, P752, ASM NEWS MADSEN EL, 1985, V50, P342, APPL ENVIRON MICROB MATSUDAIRA P, 1987, V262, P10035, J BIOL CHEM MEANS JL, 1978, V200, P1477, SCIENCE MOOS M, 1988, V263, P6005, J BIOL CHEM NATARAJAN P, 1973, V77, P2049, J PHYS CHEM-US NEIDHARDT RC, 1996, ESCHERICHIA COLI SAL NISHIYA Y, 1998, V438, P263, FEBS LETT NORTEMANN B, 1992, V58, P671, APPL ENVIRON MICROB NORTEMANN B, 1999, V51, P751, APPL MICROBIOL BIOT PARK JT, 1998, V180, P1215, J BACTERIOL PAYNE JW, 1998, V180, P3823, J BACTERIOL PAYNE JW, 1999, THESIS WASHINGTON ST PIDDINGTON CS, 1995, V61, P468, APPL ENVIRON MICROB RUDNER DZ, 1991, V173, P1388, J BACTERIOL SAMBROOK J, 1989, MOL CLONING LAB MANU SILANPAA M, 1997, V152, P85, REV ENVIRON CONTAM T SYLVANEN AC, 1996, V178, P6182, J BACTERIOL THIBAUT D, 1995, V177, P5199, J BACTERIOL THOM NS, 1975, V189, P347, P R SOC LOND B TIEDJE JM, 1977, V6, P21, J ENVIRON QUAL TIEDJE JM, 1975, V30, P327, APPL MICROBIOL TU SC, 1995, V62, P615, PHOTOCHEM PHOTOBIOL UETZ T, 1993, V3, P423, BIODEGRADATION UETZ T, 1992, V174, P1179, J BACTERIOL VERMEIJ P, 1999, V32, P913, MOL MICROBIOL WITSCHEL M, 1999, V145, P973, MICROBIOL-UK 4 WITSCHEL M, 1997, V179, P6937, J BACTERIOL XU YR, 1997, V179, P1112, J BACTERIOL XUN LY, 2000, V66, P481, APPL ENVIRON MICROB Washington State Univ,Sch Mol Biosci,Pullman//WA/99164 (REPRINT); Washington State Univ,Sch Mol Biosci,Pullman//WA/99164; Pacific NW Natl Labs,Environm Microbiol Grp,Richland//WA/99352 {? Chang, Y. J.
Peacock, A. D.
Long, P. E.
Stephen, J. R.
McKinley, J. P.
Macnaughton, S. J.
Hussain, A.
Saxton, A. M.
White, D. C. 2001j Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site 3149-3160& Applied and Environmental Microbiology 67 7 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): DISSIMILATORY SULFITE REDUCTASE; FATTY-ACID
BIOMARKERS; RIBOSOMAL-RNA; COMMUNITY STRUCTURE;
DESULFOVIBRIO-VULGARIS; HYBRIDIZATION; SEDIMENTS; PROFILES; GENES;
PCRM Microbially mediated reduction and immobilization of U(VI) to U(TV) plays a role in both natural attenuation and accelerated bioremediation of uranium contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex,, was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from F-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least,52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0, Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within F-Proteobacteria were mainly recovered from low-uranium (less than or equal to 302 ppb) samples. One Desulfotomaculum like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001), This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. Using Smart Source Parsingx *DEP EN, 2000, GJO2000169TAR UMTRA ABDELOUAS A, 1999, V38, P433, URANIUM MINERALOGY G ABDELOUAS A, 2000, V250, P21, SCI TOTAL ENVIRON AGRESTI A, 1996, ONTRO CATEGORICAL DA BRECKLINGHAUS J, 1981, V21, P65, Z ALLG MIKROBIOL CANFIELD DE, 1991, V251, P1471, SCIENCE CYPIONKA H, 2000, V54, P827, ANNU REV MICROBIOL DEVEREUX R, 1996, V20, P23, FEMS MICROBIOL ECOL DEVEREUX R, 1993, P131, SULFATE REDUCING BAC DOWLING NJE, 1986, V132, P1815, J GEN MICROBIOL EDLUND A, 1985, V26, P982, J LIPID RES EHRLICH HL, 1996, GEOMICROBIOLOGY FRUND C, 1992, V58, P70, APPL ENVIRON MICROB GUCKERT JB, 1985, V31, P147, FEMS MICROBIOL ECOL HRISTOVA KR, 2000, V2, P143, ENVIRON MICROBIOL JONES HE, 1976, V16, P425, Z ALLG MIKROBIOL KARKHOFFSCHWEIZ.RR, 1995, V61, P290, APPL ENVIRON MICROB KATES M, 1986, TECHNIQUES LIPIDOLOG KOHRING LL, 1994, V119, P303, FEMS MICROBIOL LETT LEDUC LG, 1997, V13, P453, WORLD J MICROB BIOT LLOBETBROSSA E, 1998, V64, P2691, APPL ENVIRON MICROB LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB LOVLEY DR, 1993, V113, P41, MAR GEOL MANZ W, 1998, V25, P43, FEMS MICROBIOL ECOL MCKINLEY JP, 1995, V43, P586, CLAY CLAY MINER MCKINLEY JP, 1997, V14, P23, GEOMICROBIOL J MINZ D, 1999, V65, P4666, APPL ENVIRON MICROB ODOM JM, 1993, P189, SULFATE REDUCING BAC OLEARY WM, 1988, V1, P172, MICROBIAL LIPIDS PARKES RJ, 1985, V31, P361, FEMS MICROBIOL ECOL POLZ MF, 1998, V64, P3724, APPL ENVIRON MICROB RABUS R, 1996, V62, P3605, APPL ENVIRON MICROB RAMSING NB, 1993, V59, P3840, APPL ENVIRON MICROB RAMSING NB, 1996, V62, P1391, APPL ENVIRON MICROB RINGELBERG DB, 1994, V14, P9, FEMS MICROBIOL ECOL RINGELBERG DB, 1989, V62, P39, FEMS MICROBIOL ECOL SINGLETON RJ, 1993, P1, SULFATE REDUCING BAC STACKEBRANDT E, 1997, V47, P1134, INT J SYST BACTERIOL STEPHEN JR, 1999, V65, P95, APPL ENVIRON MICROB STRUNK O, 1996, ARB SOFTWARE ENV SEQ SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB TEBO BM, 1998, V162, P193, FEMS MICROBIOL LETT TREXLER JC, 1993, V74, P1629, ECOLOGY VAINSHTEIN M, 1992, V15, P554, SYST APPL MICROBIOL VOORDOUW G, 1990, V56, P3748, APPL ENVIRON MICROB VOORDOUW, 1990, P37, MICROBIOLOGY BIOCH S WAGNER M, 1998, V180, P2975, J BACTERIOL WAWER C, 1995, V63, P4360, APPL ENVIRON MICROB WHITE DC, 1979, V40, P51, OECOLOGIA BERLIN WHITE DC, 1997, V5, P319, IN SITU ON SITE BIOR WIDDEL F, 1988, P469, BIOL ANAEROBIC MICROg Univ Tennessee,Ctr Biomarker Anal,10515 Res Dr,Suite 300/Knoxville//TN/37932 (REPRINT); Univ Tennessee,Ctr Biomarker Anal,Knoxville//TN/37932; Univ Tennessee,Dept Anim Sci,Knoxville//TN/37932; Pacific NW Natl Lab,Environm Technol,Richland//WA/99352; Hort Res Int,Crop & Weed Sci,Warwick CV35 9EF//England/; AEA Technol Environm,Abingdon OX14 3BD/Oxon/England/ R? * Chaudhuri, S. K.
Lack, J. G.
Coates, J. D. 2001E Biogenic magnetite formation through anaerobic biooxidation of Fe(II) 2844-2848& Applied and Environmental Microbiology 67 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): BANDED IRON-FORMATIONS; FERROUS IRON; NEUTRAL PH;
GREEN RUST; OXIDATION; BACTERIA; NITRATE; REDUCTION; SEDIMENTS;
AMMONIUMv The presence of isotopically Light carbonates in association with fine-grained magnetite is considered to be primarily due to the reduction of Fe(III) by Fe(III)-reducing bacteria in the environment. Here, we report on magnetite formation by biooxidation of Fe(II) coupled to denitrification, This metabolism offers an alternative environmental source of biogenic magnetite. Using Smart Source Parsing AHN JH, 1990, V250, P111, SCIENCE BAUR ME, 1985, V80, P270, ECON GEOL BAZYLINSKI DA, 1988, V334, P518, NATURE BENZ M, 1998, V169, P159, ARCH MICROBIOL BROWN DA, 1995, V33, P1321, CAN MINERAL 6 BRUCE RA, 1999, V1, P319, ENVIRON MICROBIOL CANFIELD DE, 1998, V396, P450, NATURE CASTRO LO, 1994, V89, P1384, ECON GEOL BULL SOC CLOUD PE, 1973, V68, P1135, ECON GEOL COATES JD, 1999, V65, P5234, APPL ENVIRON MICROB DOMINGO C, 1994, V165, P244, J COLLOID INTERF SCI DREVER JI, 1974, V85, P1099, GEOL SOC AM BULL DRISSI SH, 1995, V37, P2025, CORROS SCI EHRENREICH A, 1994, V60, P4517, APPL ENVIRON MICROB GIBBSEGGAR Z, 1999, V168, P1, EARTH PLANET SC LETT GOLD T, 1992, V89, P6045, P NATL ACAD SCI USA HAFENBRADL D, 1996, V166, P308, ARCH MICROBIOL HANSEN HCB, 1998, V33, P87, CLAY MINER HANSEN HCB, 1996, V30, P2053, ENVIRON SCI TECHNOL HOLLAND HD, 1984, CHEM EVOLUTION ATMOS HUNGATE RE, 1969, V3, P117, METHODS MICROBIOLO B ISLEY AE, 1995, V103, P169, J GEOL KARLIN R, 1987, V326, P490, NATURE KRISCHVINK JL, 1984, V12, P559, GEOLOGY LOVELY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVELY DR, 1987, V330, P252, NATURE LOVELY DL, 1986, V52, P751, APPL ENVIRON MICROB MANCINELLI RL, 1988, V18, P311, ORIGINS LIFE MICHAELIDOU U, 2000, P271, PERCHLORATE ENV MOLINIER M, 1997, P4061, J CHEM SOC DALT 1107 NEALSON KH, 1990, V290, P35, AM J SCI A STRAUB KL, 1996, V62, P1458, APPL ENVIRON MICROB WALKER JCG, 1984, V309, P340, NATURE WIDDEL F, 1993, V362, P834, NATURE So Illinois Univ,Dept Microbiol,Mailcode 6508/Carbondale//IL/62901 (REPRINT); So Illinois Univ,Dept Microbiol,Carbondale//IL/62901 ? X 3 Coppi, M. V.
Leang, C.
Sandler, S. J.
Lovley, D. R. 2001< Development of a genetic system for Geobacter sulfurreducens 3180-3187& Applied and Environmental Microbiology 67 7 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): ESCHERICHIA-COLI; VECTORS; REDUCTION;
TRANSFORMATION; CONSTRUCTION; PLASMIDS; ELECTROPORATION;
DESULFOVIBRIO; DERIVATIVES; EXPRESSION# Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these organisms, a genetic system was developed for Geobacter sulfurreducens, The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established. A protocol for the introduction of foreign DNA into G. sulfurreducens by electroporation was also developed, Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in G. sulfurreducens. Ln particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism, When the information and novel methods described above were utilized, the nifD gene of G, sulfurreducens was disrupted by the single-step gene replacement method, Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of G, sulfurreducens to grow in medium lacking a source of fixed nitrogen. Expression of the nifD gene in trans complemented this phenotype, This paper constitutes the first report of genetic manipulation of a member of the Geobacter genus. Using Smart Source Parsing *BETH RES LAB, 1986, V8, P9, BETHESDA RES LAB FOC AMANN E, 1983, V25, P167, GENE ANTOINE R, 1992, V6, P1785, MOL MICROBIOL BATTISTI JM, 1999, V65, P3441, APPL ENVIRON MICROB BAZYLINSKI DA, 2000, V2, P266, ENVIRON MICROBIOL BOLIVAR F, 1978, V4, P121, GENE CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB DAVISON J, 1987, V51, P275, GENE DEAN DR, 1992, P763, BIOL NITROGEN FIXATI DEHIO M, 1998, V215, P223, GENE HANAHAN D, 1983, V166, P557, J MOL BIOL KOVACH ME, 1995, V166, P175, GENE LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 2000, P3, ENV MICROBE METAL IN LOVLEY DR, 1984, V48, P81, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 2000, IN PRESS PROKARYOTES LOVLEY DR, 1999, V1, P89, ENVIRON MICROBIOL MORALES VM, 1991, V97, P39, GENE NICKOLOFF JA, 1995, V47, METHODS MOL BIOL SER ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB ROUSSET M, 1991, V5, P1735, MOL MICROBIOL ROUSSET M, 1998, V39, P114, PLASMID RUSSELL CB, 1989, V171, P2609, J BACTERIOL SAMBROOK J, 1989, MOL CLONING LAB MANU SMITH CJ, 1995, V47, P161, METHOD MOL BIOL SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL TOYAMA H, 1998, V166, P1, FEMS MICROBIOL LETT UEDA T, 1995, V41, P235, CAN J MICROBIOL YANISCHPERRON C, 1985, V33, P103, GENE Univ Massachusetts,Morrill Sci Ctr IVN 203 Dept Microbiol,Amherst//MA/01003 (REPRINT); Univ Massachusetts,Morrill Sci Ctr IVN 203 Dept Microbiol,Amherst//MA/01003 a? 9 Holmes, D. E.
Finneran, K. T.
O'Neil, R. A.
Lovley, D. R. 2002 Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments 2300-2306& Applied and Environmental Microbiology 68 5 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; SULFATE-REDUCING BACTERIA;
FE(III) REDUCTION; SULFURREDUCENS; OXIDATION; POPULATIONS;
GROUNDWATER; DNAY Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe (III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe (III) -reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments. Using Smart Source Parsing? Q Hurt, R. A.
Qiu, X. Y.
Wu, L. Y.
Roh, Y.
Palumbo, A. V.
Tiedje, J. M.
Zhou, J. H. 2001= Simultaneous recovery of RNA and DNA from soils and sediments 4495-4503& Applied and Environmental Microbiology 67 10 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): RIBOSOMAL-RNA; DIRECT EXTRACTION; MESSENGER-RNA;
BACTERIAL COMMUNITY; RNA/DNA RATIO; MICROBIAL DNA; RAPID METHOD;
DIVERSITY; PURIFICATION; MICROORGANISMS Recovery of mRNA from environmental samples for measurement of in situ metabolic activities is a significant challenge. A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting our previous grinding-based cell lysis method (Zhou et al., Appl. Environ. Microbiol. 62:316-322, 1996) for DNA extraction. One of the key differences is that the samples are ground in a denaturing solution at a temperature below 0 degreesC to inactivate nuclease activity. Two different methods were evaluated for separating RNA from DNA. Among the methods examined for RNA purification, anion exchange resin gave the best results in terms of RNA integrity, yield, and purity. With the optimized protocol, intact RNA and high-molecular-weight DNA were simultaneously recovered from 19 soil and stream sediment samples of diverse composition. The RNA yield from these samples ranged from 1.4 to 56 mug g of soil(-1) dry weight), whereas the DNA yield ranged from 23 to 435 mug g(-1). In addition, studies with the same soil sample showed that the DNA yield was, on average, 40% higher than that in our previous procedure and 68% higher than that in a commercial bead milling method. For the majority of the samples, the DNA and RNA recovered were of sufficient purity for nuclease digestion, microarray hybridization, and PCR or reverse transcription-PCR amplification. Using Smart Source Parsing ALM EW, 2000, V40, P153, J MICROBIOL METH AMANN RI, 1995, V59, P143, MICROBIOL REV AUSUBEL FM, 1995, CURRENT PROTOCOLS MO BORNEMAN J, 1997, V29, P1621, SOIL BIOL BIOCHEM BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BRAKER G, 2000, V66, P2096, APPL ENVIRON MICROB CHOMCZYNSKI P, 1987, V162, P156, ANAL BIOCHEM DELLANNO A, 1998, V64, P3238, APPL ENVIRON MICROB DUARTE GF, 1998, V32, P21, J MICROBIOL METH FABIANO M, 1995, V15, P393, POLAR BIOL FLEMING JT, 1993, V27, P1068, ENVIRON SCI TECHNOL FRIES MR, 1994, V60, P2802, APPL ENVIRON MICROB FROSTEGARD A, 1999, V65, P5409, APPL ENVIRON MICROB GEE GW, 1986, V9, P383, AGRONOMY GREAVES MP, 1969, V1, P317, SOIL BIOL BIOCHEM HOLBEN WE, 1988, V54, P703, APPL ENVIRON MICROB HUGENHOLTZ P, 1998, V180, P4765, J BACTERIOL JEFFREY WH, 1996, V10, P87, AQUAT MICROB ECOL JEFFREY WH, 1994, V60, P1814, APPL ENVIRON MICROB JOHNSTON WH, 1996, P1, MOL MICROBIAL ECOLOG KERKHOF L, 1993, V59, P1303, APPL ENVIRON MICROB KILMER VJ, 1949, V68, P15, SOIL SCI LOVELL CR, 1994, V20, P161, J MICROBIOL METH MALIK M, 1994, V20, P183, J MICROBIOL METH MANIATIS T, 1982, MOL CLONING LAB MANU MCLEAN EO, 1982, V9, P199, AGRON MONOGR MORAN MA, 1993, V59, P915, APPL ENVIRON MICROB MUTTRAY AF, 1999, V38, P348, MICROBIAL ECOL OGRAM A, 1995, V61, P763, APPL ENVIRON MICROB OGRAM A, 1988, V22, P982, ENVIRON SCI TECHNOL OGRAM A, 1987, V7, P57, J MICROBIOL METH OGRAM AV, 1994, V60, P393, APPL ENVIRON MICROB PICARD C, 1992, V58, P2717, APPL ENVIRON MICROB PICHARD SL, 1993, V59, P451, APPL ENVIRON MICROB PURDY KJ, 1996, V62, P3905, APPL ENVIRON MICROB RAUHUT R, 1999, V23, P353, FEMS MICROBIOL REV ROMANOWSKI G, 1991, V57, P1057, APPL ENVIRON MICROB SELENSKA S, 1992, V1, P41, MICROB RELEASES STACKEBRANDT E, 1993, V7, P232, FASEB J STEFFAN RJ, 1988, V54, P2908, APPL ENVIRON MICROB TEBBE CC, 1993, V59, P2657, APPL ENVIRON MICROB TIEDJE JM, 1997, P35, PROGR MICROBIAL ECOL TSAI YL, 1991, V57, P1070, APPL ENVIRON MICROB TSAI YL, 1991, V57, P765, APPL ENVIRON MICROB VESICO PA, 1995, V21, P225, J MICROBIOL METH WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV YU ZT, 1999, V45, P269, CAN J MICROBIOL ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ? j ; Korenevsky, A. A.
Vinogradov, E.
Gorby, Y.
Beveridge, T. J. 2002J Characterization of the lipopolysaccharides and capsules of Shewanella spp 4653-4657& Applied and Environmental Microbiology 68 9 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): PSEUDOMONAS-AERUGINOSA; GROWTH TEMPERATURE;
OUTER-MEMBRANE; FREEZE-SUBSTITUTION; POLYACRYLAMIDE GELS;
SERRATIA-MARCESCENS; PUTREFACIENS MR-1; CELL-WALLS; SURFACE;
ADHESION Electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis with silver staining and H-1, C-13, and P-31-nuclear magnetic resonance (NMR) were used to detect and characterize the lipopolysaccharides (LPSs) of several Shewanella species. Many expressed only rough LPS; however, approximately one-half produced smooth LPS (and/or capsular polysaccharides). Some LPSs were affected by growth temperature with increased chain length observed below 25degreesC. Maximum LPS heterogeneity was found at 15 to 20degreesC. Thin sections of freeze-substituted cells revealed that Shewanella oneidensis, S. algae, S. frigidimarina, and Shewanella sp. strain MR-4 possessed either O-side chains or capsular fringes ranging from 20 to 130 nm in thickness depending on the species. NMR detected unusual sugars in S. putrefaciens CN32 and S. algae BrYDL. It is possible that the ability of Shewanella to adhere to solid mineral phases (such as iron oxides) could be affected by the composition and length of surface polysaccharide polymers. These same polymers in S. algae may also contribute to this opportunistic pathogen's ability to promote infection. Using Smart Source Parsing ? U Lack, J. G.
Chaudhuri, S. K.
Kelly, S. D.
Kemner, K. M.
O'Connor, S. M.
Coates, J. D. 2002Z Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II) 2704-2710& Applied and Environmental Microbiology 68 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SP-NOV; FERROUS IRON; NEUTRAL PH; GEN-NOV;
(PER)CHLORATE-REDUCING BACTERIA; HUMIC SUBSTANCES; WASTE-DISPOSAL;
URANYL-ION; GREEN RUST; REDUCTION Adsorption of heavy metals and radionuclides (HMR) onto iron and manganese oxides has long been recognized as an important reaction for the immobilization of these compounds. However, in environments containing elevated concentrations of these HMR the adsorptive capacity of the iron and manganese oxides may well be exceeded, and the HMR can migrate as soluble compounds in aqueous systems. Here we demonstrate the potential of a bioremediative strategy for HMR stabilization in reducing environments based on the recently described anaerobic nitrate-dependent Fe(II) oxidation by Dechlorosoma species. Bio-oxidation of 10 mM Fe(II) and precipitation of Fe(III) oxides by these organisms resulted in-rapid adsorption and removal of 55 muM uranium and 81 muM cobalt from solution. The adsorptive capacity of the biogenic Fe(III) oxides was lower than that of abiotically produced Fe(III) oxides (100 muM for both metals), which may have been a result of steric hindrance by the microbial cells on the iron oxide surfaces. The binding capacity of the biogenic oxides for different heavy metals was indirectly correlated to the atomic radius of the bound element. X-ray absorption spectroscopy indicated that the uranium was bound to the biogenically produced Fe(III) oxides as U(VI) and that the U(VI) formed bidentate and tridentate inner-sphere complexes with the Fe(III) oxide surfaces. Dechlorosoma suillum oxidation was specific for Fe(II), and the organism did not enzymatically oxidize U(IV) or Co(II). Small amounts (less than 2.5 muM) of Cr(III) were reoxidized by D. suillum; however, this appeared to be inversely dependent on the initial concentration of the Cr(III). The results of this study demonstrate the potential of this novel approach for stabilization and immobilization of HMR in the environment. Using Smart Source Parsing ? C Liu, Y.
Louie, T. M.
Payne, J.
Bohuslavek, J.
Bolton, H.
Xun, L. Y. 2001s Identification, purification, and characterization of iminodiacetate oxidase from the EDTA-degrading bacterium BNC1 696-701& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): AMINO-ACID OXIDASE; CRYSTAL-STRUCTURE;
NITRILOTRIACETATE; METABOLISM; BIODEGRADATION; MONOOXYGENASE;
DEGRADATION; OXIDATION; BINDING; CELLSe Microbial degradation of synthetic chelating agents, such as EDTA and nitrilotriacetate (NTA), may help immobilizing radionuclides and heavy metals in the environment. The EDTA- and NTA-degrading bacterium BNC1 uses EDTA monooxygenase to oxidize NTA to iminodiacetate (IDA) and EDTA to ethylenediaminediacetate (EDDA). IDA- and EDDA-degrading enzymes have not been purified and characterized to date. In this report, an LDA oxidase was purified to apparent homogeneity from strain BNC1 by using a combination of eight purification steps. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein band of 40 kDa, and by using size exclusion chromatography, we estimated the native enzyme to be a homodimer. Flavin adenine dinucleotide was determined as its prosthetic group. The purified enzyme oxidized IDA to glycine and glyoxylate with the consumption of O-2. The temperature and pH optima for IDA oxidation were 35 degreesC and 8, respectively. The apparent K-m for IDA was 4.0 mM with a k(cat) of 5.3 s(-1). When the N-terminal amino acid sequence was determined, it matched exactly with that encoded by a previously sequenced hypothetical oxidase gene of BNC1. The gene was expressed in Escherichia coli, and the gene product as a C-terminal fusion with a His tag was purified by a one-step nickel affinity chromatography. The purified fusion protein had essentially the same enzymatic activity and properties as the native IDA oxidase. IDA oxidase also oxidized EDDA to ethylenediamine and glyoxylate. Thus, IDA oxidase is likely the second enzyme in both NTA and EDTA degradation pathways in strain BNC1. Using Smart Source Parsings *GEN COMP GROUP, 1998, PROGR MAN GCG PACK V ALTSCHUL SF, 1990, V87, P5509, P NATL ACAD SCI USA ANDERSON AH, 1996, V35, P3335, BIOCHEMISTRY-US AULING G, 1993, V16, P104, SYST APPL MICROBIOL AVERS JA, 1970, DECONTAMINATION NUCL BELLY RT, 1975, V29, P787, APPL MICROBIOL BINDA C, 1999, V7, P265, STRUCT FOLD DES BOHUSLAVEK J, 2001, V67, P688, APPL ENVIRON MICROB BRADFORD MM, 1976, V72, P248, ANAL BIOCHEM CLEVELAND JM, 1981, V200, P1506, SCIENCE CRIPPS RE, 1973, V136, P1059, BIOCHEM J DAUBARAS DL, 1996, V62, P4276, APPL ENVIRON MICROB EGLI T, 1988, V10, P297, SYSTEM APPL MICROBIO EPSTEIN S, 1972, V2, P291, ANXIETY CURRENT TREN ISHIZUKA H, 1993, V139, P425, J GEN MICROBIOL KLUNER T, 1998, V49, P194, APPL MICROBIOL BIOT LAEMMLI UK, 1970, V4, P680, NATURE LAUCAM CA, 1991, V14, P1939, J LIQ CHROMATOGR LAUFF JJ, 1990, V56, P3346, APPL ENVIRON MICROB LAVILLE J, 1998, V180, P3187, J BACTERIOL LIM CK, 1986, HPLC SMALL MOL PRACT MATTEVI A, 1996, V93, P7496, P NATL ACAD SCI USA MCFADDEN KM, 1980, ORGANIC COMPONENTS N MIZUTANI H, 1996, V120, P14, J BIOCHEM-TOKYO MULLER F, 1980, V66, P350, METHOD ENZYMOL NISHIYA Y, 1998, V438, P263, FEBS LETT NORTEMANN B, 1999, V51, P751, APPL MICROBIOL BIOT NORTEMANN B, 1992, V58, P671, APPL ENVIRON MICROB NORTEMANN B, 1991, P259, INT S ENV BIOT 22 25 PARRY RJ, 1997, V272, P23303, J BIOL CHEM PAYNE JW, 1998, V180, P3823, J BACTERIOL PAYNE JW, 1999, THESIS WASHINGTON ST PICIULO PL, 1986, RELEASE ORGANIC CHEL PICKAVER AH, 1976, V8, P13, SOIL BIOL BIOCHEM ROBINSON J, 1970, V33, P390, ANAL BIOCHEM SAMBROOK J, 1989, MOL CLONING LAB MANU SILVERMAN RB, 1995, V28, P335, ACCOUNTS CHEM RES SISTO JD, 1996, CHEM EC HDB STRICKLAND S, 1973, V248, P2944, J BIOL CHEM THOMAS RAP, 1998, V64, P1319, APPL ENVIRON MICROB TIEDJE JM, 1973, V25, P811, APPL MICROBIOL TODONE F, 1997, V36, P5853, BIOCHEMISTRY-US TRICKEY P, 1999, V7, P331, STRUCT FOLD DES UETZ T, 1993, V3, P423, BIODEGRADATION UETZ T, 1992, V174, P1179, J BACTERIOL WIERENGA RK, 1986, V187, P101, J MOL BIOL WITSCHEL M, 1997, V179, P6937, J BACTERIOL XU YR, 1997, V179, P1112, J BACTERIOL XUN LY, 2000, V66, P481, APPL ENVIRON MICROB ZANKER H, 1994, V176, P4511, J BACTERIOL Washington State Univ,Sch Mol Biosci,Pullman//WA/99164 (REPRINT); Washington State Univ,Sch Mol Biosci,Pullman//WA/99164; Battelle Mem Inst,Pacific NW Natl Labs Environm Microbiol Grp,Richland//WA/99352 ?
X Nevin, K. P.
Lovley, D. R. 2002n Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans 2294-2299& Applied and Environmental Microbiology 68 5 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): PETROLEUM-CONTAMINATED AQUIFERS; ANAEROBIC BENZENE
OXIDATION; C-TYPE CYTOCHROME; FE(III)-REDUCING BACTERIA;
ELECTRON-ACCEPTORS; HUMIC SUBSTANCES; GEOBACTER-METALLIREDUCENS;
IRON; SEDIMENTS; SULFURREDUCENS Mechanisms for Fe(III) oxide reduction were investigated in Geothrix fermentans, a dissimilatory Fe(III)reducing microorganism found within the Fe(III) reduction zone of subsurface environments. Culture filtrates of G. fermentans stimulated the reduction of poorly crystalline Fe(III) oxide by washed cell suspensions, suggesting that G. fermentans released one or more extracellular compounds that promoted Fe(III) oxide reduction. In order to determine if G. fermentans released electron-shuttling compounds, poorly crystalline Fe(III) oxide was incorporated into microporous alginate beads, which prevented contact between G. fermentans and the Fe(III) oxide. G. fermentans reduced the Fe(III) within the beads, suggesting that one of the compounds that G.fermentans releases is an electron-shuttling compound that can transfer electrons from the cell to Fe(III) oxide that is not in contact with the organism. Analysis of culture filtrates by thin-layer chromatography suggested that the electron shuttle has characteristics similar to those of a water-soluble quinone. Analysis of filtrates by ion chromatography demonstrated that there was as much as 250 muM dissolved Fe(III) in cultures of G.fermentans growing with Fe(III) oxide as the electron acceptor, suggesting that G.fermentans released one or more compounds capable of chelating and solubilizing Fe(III). Solubilizing Fe(III) is another strategy for alleviating the need for contact between cells and Fe(III) oxide for Fe(III) reduction. This is the first demonstration of a microorganism that, in defined medium without added electron shuttles or chelators, can reduce Fe(III) derived from Fe(III) oxide without directly contacting the Fe(III) oxide. These results are in marked contrast to those with Geobacter metallireducens, which does not produce electron shuttles or Fe(III) chelators. These results demonstrate that phylogenetically distinct Fe (III)-reducing microorganisms may use significantly different strategies for Fe(III) reduction. Thus, it is important to know which Fe (III) -reducing microorganisms predominate in a given environment in order to understand the mechanisms for Fe(III) reduction in the environment of interest. Using Smart Source Parsing ? j D Payne, R. B.
Gentry, D. A.
Rapp-Giles, B. J.
Casalot, L.
Wall, J. D. 2002V Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant 3129-3132& Applied and Environmental Microbiology 68 6p Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; U(VI); TECHNETIUM Previous in vitro experiments with Desulfovibrio vulgaris strain Hildenborough demonstrated that extracts containing hydrogenase and cytochrome c, could reduce uranium(VI) to uranium(IV) with hydrogen as the electron donor. To test the involvement of these proteins in vivo, a cytochrome c, mutant of D. desulfuricans strain G20 was assayed and found to be able to reduce U(VI) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. With electrons from hydrogen, the rate was more severely impaired. Cytochrome c. appears to be a part of the in vivo electron pathway to U(VI), but additional pathways from organic donors can apparently bypass this protein. Using Smart Source Parsing ? Y Qiu, X. Y.
Wu, L. Y.
Huang, H. S.
McDonel, P. E.
Palumbo, A. V.
Tiedje, J. M.
Zhou, J. Z. 2001d Evaluation of PCR-generated chimeras: Mutations, and heteroduplexes with 16S rRNA gene-based cloning 880-887& Applied and Environmental Microbiology 67 2 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): RIBOSOMAL-RNA GENES; MOLECULAR MICROBIAL DIVERSITY;
GRADIENT GEL-ELECTROPHORESIS; BACTERIAL DIVERSITY; COMMUNITY
STRUCTURE; DNA-POLYMERASE; RDNA ANALYSIS; AMPLIFICATION; SOIL;
COAMPLIFICATION To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Tag DNA polymerases examined: 20% for Z-Taq, with the highest: processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies. Using Smart Source ParsingR AVANISSAGHAJANI E, 1994, V17, P144, BIOTECHNIQUES BORNEMAN J, 1996, V62, P1935, APPL ENVIRON MICROB BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BRAKENHOFF RH, 1991, V19, P1949, NUCLEIC ACIDS RES CARIELLO NF, 1990, V99, P105, GENE CLINE J, 1996, V24, P3546, NUCLEIC ACIDS RES DELONG E, 1998, V280, P542, SCIENCE DELONG EF, 1992, V89, P5685, P NATL ACAD SCI USA DELWART EL, 1993, V262, P1257, SCIENCE DOJKA MA, 1998, V64, P3869, APPL ENVIRON MICROB ECKERT KA, 1990, V18, P3739, NUCLEIC ACIDS RES ESPEJO RT, 1998, V144, P1611, MICROBIOL-UK 6 FELSKE A, 1998, V64, P871, APPL ENVIRON MICROB FUHRMAN JA, 1993, V59, P1294, APPL ENVIRON MICROB GROSSKOPF R, 1998, V64, P960, APPL ENVIRON MICROB HEUER H, 1997, V63, P3233, APPL ENVIRON MICROB HUGENHOLTZ P, 1998, V180, P4765, J BACTERIOL KOPCZYNSKI ED, 1994, V60, P746, APPL ENVIRON MICROB LEE DH, 1996, V62, P3112, APPL ENVIRON MICROB LIESACK W, 1991, V21, P191, MICROBIAL ECOL LIU WT, 1997, V63, P4516, APPL ENVIRON MICROB LOWELL JL, 2000, V28, P676, BIOTECHNIQUES MASSOLDEYA A, 1997, V63, P270, APPL ENVIRON MICROB MEYERHANS A, 1990, V18, P1687, NUCLEIC ACIDS RES MOYER CL, 1994, V60, P871, APPL ENVIRON MICROB MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NUBEL U, 1996, V178, P5636, J BACTERIOL PAABO S, 1990, V265, P4718, J BIOL CHEM REYSENBACH AL, 1994, V60, P2113, APPL ENVIRON MICROB SNYDER L, 1997, MOL GENETICS BACTERI STACKEBRANDT E, 1993, V7, P232, FASEB J SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB WANG GCY, 1997, V63, P4645, APPL ENVIRON MICROB WANG GCY, 1996, V142, P1107, MICROBIOL-UK 5 WEISBURG WG, 1991, V173, P697, J BACTERIOL WHITE MB, 1992, V12, P301, GENOMICS WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV WISE MG, 1997, V63, P1505, APPL ENVIRON MICROB ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ?
j & Sani, R. K.
Peyton, B. M.
Brown, L. T. 2001 Copper-induced inhibition of growth of Desulfovibrio desulfuricans G20: Assessment of its toxicity and correlation with those of zinc and lead 4765-4772& Applied and Environmental Microbiology 67 10 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; METAL-IONS;
PLASMA-MEMBRANE; HEAVY-METALS; SEDIMENTS; METHANOGENESIS;
RESISTANCE; REDUCTION; HYDROGEN; WATER The toxicity of copper [Cu(II)] to sulfate-reducing bacteria (SRB) was studied by using Desulfovibrio desulfuricans G20 in a medium (MTM) developed specifically to test metal toxicity to SRB (R. K. Sani, G. Geesey, and B. M. Peyton, Adv. Environ. Res. 5:269-276, 2001). The effects of Cu(II) toxicity were observed in terms of inhibition in total cell protein, longer lag times, lower specific growth rates, and in some cases no measurable growth. At only 6 muM, Cu(II) reduced the maximum specific growth rate by 25% and the final cell protein concentration by 18% compared to the copper-free control. Inhibition by Cu(II) of cell yield and maximum specific growth rate increased with increasing concentrations. The Cu(II) concentration causing 50% inhibition in final cell protein was evaluated to be 16 muM. A Cu(II) concentration of 13.3 muM showed 50% inhibition in maximum specific growth rate. These results clearly show significant Cu(II) toxicity to SRB at concentrations that are 100 times lower than previously reported. No measurable growth was observed at 30 muM Cu(II) even after a prolonged incubation of 384 h. In contrast, Zn(II) and Pb(II), at 16 and 5 muM, increased lag times by 48 and 72 h, respectively, but yielded final cell protein concentrations equivalent to those of the zinc- and lead-free controls. Live/dead staining, based on membrane integrity, indicated that while Cu(II), Zn(II), and Pb(II) inhibited growth, these metals did not cause a loss of D. desulfuricans membrane integrity. The results show that D. desulfuricans in the presence of Cu(II) follows a growth pattern clearly different from the pattern followed in the presence of Zn(II) or Pb(II). It is therefore likely that Cu(II) toxicity proceeds by a mechanism different from that of Zn(II) or Pb(II) toxicity. Using Smart Source Parsing ABRAM JW, 1978, V117, P89, ARCH MICROBIOL ALLISON JD, 1991, EPA600391021 US EPA AVERY SV, 1995, V312, P811, BIOCHEM J 3 AVERY SV, 1996, V62, P3960, APPL ENVIRON MICROB BARNES SP, 1998, V15, P67, GEOMICROBIOL J BEECH IB, 1995, V35, P59, INT BIODETER BIODEGR BHARATHI PAL, 1990, V67, P361, ENVIRON POLLUT BHATTACHARYA D, 1981, V209, P31, AICHE S SER BOOTH GH, 1963, V199, P622, NATURE BOULOS L, 1999, V37, P77, J MICROBIOL METH CAPONE DG, 1983, V45, P1586, APPL ENVIRON MICROB CERVANTES C, 1994, V14, P121, FEMS MICROBIOL REV CHEN L, 1993, V216, P443, EUR J BIOCHEM CHEN BY, 2000, V46, P11, INT BIODETER BIODEGR CYPIONKA H, 2000, V54, P827, ANNU REV MICROBIOL DUFFY G, 1998, V31, P167, J MICROBIOL METH ERARDI FX, 1987, V53, P1951, APPL ENVIRON MICROB FERNANDEZ VM, 1989, V185, P449, EUR J BIOCHEM FITZ RM, 1991, V155, P444, ARCH MICROBIOL FLORIN THJ, 1991, V196, P127, CLIN CHIM ACTA FOGO JK, 1949, V21, P732, ANAL CHEM GADD GM, 1993, V124, P25, NEW PHYTOL GADD GM, 1992, V100, P197, FEMS MICROBIOL LETT GRIEG R, 1977, V8, P188, MAR POLLUT B HAO OJ, 1994, V46, P197, TOXICOL ENVIRON CHEM HAZEL JR, 1990, V29, P167, PROG LIPID RES HUGHES MN, 1989, METALS MICROORGANISM JALALI K, 2000, V34, P797, WATER RES KUO CW, 1996, V62, P2317, APPL ENVIRON MICROB LLOYD JR, 1998, V64, P4607, APPL ENVIRON MICROB LOVLEY DR, 1994, V60, P726, APPL ENVIRON MICROB LOVLEY DR, 1982, V43, P1373, APPL ENVIRON MICROB LOVLEY DR, 1992, V58, P850, APPL ENVIRON MICROB MORTON JD, 2000, V66, P1730, APPL ENVIRON MICROB NIES DH, 1999, V51, P730, APPL MICROBIOL BIOT OCHIAI EI, 1987, GEN PRINCIPLES BIOCH OHSUMI Y, 1988, V170, P2676, J BACTERIOL POSTGATE JR, 1984, SULPHATE REDUCING BA POULSON SR, 1997, V14, P41, GEOMICROBIOL J RILEY RG, 1992, DOEER0547T US DEP EN SAID WA, 1991, V57, P1498, APPL ENVIRON MICROB SALEH AM, 1964, V27, P281, J APPL BACTERIOL SANI RK, 2001, V5, P269, ADV ENVIRON RES SANI RK, 1999, V44, P367, FOLIA MICROBIOL SASS H, 1998, V21, P212, SYST APPL MICROBIOL SONG YC, 1998, V38, P187, WATER SCI TECHNOL STAUBER JL, 1986, V8, P223, AQUAT TOXICOL STAUBER JL, 1987, V94, P511, MAR BIOL STOHS SJ, 1995, V18, P321, FREE RADICAL BIO MED TEMPLE KL, 1964, V59, P271, ECON GEOL THAUER RK, 1977, V41, P100, BACTERIOL REV TWIGG RS, 1945, V155, P401, NATURE VALLEE BL, 1972, V41, P91, ANNU REV BIOCHEM WIJAYA S, 1993, P469, P 48 PURD IND WAST C WILLIAMS SC, 1978, V6, P195, MAR CHEM WINFREY MR, 1977, V33, P275, APPL ENVIRON MICROB ZEVENHUIZEN LPT, 1979, V5, P139, MICROBIAL ECOL Washington State Univ,Ctr Multiphase Environm Res Dept Chem Engn,Dana Hall,Rm 118/Pullman//WA/99164 (REPRINT); Washington State Univ,Ctr Multiphase Environm Res Dept Chem Engn,Pullman//WA/99164 S? 3 Snoeyenbos-West, O.
Van Praagh, C. G.
Lovley, D. R. 2001B Trichlorobacter thiogenes should be renamed as a Geobacter species 1020-1021& Applied and Environmental Microbiology 67 2a Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): TETRACHLOROETHYLENE; BACTERIA Using Smart Source Parsing AMANN RI, 1992, V58, P614, APPL ENVIRON MICROB DEWEVER H, 2000, V66, P2297, APPL ENVIRON MICROB KRUMHOLZ LR, 1996, V62, P4108, APPL ENVIRON MICROB KRUMHOLZ LR, 1997, V47, P1262, INT J SYST BACTERIOL LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 2000, P1, PROKARYOTES LOVLEY DR, 2000, P3, ENV MICROBAMETAL INT LOVLEY DR, 1997, P187, IRON RELATED TRANSIT MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES VANDEPEER Y, 1994, V10, P569, COMPUT APPL BIOSCI Univ Massachusetts,Dept Microbiol Morrill Sci Ctr IVN 203,Box 35720/Amherst//MA/01003 (REPRINT); Univ Massachusetts,Dept Microbiol Morrill Sci Ctr IVN 203,Amherst//MA/01003 ? Spiro, A.
Lowe, M. 2002_ Quantitation of DNA sequences in environmental PCR products by a multiplexed, bead-based method 1010-1013& Applied and Environmental Microbiology 68 2M Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): DIVERSITYZ A first application of a multiplexed, bead-based method is described for determining the abundances of target sequences in an environmental PCR product. Target sequences as little as 0.3% of the total amount of DNA can be quantified. Tests were conducted on 16S ribosomal DNA sequences from microorganisms collected from contaminated groundwater. Using Smart Source Parsing1? X 8 Steger, J. L.
Vincent, C.
Ballard, J. D.
Krumholz, L. R. 2002g Desulfovibrio sp genes involved in the respiration of sulfate during metabolism of hydrogen and lactate 1932-1937& Applied and Environmental Microbiology 68 4 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SUBSP VULGARIS HILDENBOROUGH; HMC OPERON;
MALATE-DEHYDROGENASE; REDUCING BACTERIA; IDENTIFICATION; EXPRESSION;
DELETION; COMPLEX To develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or hydrogen as an electron donor. RNA extracts of Desulfovibrio desulfuricans subsp. aestuarii were analyzed by using random arbitrarily primed PCR. RNA was reverse transcribed under low-stringency conditions with a set of random primers, and candidate cDNAs were cloned, sequenced, and characterized by BLAST analysis. Putative differentially expressed transcripts were confirmed by Northern blot analysis. Interestingly, dissimilatory bisulfite reductase was upregulated in the presence of hydrogen. To link these transcriptional changes to the physiology of sulfate-reducing bacteria, sulfide was measured during growth of several strains of Desulfovibrio on hydrogen or lactate, and this revealed that hydrogen-grown cells produced more sulfide per unit of cell mass than lactate-grown cells. Transcription of other redox proteins was characterized by Northern blotting to determine whether or not they were also transcribed to higher levels in hydrogen-grown cells. Growth on lactate produced greater transcription of [NiFe] hydrogenase. H-2-grown cells transcribed the adenylylsulfate reductase b subunit and HmcA to higher levels. The results we describe here provide new insight into the continuing debate over how Desulfovibrio species utilize redox components to generate membrane potential and to channel electrons to sulfate, the final electron acceptor. Using Smart Source Parsingu? I Stults, J. R.
Snoeyenbos-West, O.
Methe, B.
Lovley, D. R.
Chandler, D. P. 2001{ Application of the 5 ' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments 2781-2789& Applied and Environmental Microbiology 67 6 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): POLYMERASE CHAIN-REACTION; REVERSE TRANSCRIPTION-PCR;
C VIRUS-RNA; LISTERIA-MONOCYTOGENES; MICROBIAL COMMUNITIES;
5'-NUCLEASE ASSAYS; COMPETITIVE PCR; RT-PCR; SOIL; QUANTIFICATION In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of Geobacter spp, and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or less than or equal to2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated; amended aquifer sediments were significantly lower (P < 0.0002) than traces for the external standard curve, We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (P < 0.0001), If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (C-t) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation, Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples. Using Smart Source Parsingx AUSUBEL FM, 1995, CURRENT PROTOCOLS MO BASSLER HA, 1995, V61, P3724, APPL ENVIRON MICROB BECKER A, 1996, V237, P204, ANAL BIOCHEM BECKER S, 2000, V66, P4945, APPL ENVIRON MICROB BELGRADER P, 1998, V44, P2191, CLIN CHEM CHANDLER DP, 1998, V64, P669, APPL ENVIRON MICROB CHANDLER DP, 1999, V49, P969, TALANTA CHANDLER DP, 1998, V21, P128, J IND MICROBIOL BIOT CHEN S, 1997, V35, P239, INT J FOOD MICROBIOL COTTREZ F, 1994, V22, P2712, NUCLEIC ACIDS RES DESJARDIN LE, 1998, V36, P1964, J CLIN MICROBIOL FELSKE A, 1998, V64, P4581, APPL ENVIRON MICROB FREDRICKSON JK, 1997, V14, P183, GEOMICROBIOL J GUT M, 1999, V77, P37, J VIROL METHODS HAUGLAND RA, 1999, V13, P329, MOL CELL PROBE HEID CA, 1996, V6, P986, GENOME RES HOLLAND PM, 1991, V88, P7276, P NATL ACAD SCI USA INNIS MA, 1995, PCR STRATEGIES JANSSON JK, 1996, MOL MICROBIOL ECOLOG JEAN L, 1996, V234, P224, ANAL BIOCHEM JOHNSEN K, 1999, V65, P1786, APPL ENVIRON MICROB KALININA O, 1997, V25, P1999, NUCLEIC ACIDS RES KIMURA B, 1999, V62, P329, J FOOD PROTECT LARRICK JW, 1995, REVERSE TRANSCRIPTAS LEE SY, 1996, V62, P3787, APPL ENVIRON MICROB LIE YS, 1998, V9, P43, CURR OPIN BIOTECH LOVLEY DR, 1996, V382, P445, NATURE MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MARTELL M, 1999, V37, P327, J CLIN MICROBIOL MAUDRU T, 1998, V25, P972, BIOTECHNIQUES MOLLER A, 1997, V22, P512, BIOTECHNIQUES MORRIS T, 1996, V34, P2933, J CLIN MICROBIOL NORTON DM, 1999, V65, P2122, APPL ENVIRON MICROB NORTHRUP MA, 1998, V70, P918, ANAL CHEM OBERST RD, 1998, V64, P3389, APPL ENVIRON MICROB ORLANDO C, 1998, V36, P255, CLIN CHEM LAB MED PICARD C, 1996, MOL MICROBIOL ECOLOG RIEDY MC, 1995, V18, P70, BIOTECHNIQUES ROONEYVARGA JN, 1999, V65, P3056, APPL ENVIRON MICROB SHARMA VK, 1999, V13, P291, MOL CELL PROBE SNOEYENBOSWEST OL, 2000, V39, P153, MICROBIAL ECOL SUZUKI MT, 2000, V66, P4605, APPL ENVIRON MICROB TAKAI K, 2000, V66, P5066, APPL ENVIRON MICROB TAYLOR TB, 1997, V25, P3164, NUCLEIC ACIDS RES TEBBE CC, 1993, V59, P2657, APPL ENVIRON MICROB TORANZOS GA, 1997, ENV APPL NUCL ACID A VANELSAS JD, 1997, V24, P188, BIOL FERT SOILS WILSON IG, 1997, V63, P3741, APPL ENVIRON MICROB WOO THS, 1998, V256, P132, ANAL BIOCHEM 900 Battele Blvd,Mail Stop P7-50/Richland//WA/99352 (REPRINT); Pacific NW Natl Lab,Environm Microbiol Grp,Richland//WA/99352; Univ Massachusetts,Dept Microbiol,Amherst//MA/01003 ? k Thompson, D. K.
Beliaev, A. S.
Giometti, C. S.
Tollaksen, S. L.
Khare, T.
Lies, D. P.
Nealson, K. H.
Lim, J.
Yates, J.
Brandt, C. C.
Tiedje, J. M.
Zhou, J. Z. 2002 Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress 881-892& Applied and Environmental Microbiology 68 2# Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): UPTAKE REGULATION PROTEIN; 6FE-6S PRISMANE-CLUSTER;
OUTER-MEMBRANE PROTEIN; EXOTOXIN-A PRODUCTION; INFLUENZAE TYPE-B;
ESCHERICHIA-COLI; PSEUDOMONAS-AERUGINOSA; VIBRIO-CHOLERAE;
SUPEROXIDE-DISMUTASE; SIDEROPHORE BIOSYNTHESIS The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC,fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems. Using Smart Source Parsing ? I Wu, L. Y.
Thompson, D. K.
Li, G. S.
Hurt, R. A.
Tiedje, J. M.
Zhou, J. Z. 2001g Development and evaluation of functional gene arrays for detection of selected genes in the environment 5780-5790& Applied and Environmental Microbiology 67 12 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): SACCHAROMYCES-CEREVISIAE; DENITRIFYING BACTERIA;
MICROARRAY ANALYSIS; EXPRESSION ANALYSIS; ESCHERICHIA-COLI; DNA;
GENOME; HYBRIDIZATION; SEDIMENTS; SCALE To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (PmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65 degreesC). The detection limit for nirS genes was approximately I ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r(2) = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of I to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity. Using Smart Source ParsingQ *NRC, 1993, IN SIT BIOR WHEN DOE AMANN RI, 1995, V59, P143, MICROBIOL REV BARTOSIEWICZ M, 2000, V376, P66, ARCH BIOCHEM BIOPHYS BRAKER G, 2000, V66, P2096, APPL ENVIRON MICROB CHEE M, 1996, V274, P610, SCIENCE CURTIS PS, 1994, V165, P45, PLANT SOIL DAQUILA RT, 1991, V19, P3749, NUCLEIC ACIDS RES DERISI JL, 1997, V278, P680, SCIENCE FRIES MR, 1994, V60, P2802, APPL ENVIRON MICROB FUTCHER B, 2000, V12, P710, CURR OPIN CELL BIOL GIBSON DT, 1992, SCI FDN BIOREMEDIATI GUSCHIN DY, 1997, V63, P2397, APPL ENVIRON MICROB HACIA JG, 1999, V21, P42, NAT GENET S KHODURSKY AB, 2000, V97, P12170, P NATL ACAD SCI USA LASHKARI DA, 1997, V94, P13057, P NATL ACAD SCI USA LOCKHART DJ, 1996, V14, P1675, NAT BIOTECHNOL NOLD SC, 2000, V66, P4532, APPL ENVIRON MICROB OGRAM A, 1995, V61, P763, APPL ENVIRON MICROB OGRAM A, 1987, V7, P57, J MICROBIOL METH PINKEL D, 1998, V20, P207, NAT GENET PORTEOUS LA, 1991, V22, P345, CURR MICROBIOL QIU XY, 2001, V67, P880, APPL ENVIRON MICROB RAMSAY G, 1998, V16, P40, NAT BIOTECHNOL RICHMOND CS, 1999, V27, P3821, NUCLEIC ACIDS RES SHALON D, 1996, V6, P639, GENOME RES SMITH GB, 1992, V58, P376, APPL ENVIRON MICROB SUDARSANAM P, 2000, V97, P3364, P NATL ACAD SCI USA TANIGUCHI M, 2001, V71, P34, GENOMICS TIEDJE JM, 2000, P393, SUSTAINABLE MANAGEME VOORDOUW G, 1993, V59, P4101, APPL ENVIRON MICROB WANG DG, 1998, V280, P1077, SCIENCE WHITE KP, 1999, V286, P2179, SCIENCE WODICKA L, 1997, V15, P1359, NAT BIOTECHNOL YE RW, 2000, V182, P4458, J BACTERIOL ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824? g Zhou, J. Z.
Xia, B. C.
Treves, D. S.
Wu, L. Y.
Marsh, T. L.
O'Neill, R. V.
Palumbo, A. V.
Tiedje, J. M. 2002I Spatial and resource factors influencing high microbial diversity in soil 326-334& Applied and Environmental Microbiology 68 1 Biotechnology & applied microbiology; microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; BACTERIAL COMMUNITY; PCR
COAMPLIFICATION; CHIMERIC MOLECULES; RDNA ANALYSIS; GENES; DNA;
AMPLIFICATION; MICROORGANISMS; ENVIRONMENTT To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently, exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility. Using Smart Source Parsing BALKWILL DL, 1989, V55, P1058, APPL ENVIRON MICROB BINTRIM SB, 1997, V94, P277, P NATL ACAD SCI USA BORNEMAN J, 1997, V63, P2647, APPL ENVIRON MICROB BORNEMAN J, 1996, V62, P1935, APPL ENVIRON MICROB CHO JC, 2000, V66, P5448, APPL ENVIRON MICROB DUNBAR J, 1999, V65, P1662, APPL ENVIRON MICROB ELLIS DE, 2000, V34, P2254, ENVIRON SCI TECHNOL FARRELLY V, 1995, V61, P2798, APPL ENVIRON MICROB FELSKE A, 1998, V64, P871, APPL ENVIRON MICROB HEWITT AD, 1990, V11, P187, ATOM SPECTROSC HUSTON MA, 1994, BIOL DIVERSITY COEXI KOPCZYNSKI ED, 1994, V60, P746, APPL ENVIRON MICROB KUSKE CR, 1997, V63, P3614, APPL ENVIRON MICROB KWOK S, 1989, V339, P237, NATURE LIESACK W, 1991, V21, P191, MICROBIAL ECOL LIESACK W, 1992, V174, P5072, J BACTERIOL LOLLAR BS, 2001, V35, P261, DOVER AIR FORCE BASE MAGURRAN E, 1988, ECOLOGICAL DIVERSITY MOYER CL, 1994, V60, P871, APPL ENVIRON MICROB MOYER CL, 1996, V62, P2501, APPL ENVIRON MICROB NUSSLEIN K, 1998, V64, P1283, APPL ENVIRON MICROB PETTERSSON B, 1994, V60, P2456, APPL ENVIRON MICROB QIU XY, 2001, V67, P880, APPL ENVIRON MICROB RASHIT E, 1987, V14, P101, MICROBIAL ECOL STACKEBRANDT E, 1993, V7, P232, FASEB J SUZUKI M, 1998, V64, P4522, APPL ENVIRON MICROB SUZUKI MT, 1996, V62, P625, APPL ENVIRON MICROB TAYLOR LR, 1978, P1, DIVERSITY INSECT FAU TIEDJE JM, 1997, P35, PROGR MICROBIAL ECOL TORSVIK V, 1990, V56, P782, APPL ENVIRON MICROB UEDA T, 1995, V46, P415, EUR J SOIL SCI WANG GCY, 1997, V63, P4645, APPL ENVIRON MICROB WANG GCY, 1996, V142, P1107, MICROBIOL-UK 5 WAYNE LG, 1987, V37, P463, INT J SYST BACTERIOL WELSBURG WW, 1991, V173, P697, J BACTERIOL WINTZINGERODE F, 1997, V21, P213, FEMS MICROBIOL REV ZHOU JZ, 1997, V143, P3913, MICROBIOL-UK 12 ZHOU JZ, 1995, V45, P500, INT J SYST BACTERIOL ZHOU JZ, 1996, V62, P316, APPL ENVIRON MICROB Oak Ridge Natl Lab,Div Environm Sci,POB 2008/Oak Ridge//TN/37831 (REPRINT); Oak Ridge Natl Lab,Div Environm Sci,Oak Ridge//TN/37831; Michigan State Univ,Ctr Microbial Ecol,E Lansing//MI/48824 ? ( Bang, S. W.
Clark, D. S.
Keasling, J. D. 2000 Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium in Escherichia coli 3939-3944 Appl. Environ. Microbiol. 66 9 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): SULFATE-REDUCING BACTERIA; VECTORS USEFUL;
PURIFICATION; CULTURE; STRAIN[ The thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium was expressed in Escherichia coli to overproduce hydrogen sulfide from thiosulfate for heavy metal removal (or precipitation). A 5.1-kb DNA fragment containing phsABC was inserted into the pMB1-based, high-copy, isopropyl-beta-D-thiogalactopyranoside-inducible expression vector pTrc99A and the RK2-based, medium-copy, m-toluate-inducible expression vector pJB866, resulting in plasmids pSB74 and pSB77. A 3.7-kb DNA fragment, excluding putative promoter and regulatory regions, was inserted into the same vectors, making plasmids pSB103 and pSB107. E. coli DH5 alpha strains harboring the phsABC constructs showed higher thiosulfate reductase activity and produced significantly more sulfide than the control strains under both aerobic and anaerobic conditions. Among the four phsABC constructs, E, coli DH5 alpha (pSB74) produced thiosulfate reductase at the highest level and removed the most cadmium from solution under anaerobic conditions: 98% of all concentrations up to 150 mu M and 91% of 200 mu M. In contrast, a negative control did not produce any measurable sulfide and removed very little cadmium from solution. Energy-dispersive X-ray spectroscopy revealed that the metal removed from solution precipitated as a complex of cadmium and sulfur, most likely cadmium sulfide. Using Smart Source ParsingY AKETAGAWA J, 1985, V97, P1025, J BIOCHEM-TOKYO AMANN E, 1988, V69, P301, GENE BIRNBOIM HC, 1979, V7, P1513, NUCLEIC ACIDS RES BLATNY JM, 1997, V38, P35, PLASMID BOLTON H, 1995, P1, BIOREMEDIATION INORG CHAUNCEY TR, 1987, V143, P350, METHOD ENZYMOL CLARK MA, 1987, V169, P2391, J BACTERIOL ESAU K, 1979, V66, P11, J ULTRASTRUCT RES FONG CLW, 1993, V175, P6368, J BACTERIOL FORD T, 1995, P1, BIOEXTRACTION BIODET FORTIN D, 1995, V14, P178, J IND MICROBIOL HANAHAN D, 1983, V166, P557, J MOL BIOL HARD BC, 1997, V152, P65, MICROBIOL RES HATCHIKIAN EC, 1975, V105, P249, ARCH MICROBIOL HEINZINGER NK, 1995, V177, P2813, J BACTERIOL HOCKETT JR, 1996, V15, P1687, ENVIRON TOXICOL CHEM KING TE, 1967, V10, P634, METHOD ENZYMOL LEFAOU A, 1990, V6, P351, FEMS MICROBIOL REV MAGYAROSY AC, 1976, V57, P486, PLANT PHYSIOL NEIDHARDT FC, 1974, V119, P736, J BACTERIOL SASAHARA KC, 1997, V179, P6736, J BACTERIOL SPEIGHT JG, 1996, ENV TECHNOLOGY HDB SUGIO T, 1997, V61, P470, BIOSCI BIOTECH BIOCH WANG CL, 1997, V63, P4075, APPL ENVIRON MICROB WEBB JS, 1998, V84, P240, J APPL MICROBIOL WHITE C, 1998, P233, EXTREMOPHILES MICROB UNIV CALIF BERKELEY,DEPT CHEM ENGN, 201 GILMAN HALL/BERKELEY//CA/94720 (REPRINT); UNIV CALIF BERKELEY,DEPT CHEM ENGN/BERKELEY//CA/94720 ? j ) Cord-Ruwisch, R.
Lovley, D. R.
Schink, B. 1998t Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners 2232-2236 Appl. Environ. Microbiol. 64 6 Microbiology; biotechnology & applied microbiology
TERMINAL ELECTRON-ACCEPTOR; SP-NOV; SUCCINOGENES; REDUCTION; RESPIRATION; MANGANESE; FUMARATE; BACTERIA; IRONI Pure cultures of Geobacter sulfurreducens and other Fe(III)-reducing bacteria accumulated hydrogen to partial pressures of 5 to 70 Pa with acetate, butyrate, benzoate, ethanol, lactate, or glucose as the electron donor if electron release to an acceptor was limiting, G. sulfurreducens coupled acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron or other electron accepters. Cocultures of G. sulfurreducens and Wolinella succinogenes with nitrate as the electron acceptor degraded acetate efficiently and grew with doubling times of 6 to 8 h, The hydrogen partial pressures in these acetate-degrading cocultures were considerably lower, in the range of 0.02 to 0.04 Pa. From these values and the concentrations of the other reactants, it was calculated that in this cooperation the free energy change available to G. sulfurreducens should be about -53 kJ per mol of acetate oxidized, assuming complete conversion of acetate to CO2 and H-2, However, growth yields (18.5 g of dry mass per mol of acetate for the coculture, about 14 g for G. sulfurreducens) indicated considerably higher energy gains. These yield data, measurement of hydrogen production rates, and calculation of the diffusive hydrogen flux indicated that electron transfer in these cocultures may not proceed exclusively via interspecies hydrogen transfer but may also proceed through an alternative carrier system with higher redox potential, e.g., a c-type cytochrome that was found to be excreted by G. sulfurreducens into the culture fluid. Syntrophic acetate degradation was also possible with G. sulfurreducens and Desulfovibrio desulfuricans CSN but only with nitrate as electron acceptor. These cultures produced cell yields of 4.5 g of dry mass per mol of acetate, to which both partners contributed at about equal rates, These results demonstrate that some Fe(III)-reducing bacteria can oxidize organic compounds under Fe(LII) limitation with the production of hydrogen, and they provide the first example of rapid acetate oxidation via interspecies election transfer at moderate temperature. BOKRANZ M, 1983, V135, P36, ARCH MICROBIOL BRONDER M, 1982, V131, P216, ARCH MICROBIOL BRYANT MP, 1979, V48, P193, J ANIM SCI CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB DAWSON RMC, 1969, DATA BIOCH RES GERTZ KH, 1954, V9, P1, Z NATURFORSCH B KREKELER D, 1995, V17, P271, FEMS MICROBIOL ECOL LEE MJ, 1988, V54, P124, APPL ENVIRON MICROB LOVLEY DR, 1995, V54, P175, ADV AGRON LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1997, P187, IRON RELATED TRANSIT LOVLEY DR, 1995, V33, P365, REV GEOPHYS MACY JM, 1986, V144, P147, ARCH MICROBIOL MCINERNEY MJ, 1988, P373, BIOL ANAEROBIC MICRO MYERS CR, 1990, V172, P6232, J BACTERIOL NEALSON KH, 1994, V48, P311, ANNU REV MICROBIOL ROZANOVA E, 1990, P469, MICROBIOLOGY BIOCH S SCHINK B, 1994, P197, ACETOGENESIS SCHINK B, 1990, V2, P63, BIOTECHNOLOGY FOCUS SCHINK B, 1997, V61, P262, MICROBIOL MOL BIOL R SCHINK B, 1991, P276, PROKARYOTES SCHNUERER A, 1997, V46, P1145, INT J SYST BACTERIOL SEELIGER S, UNPUB PERIPLASMIC EX STOUTHAMER AH, 1979, V21, P1, INT REV BIOCHEM STRICKLAND JDH, 1972, PRACTICAL HDB SEAWAT THAUER RK, 1977, V41, P100, BACTERIOL REV WIDDEL F, 1981, V129, P395, ARCH MICROBIOL ZINDER SH, 1984, V138, P263, ARCH MICROBIOL UNIV KONSTANZ,FAK BIOL, POSTFACH 5560/D-78457 CONSTANCE GERMANY/ (REPRINT); UNIV KONSTANZ,FAK BIOL/D-78457 CONSTANCE GERMANY/; MURDOCH UNIV,/MURDOCH/WA 6150/AUSTRALIA/; UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST MA/01003? ] Cummings, D. E.
March, A. W.
Bostick, B.
Spring, S.
Caccavo, F.
Fendorf, S.
Rosenzweig, R. F. 2000n Evidence for microbial Fe(III) reduction in anoxic, mining-impacted lake sediments (Lake Coeur d'Alene, Idaho) 154-162 Appl. Environ. Microbiol. 66 1 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): IRON-REDUCING BACTERIA; FERRIC IRON;
FE(III)-REDUCING BACTERIA; THIOBACILLUS-FERROOXIDANS; SULFATE
REDUCTION; MINE TAILINGS; ADSORPTION; MAGNETITE; OXYHYDROXIDES;
ENVIRONMENTS Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hvdr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)reducing bacteria in this habitat. The concentration of mild-acid-extractable Fem) increased with sediment depth up to 50 g kg(-1), suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter(-1)) occurred 10 to 15 cm beneath the sediment-cater interface, suggesting that sulfidogenesis may not be the predominant terminal electron-accepting process in this environment and that dissolved Fe(II) arises from biological reductive dissolution of iron (hydr)oxides. The concentration of sedimentary magnetite (Fe3O4), a common product of bacterial Fe(III) hydroxide reduction, was as much as 15.5 g kg(-1). Most-probable-number enrichment cultures revealed that the mean density of Fe(III)-reducing bacteria was 8.3 x 10(5) cells g (dry weight) of sediment(-1). Two new strains of dissimilatory Fe(III)-reducing bacteria were isolated from surface sediments. Collectively, the results of this study support the hypothesis that dissimilatory reduction of iron has been and continues to be an important biogeochemical process in the environment examined. Using Smart Source Parsingv
BALCH WE, 1976, V32, P781, APPL ENVIRON MICROB BALCH WE, 1979, V43, P260, MICROBIOL REV BEARD BL, 1999, V285, P1889, SCIENCE BELL PE, 1987, V53, P2610, APPL ENVIRON MICROB BELZILE N, 1990, V54, P103, GEOCHIM COSMOCHIM AC BLAKEMORE RP, 1975, V190, P377, SCIENCE BROCK TD, 1976, V32, P567, APPL ENVIRON MICROB BRYANT MP, 1972, V25, P1324, AM J CLIN NUTR CACCAVO F, 1996, V62, P4678, APPL ENVIRON MICROB CHAPELLE FH, 1992, V30, P29, GROUND WATER COATES JD, 1998, V64, P1504, APPL ENVIRON MICROB COCHRAN WG, 1950, V6, P105, BIOMETRICS COEY JMD, 1974, V11, P1489, CAN J EARTH SCI CUMMINGS DE, 1999, V171, P183, ARCH MICROBIOL CUMMINGS DE, 1999, V33, P723, ENVIRON SCI TECHNOL CUMMINGS DE, UNPUB DAS A, 1996, V45, P377, APPL MICROBIOL BIOT DAS A, 1992, V97, P167, FEMS MICROBIOL LETT ELLIS MM, 1940, 1 US BUR FISH FELSENSTEIN J, 1982, V57, P379, Q REV BIOL FORTIN D, 1995, V14, P178, J IND MICROBIOL FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH GIBBSEGGAR Z, 1999, V168, P1, EARTH PLANET SC LETT HARRINGTON JM, 1998, V32, P650, ENVIRON SCI TECHNOL HOBBIE JE, 1977, V33, P1225, APPLIED ENV MICROBIO HOBBS SW, 1965, 478 USGS HOROWITZ AJ, 1995, V52, P135, J GEOCHEM EXPLOR KENNEDY LG, 1998, V2, P259, BIOREMED J KOSTKA JE, 1996, V44, P522, CLAY CLAY MINER LAKIND JS, 1989, V53, P961, GEOCHIM COSMOCHIM AC LONERGAN DJ, 1996, V178, P2402, J BACTERIOL LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1986, V51, P683, APPL ENVIRON MICROB LOVLEY DR, 1987, V53, P2636, APPL ENVIRON MICROB LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LUDWIG W, 1999, ARB SOFTWARE ENV SEQ MAIDAK BL, 1996, V24, P82, NUCLEIC ACIDS RES MANNING BA, 1997, V31, P2005, ENVIRON SCI TECHNOL MANNING BA, 1998, V32, P2383, ENVIRON SCI TECHNOL MCGEEHAN SL, 1994, V58, P337, SOIL SCI SOC AM J MOORE JN, 1988, V22, P432, ENVIRON SCI TECHNOL MUDROCH A, 1994, HDB TECHNIQUES AQUAT OTTOW JCG, 1970, V225, P103, NATURE PRONK JT, 1992, V10, P153, GEOMICROBIOL J RAVEN KP, 1998, V32, P344, ENVIRON SCI TECHNOL RIBET I, 1995, V17, P239, J CONTAM HYDROL ROCHETTE EA, 1998, V62, P1530, SOIL SCI SOC AM J SCHIPPERS A, 1995, V61, P2930, APPL ENVIRON MICROB STOOKEY LL, 1970, V42, P779, ANAL CHEM STRAUB KL, 1998, V21, P442, SYST APPL MICROBIOL STUMM W, 1985, CHEM PROCESSES LAKES TESSIER A, 1985, V49, P183, GEOCHIM COSMOCHIM AC THIBEAU RJ, 1978, V32, P532, APPL SPECTROSC THOMAS HA, 1942, V34, P572, J AM WATER WORKS ASS TORRELLA F, 1981, V41, P518, APPL ENVIRON MICROB TOWNSEND HE, 1994, V50, P546, CORROSION WALLNER G, 1997, V63, P4223, APPL ENVIRON MICROB WIELINGA B, 1999, V65, P1548, APPL ENVIRON MICROB WOODS PF, 1989, 894032 USGS ZHANG CL, 1997, V61, P4621, GEOCHIM COSMOCHIM AC: UNIV IDAHO,DEPT BIOL SCI/MOSCOW//ID/83844 (REPRINT); UNIV IDAHO,DEPT BIOL SCI/MOSCOW//ID/83844; UNIV IDAHO,DEPT MICROBIOL MOL BIOL & BIOCHEM/MOSCOW//ID/83844; UNIV IDAHO,SOIL SCI DIV/MOSCOW//ID/83844; TECH UNIV MUNICH,LEHRSTUHL MIKROBIOL/D-80290 MUNICH//GERMANY/; UNIV NEW HAMPSHIRE,DEPT MICROBIOL/DURHAM//NH/03824? H Deflaun, M. F.
Oppenheimer, S. R.
Streger, S.
Condee, C. W.
Fletcher, M. 1999e Alterations in adhesion, transport, and membrane characteristics in an adhesion-deficient pseudomonad 759-765. Appl. Environ. Microbiol. 65 2 Microorganisms
Bacteria
Eubacteria
Cell Biology
Pollution Assessment Control and Management
Adhesion-Defective Mutants
Aquifer Sediments
Bacterial Adhesion Alterations
Transport
Transport Rates A stable adhesion-deficient mutant of Burkholderia cepacia G4, a soil pseudomonad, was selected in a sand column assay. This mutant (ENV435) was compared to the wild-type strain by examining the adhesion of the organisms to silica sand and their transport through two aquifer sediments that differed in their sand, silt, and clay contents. We compared the longitudinal transport of the wild type and the adhesion mutant to the transport of a conservative chloride tracer in 25-cm-long glass columns. The transport of the wild-type strain was severely retarded compared to the transport of the conservative tracer in a variety of aquifer sediments, while the adhesion mutant and the conservative tracer traveled at similar rates. An intact sediment core study produced similar results; ENV435 was transported at a faster rate and in much greater numbers than G4. The results of hydrophobic interaction chromatography revealed that G4 was significantly more hydrophobic than ENV435, and polyacrylamide gel electrophoresis revealed significant differences in the lipopolysaccharide O-antigens of the adhesion mutant and the wild type. Differences in this cell surface polymer may explain the decreased adhesion of strain ENV435. Journal article ? E Elias, Dwayne A.
Krumholz, Lee R.
Tanner, Ralph S.
Suflita, Joseph M. 1999> Estimation of methanogen biomass by quantitation of coenzyme M
5541-5545. Appl. Environ. Microbiol. 65 12 Microorganisms
Archaeobacteria
Bacteria
Enzymology (Biochemistry and Molecular Biophysics)
Ecology (Environmental Sciences)
Metabolism
Anaerobic Ecosystem
Bacterial BiomassB Determination of the role of methanogenic bacteria in an anaerobic ecosystem often requires quantitation of the organisms. Because of the extreme oxygen sensitivity of these organisms and the inherent limitations of cultural techniques, an accurate biomass value is very difficult to obtain. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363-370, 1990) was modified in order to quantify CoM in pure cultures, sediments, and sewage water samples. The identity of the CoM derivative was verified by using liquid chromatography-mass spectroscopy. The assay was linear for CoM amounts ranging from 2 to 2,000 pmol, and the detection limit was 2 pmol of CoM/ml of sample. CoM was not adsorbed to sediments. The methanogens tested contained an average of 19.5 nmol of CoM/mg of protein and 0.39 plus-minus 0.07 fmol of CoM/cell. Environmental samples contained an average of 0.41 plus-minus 0.17 fmol/cell based on most-probable-number estimates. CoM was extracted by using 1% tri-(N)-butylphosphine in isopropanol. More than 90% of the CoM was recovered from pure cultures and environmental samples. We observed no interference from sediments in the CoM recovery process, and the method could be completed aerobically within 3 h. Freezing sediment samples resulted in 46 to 83% decreases in the amounts of detectable CoM, whereas freezing had no effect on the amounts of CoM determined in pure cultures. The method described here provides a quick and relatively simple way to estimate methanogenic biomass. Journal article? j M Fredrickson, J. K.
Kostandarithes, H. M.
Li, S. W.
Plymale, A. E.
Daly, M. J. 2000N Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1 2006-2011 Appl. Environ. Microbiol. 66 5 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): SHEWANELLA-PUTREFACIENS MR-1; C-TYPE CYTOCHROME;
DISSIMILATORY REDUCTION; RADIATION-RESISTANT; MICROBIAL REDUCTION;
ELECTRON-ACCEPTORS; HUMIC SUBSTANCES; IONIZING-RADIATION; METAL
REDUCTION; OUTER-MEMBRANE Deinococcus radiodurans is an exceptionally radiation-resistant microorganism capable of surviving acute exposures to ionizing radiation doses of 15,000 Gy and previously described as having a strictly aerobic respiratory metabolism. Under strict anaerobic conditions, D. radiodurans R1 reduced Fe(III)-nitrilotriacetic acid coupled to the oxidation of lactate to CO2 and acetate but was unable to link this process to growth. D. radiodurans reduced the humic acid analog anthraquinone-2,6-disulfonate (AQDS) to its dihydroquinone form, AH(2)DS. which subsequently transferred electrons to the Fe(III) oxides hydrous ferric oxide and goethite via a previously described electron shuttle mechanism. D. radiodurans reduced the solid phase Fe(III) oxides in the presence of either 0.1 mM AQDS or leonardite humic acids (2 mg ml(-1)) but not in their absence. D, radiodurans also reduced U(VI) and Tc(VII) in the presence of AQDS. In contrast, Cr(VI) was directly reduced in anaerobic cultures with lactate although the rate of reduction was higher in the presence of AQDS. The results are the first evidence that D. radiodurans can reduce Fe(III) coupled to the oxidation of lactate or other organic compounds. Also, D. radiodurans, in combination with humic acids or synthetic electron shuttle agents, can reduce U and Te and thus has potential applications for remediation of metal- and radionuclide-contaminated sites where ionizing radiation or other DNA-damaging agents may restrict the activity of more sensitive organisms. Using Smart Source Parsing BALL JW, 1998, V43, P895, J CHEM ENG DATA BATTISTA JR, 1997, V51, P203, ANNU REV MICROBIOL BRIM H, 2000, V18, P85, NAT BIOTECHNOL BRINA R, 1992, V64, P1413, ANAL CHEM CAMPOS J, 1995, V68, P203, ANTON LEEUW INT J G DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL DOBBIN PS, 1995, V8, P163, BIOMETALS EMBLEY TM, 1993, V16, P25, SYST APPL MICROBIOL FERREIRA AC, 1997, V47, P939, INT J SYST BACTERIOL FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, IN PRESS GEOCHIM COS HENSEL R, 1986, V36, P444, INT J SYST BACTERIOL KIEFT TL, 1999, V65, P1214, APPL ENVIRON MICROB KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1999, V65, P4252, APPL ENVIRON MICROB LOVLEY DR, 1995, V14, P85, J IND MICROBIOL LOVLEY DR, 1991, V350, P413, NATURE LOVLEY DR, 1996, V382, P445, NATURE MATTIMORE V, 1996, V178, P633, J BACTERIOL MINTON KW, 1996, V363, P1, MUTAT RES-DNA REPAIR MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1992, V174, P3429, J BACTERIOL RILEY RG, 1992, DOEER0547T RODEN EE, 1996, V30, P1618, ENVIRON SCI TECHNOL RUSIN PA, 1994, V28, P1686, ENVIRON SCI TECHNOL SCOTT DT, 1998, V32, P2984, ENVIRON SCI TECHNOL SEELIGER S, 1998, V180, P3686, J BACTERIOL SMITH MD, 1988, V170, P2126, J BACTERIOL STOOKEY LL, 1970, V42, P779, ANAL CHEM TRATNYEK PG, 1989, V37, P248, J AGR FOOD CHEM TRIBALAT S, 1953, V8, P22, ANAL CHIM ACTA URONE PF, 1955, V27, P1354, ANAL CHEM VENKATESWARAN K, 1999, V49, P705, INT J SYST BACTERIOL WHITE O, 1999, V286, P1571, SCIENCE WILDUNG RE, IN PRESS APPL ENV MI ZACHARA JM, 1998, V83, P1426, AM MINERAL BATTELLE MEM INST,PACIFIC NW LABS, MSIN P7-50, POB 999/RICHLAND//WA/99352 (REPRINT); UNIFORMED SERV UNIV HLTH SCI,/BETHESDA//MD/20814 ? j Kieft, T. L.
Fredrickson, J. K.
Onstott, T. C.
Gorby, Y. A.
Kostandarithes, H. M.
Bailey, T. J.
Kennedy, D. W.
Li, S. W.
Plymale, A. E.
Spadoni, C. M.
Gray, M. S. 1999T Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate
1214-1221. Appl. Environ. Microbiol. 65 3- Microorganisms
Bacteria
Eubacteria
Metabolism A thermophilic bacterium that can use O2, NO3-, Fe(III), and S0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(HI) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H2. Both strains were also able to mineralize NTA to CO2 and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65degreeC; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S. Journal article? J Konopka, A.
Zakharova, T.
Bischoff, M.
Oliver, L.
Nakatsu, C.
Turco, R. F. 19998 Microbial biomass and activity in lead-contaminated soil
2256-2259. Appl. Environ. Microbiol. 65 5 Microorganisms
Biodiversity
Pollution Assessment Control and Management
Soil Science
Toxicology
Microbial Activity
Microbial Biomass
Microbial Community Diversity
Microbial Metal Resistance
Soil Contamination
Soil Pollution Microbial community diversity, potential microbial activity, and metal resistance were determined in three soils whose lead contents ranged from 0.00039 to 48 mmol of Pb kg of soil-1. Biomass levels were directly related to lead content. A molecular analysis of 16S rRNAs suggested that each soil contained a complex, diverse microbial community. A statistical analysis of the phospholipid fatty acids indicated that the community in the soil having the highest lead content was not related to the communities in the other soils. All of the soils contained active microbial populations that mineralized (14C) glucose. In all samples, 10 to 15% of the total culturable bacteria were Pb resistant and had MIC of Pb for growth of 100 to 150 muM. Journal article@ ? D Krumholz, Lee R.
Harris, Steve H.
Tay, Stephen T.
Suflita, Joseph M. 1999 Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles
2300-2306. Appl. Environ. Microbiol. 65 6 Microorganisms
Bacteria
Eubacteria
Bacteriology
Ecology (Environmental Sciences)
Systematics and Taxonomy
Subsurface Sandstone Ecosystem We examined the relative roles of acetogenic and sulfate-reducing bacteria H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S and rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.( Journal article; molecular sequence data? : Lloyd, J. R.
Sole, V. A.
VanPraagh, C. V. G.
Lovley, D. R. 2000O Direct and Fe(II)-mediated reduction of technetium by Fe(III)-reducing bacteria 3743-3749 Appl. Environ. Microbiol. 66 9 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): 16S RIBOSOMAL-RNA; GRADIENT GEL-ELECTROPHORESIS;
ESRF BEAMLINE ID26; X-RAY-ABSORPTION; GEOBACTER-SULFURREDUCENS;
MICROBIAL-POPULATIONS; IRON; PERTECHNETATE; FE(III); TCb The dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens reduced and precipitated Tc(Vn) by two mechanisms. Washed cell suspensions coupled the oxidation of hydrogen to enzymatic reduction of Tc(MI) to Tc(IV), leading to the precipitation of TcO2 at the periphery of the cell. An indirect, Fe(II)-mediated mechanism was also identified. Acetate, although not utilized efficiently as an electron donor for direct cell-mediated reduction of technetium, supported the reduction of Fe(III), and the Fe(II) formed was able to transfer electrons abiotically to Tc(VII), Tc(VII) reduction was comparatively inefficient via this indirect mechanism when soluble Fe(III) citrate was supplied to the cultures but was enhanced in the presence of solid Fe(III) oxide. The rate of Tc(VII) reduction was optimal, however, when Fe(III) oxide reduction was stimulated by the addition of the humic analog and electron shuttle anthaquinone-2,6-disulfonate, leading to the rapid formation of the Fe(II)-bearing mineral magnetite, Under these conditions, Tc(VII) was reduced and precipitated abiotically on the nanocrystals of biogenic magnetite as TcO2 and was removed from solution to concentrations below the limit of detection by scintillation counting. Cultures of Fe(III)-reducing bacteria enriched from radionuclide-contaminated sediment using Fe(III) oxide as an electron acceptor in the presence of 25 mu M Tc(VII) contained a single Geobacter sp, detected by 16S ribosomal DNA analysis and were also able to reduce and precipitate the radionuclide via biogenic magnetite, Fe(III) reduction was stimulated in aquifer material, resulting in the formation of Fe(II)-containing minerals that were able to reduce and precipitate Tc(VII). These results suggest that Fe(III)-reducing bacteria may play an important role in immobilizing technetium in sediments via direct and indirect mechanisms. Using Smart Source Parsing ALLEN PG, 1997, V76, P77, RADIOCHIM ACTA AMANN RI, 1990, V56, P1919, APPL ENVIRON MICROB ANDERSON RT, 1998, V32, P1222, ENVIRON SCI TECHNOL BONDIETTI EA, 1979, V203, P1337, SCIENCE CACCAVO F, 1994, V60, P3752, APPL ENVIRON MICROB CATALDO DA, 1989, V57, P281, HEALTH PHYS CUI DQ, 1996, V30, P2259, ENVIRON SCI TECHNOL CUI DQ, 1996, V30, P2263, ENVIRON SCI TECHNOL FARRELL J, 1999, V33, P1244, ENVIRON SCI TECHNOL GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GAUTHIER C, 1999, V6, P164, J SYNCHROTRON RADIAT HAINES RI, 1987, V1, P32, NUCL J CAN HENROT J, 1989, V57, P239, HEALTH PHYS LANE DJ, 1985, V82, P6955, P NATL ACAD SCI USA LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LLOYD JR, 1999, V66, P123, BIOTECHNOL BIOENG LLOYD JR, 2000, P277, ENV MICROBE METAL IN LLOYD JR, 1998, V15, P43, GEOMICROBIOL J LLOYD JR, 1997, V179, P2014, J BACTERIOL LLOYD JR, 1999, V181, P7647, J BACTERIOL LLOYD JR, 1997, V148, P530, RES MICROBIOL LOVLEY DR, 1986, V52, P751, APPL ENVIRON MICROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1990, P151, IRON BIOMINERALS LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1996, V382, P445, NATURE MACASKIE LE, 1991, V11, P41, CRIT REV BIOTECHNOL MAGEE RJ, 1985, P439, STANDARD POTENTIALS MAGNUSON TS, 1999, V185, P205, FEMS MICROBIOL LETT MAIDAK BL, 1999, V27, P171, NUCLEIC ACIDS RES MCCULLOUGH J, 1999, BIOREMEDIATION METAL MURRAY AE, 1996, V62, P2676, APPL ENVIRON MICROB MUYZER G, 1993, V59, P695, APPL ENVIRON MICROB NEIDHARDT FC, 1990, PHYSL BACTERIAL CELL NEVIN KP, 2000, V34, P2472, ENVIRON SCI TECHNOL PIGNOLET L, 1989, V57, P791, HEALTH PHYS SHUKLA SK, 1966, V21, P92, J CHROMATOGR SMITH PK, 1985, V150, P76, ANAL BIOCHEM SNOEYENBOSWEST O, 2000, V39, P153, MICROBIAL ECOL SOLE VA, 1999, V6, P174, J SYNCHROTRON RADIAT SPARKS NHC, 1990, V98, P14, EARTH PLANET SC LETT VONWINTZINGERODE F, 1999, V65, P283, APPL ENVIRON MICROB WATSON JHP, 1994, V7, P1017, MINER ENG YANKE LJ, 1995, V1, P61, ANAEROBEh UNIV MASSACHUSETTS,DEPT MICROBIOL/AMHERST//MA/01003 (REPRINT); ESRF EXAFS GRP,/F-38043 GRENOBLE//FRANCE/ ? + Lovley, Derek R.
Blunt-Harris, Elizabeth L. 1999Y Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction
4252-4254. Appl. Environ. Microbiol. 65 9c Microorganisms
Bacteria
Eubacteria
Bioenergetics (Biochemistry and Molecular Biophysics)
MetabolismT The dissimilatory Fe(III) reducer Geobacter metallireducens reduced Fe(III) bound in humic substances, but the concentrations of Fe(III) in a wide range of highly purified humic substances were too low to account for a significant portion of the electron-accepting capacities of the humic substances. Furthermore, once reduced, the iron in humic substances could not transfer electrons to Fe(III) oxide. These results suggest that other electron-accepting moieties in humic substances, such as quinones, are the important electron-accepting and shuttling agents under Fe(III)-reducing conditions. Journal article?! j Macnaughton, Sarah J.
Stephen, John R.
Venosa, Albert D.
Davis, Gregory A.
Chang, Yun-Juan
White, David C. 1999O Microbial population changes during bioremediation of an experimental oil spill
3566-3574. Appl. Environ. Microbiol. 65 8b Microorganisms
Bacteria
Eubacteria
Bioprocess Engineering
Methods and Techniques
Coastal Oil Spill= Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the alpha-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. alpha-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained. Journal article ?" Y Nevin, K. P.
Lovley, D. R. 2000 Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens 2248-2251 Appl. Environ. Microbiol. 66 5 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): C-TYPE CYTOCHROME; FE(III)-REDUCING BACTERIUM; HUMIC
SUBSTANCES; IRON; SULFURREDUCENS; MICROORGANISM; MECHANISMS;
ACCEPTORS; SEDIMENTS Studies with the dissimilatory Fe(III)-reducing microorganism Geobacter metallireducens demonstrated that the common technique of separating Fe(III)-reducing microorganisms and Fe(III) oxides with semipermeable membranes in order to determine whether the Fe(III) reducers release electron-shuttling compounds and/or Fe(III) chelators is invalid. This raised doubts about the mechanisms for Fe(III) oxide reduction by this organism. However, several experimental approaches indicated that G. metallireducens does not release electron-shuttling compounds and does not significantly solubilize Fe(III) during Fe(III) oxide reduction. These results suggest that G. merallireducens directly reduces insoluble Fe(III) oxide. Using Smart Source Parsing *DION CORP, 1999, DET TRANS MET ION CH ARNOLD RG, 1988, V32, P1081, BIOTECHNOL BIOENG BIRNBAUM S, 1981, V3, P393, BIOTECHNOL LETT CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CACCAVO F, 1997, V63, P3837, APPL ENVIRON MICROB CHEETHAM PSJ, 1979, V21, P2155, BIOTECHNOL BIOENG COATES JD, 1999, V49, P1615, INT J SYST BACTERIOL GASPARD S, 1998, V64, P3188, APPL ENVIRON MICROB GORBY YA, 1991, V57, P867, APPL ENVIRON MICROB LLOYD JR, 1999, V181, P7647, J BACTERIOL LOVLEY DR, 1998, V26, P152, ACTA HYDROCH HYDROB LOVLEY DR, 1988, V54, P1472, APPL ENVIRON MICROB LOVLEY DR, 1996, V132, P19, CHEM GEOL LOVLEY DR, 1991, V25, P1062, ENVIRON SCI TECHNOL LOVLEY DR, 1991, V55, P259, MICROBIOL REV LOVLEY DR, 1987, V330, P252, NATURE LOVLEY DR, 1994, V370, P128, NATURE LOVLEY DR, 1996, V382, P445, NATURE MAGNUSON TS, IN PRESS FEMS MICROB MUNCH JC, 1983, V35, P383, ECOL B STOCKHOLM SEELIGER S, 1998, V180, P3686, J BACTERIOL TUGEL JB, 1986, V52, P1167, APPL ENVIRON MICROB UNIV MASSACHUSETTS,DEPT MICROBIOL, MORRILL SCI CTR 4 203/AMHERST//MA/01003 (REPRINT); UNIV MASSACHUSETTS,DEPT MICROBIOL, MORRILL SCI CTR 4 203/AMHERST//MA/01003 ?# i > Sharma, P. K.
Balkwill, D. L.
Frenkel, A.
Vairavamurthy, M. A. 2000} A new Klebsiella planticola strain (Cd-1) grows anaerobically at high cadmium concentrations and precipitates cadmium sulfide 3083-3087 Appl. Environ. Microbiol. 66 7 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): X-RAY-ABSORPTION; ESCHERICHIA-COLI; RESISTANT;
BACTERIA; CULTURE Heavy metal resistance by bacteria is a topic of much importance to the bioremediation of contaminated soils and sediments. We report here the isolation of a highly cadmium-resistant Klebsiella planticola strain, Cd-1, from reducing salt marsh sediments. The strain grows in up to 15 mM CdCl2 under a wide range of NaCl concentrations and at acidic or neutral pH. In growth medium amended with thiosulfate, it precipitated significant amounts of cadmium sulfide (CdS), as confirmed by x-absorption spectroscopy. In comparison with various other strains tested, Cd-1 is superior for precipitating CdS in cultures containing thiosulfate. Thus, our results suggest that Cd-1 is a good candidate for the accelerated bioremediation of systems contaminated by high levels of cadmium. Using Smart Source Parsing BALKWILL DL, 1997, V20, P201, FEMS MICROBIOL REV BHATTACHARYYA G, 1989, V27, P574, INDIAN J EXP BIOL BRIM H, 1999, V22, P258, SYST APPL MICROBIOL CAMINITI R, 1981, V35, P373, ACTA CHEM SCAND A CHOUDHURY P, 1998, V44, P186, CAN J MICROBIOL COLLINS YE, 1989, P31, METAL IONS BACTERIA DESOETE G, 1983, V48, P621, PSYCHOMETRIKA FELSENTEIN J, 1993, PHYLIP PHYLOGENY INF FERIANC P, 1998, V144, P1045, MICROBIOL-UK FITCH WM, 1967, V155, P279, SCIENCE HOLMES JD, 1995, V163, P143, ARCH MICROBIOL JUKES TH, 1963, P21, MAMMALIAN PROTEIN ME KARPEL R, 1991, V266, P21753, J BIOL CHEM POULSON SR, 1997, V14, P41, GEOMICROBIOL J STERN EA, 1983, P955, HDB SYNCHROTRON RAD STERN EA, 1995, V208, P117, PHYSICA B SWOFFORD DL, 1993, PAUP PHYLOGENETIC AN VAIRAVAMURTHY A, 1998, V54, P2009, SPECTROCHIM ACTA A VAIRAVAMURTHY MA, 1997, V11, P546, ENERG FUEL WANG CL, 1997, V63, P4075, APPL ENVIRON MICROB WEISBURG WG, 1991, V173, P697, J BACTERIOL WHITE C, 1998, V144, P1407, MICROBIOL-UK WYCOKOFF R, 1964, V1, CRYSTAL STRUCTURES BROOKHAVEN NATL LAB,DEPT APPL SCI, BLDG 815/UPTON//NY/11973 (REPRINT); BROOKHAVEN NATL LAB,DEPT APPL SCI/UPTON//NY/11973; FLORIDA STATE UNIV,DEPT BIOL SCI/TALLAHASSEE//FL/32306 J?$ Spiro, A.
Lowe, M.
Brown, D. 2000i A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry 4258-4265 Appl. Environ. Microbiol. 66 10 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): NUCLEIC-ACIDS; HYBRIDIZATION; SYSTEM; MICROBIOLOGY;
FLUORESCEIN; STANDARDS; SUPPORT; ASSAYP A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-mu m diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and how cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte, Tn this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation. Using Smart Source Parsing BOGDANOV VL, 1997, V2985, P129, P SOC PHOTO-OPT INS DERBALIAN GP, 1988, V173, P59, ANAL BIOCHEM DOKTYCZ MJ, 1997, P205, AUTOMATED TECHNOLOGI EGGERS MD, 1997, SAE TECHNICAL PAPER FULTON RJ, 1997, V43, P1749, CLIN CHEM GURTLER V, 1996, V142, P3, MICROBIOL-UK GUSCHIN DY, 1997, V63, P2397, APPL ENVIRON MICROB IANNONE MA, 2000, V39, P131, CYTOMETRY IMAI T, 1996, V177, P245, J COLLOID INTERF SCI JACOBSEN CS, 1995, V61, P3347, APPL ENVIRON MICROB KLONIS N, 1996, V6, P147, J FLUORESCENCE KUMKE MU, 1995, V67, P3945, ANAL CHEM MADSEN EL, 1998, V32, P429, ENVIRON SCI TECHNOL NIKIFOROV TT, 1994, V3, P285, PCR METH APPL NUNNALLY BK, 1997, V69, P2392, ANAL CHEM ROGERS YH, 1999, V266, P23, ANAL BIOCHEM SCHWARTZ A, 1993, V677, P28, ANN NY ACAD SCI SCHWARTZ A, 1998, V33, P106, CYTOMETRY SJOBACK R, 1995, V51, PL7, SPECTROCHIM ACTA A SMITH PL, 1998, V44, P2054, CLIN CHEM WOOD WI, 1985, V82, P1585, P NATL ACAD SCI USA ZAMMATTEO N, 1997, V253, P180, ANAL BIOCHEM LOYOLA COLL,DEPT PHYS/BALTIMORE//MD/21210 (REPRINT); LOYOLA COLL,DEPT PHYS/BALTIMORE//MD/21210; UNIV MARYLAND,CTR MARINE BIOTECHNOL, INST BIOTECHNOL/BALTIMORE//MD/21202
?% | Stephen, John R.
Chang, Yun-Juan
Macnaughton, Sarah J.
Kowalchuk, George A.
Leung, Kam T.
Flemming, Cissy A.
White, David C. 1999 Effect of toxic metals on indigenous soil beta-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria 95-101. Appl. Environ. Microbiol. 65 1 Microorganisms
Bacteria
Eubacteria
Microbiology
Pollution Assessment Control and Management
Toxicology
Waste Management (Sanitation)
Biodegradation
Bioremediation
Microbial Community Structure
Nitrogen Cycling
Soil Contamination
Soils
Toxicity Protection Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (beta-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4+ levels in soil samples. The gene encoding the alpha-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the beta-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of beta-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of beta-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment. Journal article ?& X p Venkateswaran, A.
McFarlan, S. C.
Ghosal, D.
Minton, K. W.
Vasilenko, A.
Makarova, K.
Wackett, L. P.
Daly, M. J. 2000K Physiologic determinants of radiation resistance in Deinococcus radiodurans 2620-2626 Appl. Environ. Microbiol. 66 6 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): IONIZING-RADIATION; STREPTOCOCCUS-EQUISIMILIS;
REPAIR; DNA; RECOMBINATION; DAMAGE Immense volumes of radioactive wastes, which were generated during nuclear weapons production, were disposed of directly in the ground during the Cold War, a period when national security priorities often surmounted concerns over the environment, The bacterium Deinococcus radiodurans is the most radiation-resistant organism known and is currently being engineered for remediation of the toxic metal and organic components of these environmental wastes. Understanding the biotic potential of D. radiodurans and its global physiological integrity in nutritionally restricted radioactive environments is important in development of this organism for in situ bioremediation, We have previously shown that D. radiodurans can grow on rich medium in the presence of continuous radiation (6,000 rads/h) without lethality. In this study we developed a chemically defined minimal medium that can be used to analyze growth of this organism in the presence and in the absence of continuous radiation; whereas cell growth was not affected in the absence of radiation, cells did not grow and were killed in the presence of continuous radiation. Under nutrient-limiting conditions, DNA repair was found to be limited by the metabolic capabilities of D. radiodurans and not by any nutritionally induced defect in genetic repair. The results of our growth studies and analysis of the complete D. radiodurans genomic sequence support the hypothesis that there are several defects in D, radiodurans global metabolic regulation that limit carbon, nitrogen, and DNA metabolism. We identified key nutritional constituents that restore growth of D. radiodurans in nutritionally limiting radioactive environments. Using Smart Source Parsingb ALTSCHUL SF, 1997, V25, P3389, NUCLEIC ACIDS RES BRIM HS, 2000, V18, P85, NAT BIOTECHNOL BROOKS BW, 1980, V30, P627, INT J SYST BACTERIOL CASHEL M, 1996, P1410, CELL MOL BIOL CASHEL M, 1994, V3, P341, METH MOL G CHOU FI, 1990, V172, P2029, J BACTERIOL DALY MJ, 1994, V176, P3508, J BACTERIOL DALY MJ, 1994, V176, P7506, J BACTERIOL DALY MJ, 1995, V177, P5495, J BACTERIOL DALY MJ, 1996, V178, P4461, J BACTERIOL DARDALHONSAMSON.M, 1980, V38, P31, INT J RADIOL BIOL DARZYNKIEWICZ Z, 1994, V41, P401, METHOD CELL BIOL HANSEN MT, 1978, V134, P71, J BACTERIOL LANGE CC, 1998, V16, P929, NAT BIOTECHNOL LIN JY, 1999, V285, P1558, SCIENCE MACILWAIN C, 1996, V383, P375, NATURE MATTIMORE V, 1995, V177, P5232, J BACTERIOL MATTIMORE V, 1996, V178, P633, J BACTERIOL MCCULLOUGH J, 1999, BIOREMEDIATION METAL MECHOLD U, 1996, V178, P1401, J BACTERIOL MECHOLD U, 1997, V179, P2658, J BACTERIOL MINTON KW, 1995, V17, P457, BIOESSAYS MINTON KW, 1994, V13, P9, MOL MICROBIOL MINTON KW, 1996, V363, P1, MUTAT RES-DNA REPAIR RAJ HD, 1960, V6, P289, CAN J MICROBIOL RICHMOND RC, 1999, V3755, P210, SPIE RILEY RG, 1992, CHEM CONTAMINANTS DO SHAPIRO A, 1977, V33, P1129, APPL ENVIRON MICROB SMITH MD, 1988, V170, P2126, J BACTERIOL SOBEL ME, 1973, V113, P907, J BACTERIOL THORNLEY MJ, 1963, V26, P334, J APPL BACTERIOL WENDRICH TM, 1977, V26, P65, MOL MICROBIOL WHITE O, 1999, V286, P1571, SCIENCEz UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL, RM B3153, 4301 JONES BRIDGE RD/BETHESDA//MD/20814 (REPRINT); UNIFORMED SERV UNIV HLTH SCI,DEPT PATHOL/BETHESDA//MD/20814; UNIV MINNESOTA,DEPT BIOCHEM, BIOL PROC TECHNOL INST/ST PAUL//MN/55108; UNIV MINNESOTA,GORTNER LAB, CTR BIODEGRADAT RES & INFORMAT/ST PAUL//MN/55108; NIH,NATL CTR BIOTECHNOL INFORMAT, NATL LIB MED/BETHESDA//MD/20894 l ?' F Wang, C. L.
Maratukulam, P. D.
Lum, A. M.
Clark, D. S.
Keasling, J. D. 2000 Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface 4497-4502 Appl. Environ. Microbiol. 66 10| Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): TREPONEMA-DENTICOLA; EXPRESSION; SULFIDE; GENE;
PROMOTER The conversion of sulfate to an excess of free sulfide requires stringent reductive conditions. Dissimilatory sulfate reduction is used in nature by sulfate-reducing bacteria for respiration and results in the conversion of sulfate to sulfide. However, this dissimilatory sulfate reduction pathway is inhibited by oxygen and is thus limited to anaerobic environments. As an alternative, we have metabolically engineered a novel aerobic sulfate reduction pathway for the secretion of sulfides. The assimilatory sulfate reduction pathway was redirected to overproduce cysteine, and excess cysteine was converted to sulfide by cysteine desulfhydrase. As a potential application for this pathway, a bacterium was engineered with this pathway and was used to aerobically precipitate cadmium as cadmium sulfide, which was deposited on the cell surface. To maximize sulfide production and cadmium precipitation, the production of cysteine desulfhydrase was modulated to achieve an optimal balance between the production and degradation of cysteine. Using Smart Source Parsing AIKING H, 1982, V44, P938, APPL ENVIRON MICROB BARTON LL, 1995, P1, SULFATE REDUCING BAC CARRIER T, 1998, V59, P666, BIOTECHNOL BIOENG CHU L, 1995, V63, P4448, INFECT IMMUN CHU L, 1997, V65, P3231, INFECT IMMUN DENK D, 1987, V133, P515, J GEN MICROBIOL FORTIN D, 1994, V14, P121, FEMS MICROBIOL ECOL GAITONDE MK, 1967, V104, P627, BIOCHEM J GUZMAN LM, 1995, V177, P4121, J BACTERIOL HOLMES JD, 1997, V143, P2521, MICROBIOL-UK KREDICH NM, 1996, V1, P514, ESCHERICHIA COLI SAL MCFALL E, 1996, V1, P358, ESCHERICHIA COLI SAL NEIDHARDT FC, 1974, V119, P736, J BACTERIOL PETERS RW, 1985, V91, P165, AM I CHEM ENG S SER PEYTON BM, 1995, PNWD2315 SMITH A, 1999, HARNESSING NATURE CL WANNER BL, 1977, V130, P212, J BACTERIOL WHITE C, 1998, V144, P1407, MICROBIOL-UK WHITE C, 1996, V142, P2197, MICROBIOLOGY UNIV CALIF BERKELEY,DEPT CHEM ENGN, 201 GILMAN HALL/BERKELEY//CA/94720 (REPRINT); UNIV CALIF BERKELEY,DEPT CHEM ENGN/BERKELEY//CA/94720L ?( Y q Wildung, R. E.
Gorby, Y. A.
Krupka, K. M.
Hess, N. J.
Li, S. W.
Plymale, A. E.
McKinley, J. P.
Fredrickson, J. K. 2000 Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens 2451-2460 Appl. Environ. Microbiol. 66 6 Microbiology; biotechnology & applied microbiology
KeyWord Plus(R): MULTIPLE-SCATTERING CALCULATIONS; REDUCING BACTERIA;
METAL REDUCTION; MR-1; CYTOCHROME; BEHAVIORR To help provide a fundamental basis for use of microbial dissimilatory reduction processes in separating or immobilizing Tc-99 in waste or groundwaters, the effects of electron donor and the presence of the bicarbonate ion on the rate and extent of pertechnetate ion [Tc(VII)O-4(-)] enzymatic reduction by the subsurface metal-reducing bacterium Shewanella putrefaciens CN32 were determined, and the forms of aqueous and solid-phase reduction products were evaluated through a combination of high-resolution transmission electron microscopy, X-ray absorption spectroscopy, and thermodynamic calculations. When H-2 served as the electron donor, dissolved Tc(VII) was rapidly reduced to amorphous Tc(IV) hydrous oxide, which was largely associated with the cell in unbuffered 0.85% NaCl and with extracellular particulates (0.2 to 0.001 mu m) in bicarbonate buffer. Cell-associated Tc was present principally in the periplasm and outside the outer membrane. The reduction rate was much lower when lactate was the electron donor, with extracellular Tc(IV) hydrous oxide the dominant solid-phase reduction product, but in bicarbonate systems much less Tc(IV) was associated directly with the cell and solid-phase Tc(IV) carbonate may have been present. in the presence of carbonate, soluble (<0.001 pm) electronegative, Tc(IV) carbonate complexes were also formed that exceeded Tc(VII)O-4(-) in electrophoretic mobility. Thermodynamic calculations indicate that the dominant reduced Tc species identified in the experiments would be stable over a range of E-h and pH conditions typical of natural waters. Thus, carbonate complexes may represent an important pathway for Tc transport in anaerobic subsurface environments, where it has generally been assumed that Tc mobility is controlled by low-solubility Tc(IV) hydrous oxide and adsorptive, aqueous Tc(IV) hydrolysis products. Using Smart Source ParsingJ ALLISON JD, 1991, EPA600391021 BREZNAKJA, 1994, P137, METHODS GEN MOL BACT CACCAVO F, 1992, V58, P3211, APPL ENVIRON MICROB CUI DQ, 1996, V30, P2263, ENVIRON SCI TECHNOL ERIKSEN TE, 1992, V58, P67, RADIOCHIM ACTA FREDRICKSON JK, 1996, V7, P287, CURR OPIN BIOTECH FREDRICKSON JK, 1998, V62, P3239, GEOCHIM COSMOCHIM AC FREDRICKSON JK, 1999, V62, P3239, GEOCHIM COSMOCHIM AC HAINES RI, 1987, V1, P32, NUCL J CAN HARTMAN MJ, 1988, PNNL11973 JACKSON GE, 1994, V45, P581, APPL RADIAT ISOTOPES KOSTKA JE, 1995, V29, P2535, ENVIRON SCI TECHNOL LANGMUIR D, 1997, AQUEOUS ENV GEOCHEMI LEISER KH, 1987, V42, P213, RADIOCHIM ACTA LEMIRE RJ, 1996, V412, P873, MATER RES SOC SYMP P LLOYD JR, 1996, V62, P578, APPL ENVIRON MICROB LLOYD JR, 1999, V65, P2691, APPL ENVIRON MICROB LLOYD JR, 1998, V15, P45, GEOMICROBIOL J LOVLEY DR, 1993, V47, P263, ANNU REV MICROBIOL LOVLEY DR, 1993, V59, P3572, APPL ENVIRON MICROB LOVLEY DR, 1995, V14, P85, J IND MICROBIOL MCMASTER WH, 1969, UCRL50174 L LIV NAT MEYER RE, 1986, ORNL6199 MEYER RE, 1991, V55, P11, RADIOCHIM ACTA MYERS CR, 1997, V1326, P307, BBA-BIOMEMBRANES MYERS CR, 1993, V108, P15, FEMS MICROBIOL LETT MYERS CR, 1993, V114, P215, FEMS MICROBIOL LETT MYERS JM, 1998, V1373, P237, BBA-BIOMEMBRANES NORDSTROM DK, 1985, GEOCHEMICAL THERMODY PACQUETTE J, 1985, V63, P2639, CAN J CHEM RARD JA, 1983, UCRL53440 L LIV NAT REHR JJ, 1992, V69, P3397, PHYS REV LETT TRIBALAT S, 1953, V8, P22, ANAL CHIM ACTA WILDENTHAL BH, 1984, V11, P5, PROG PART NUCL PHYS WILDUNG RE, 1979, V8, P156, J ENVIRON QUAL WILDUNG RE, 1997, 1 ANN INT BIOM S CAL ZABINSKY SI, 1995, V52, P2995, PHYS REV BN PACIFIC NW NATL LAB,ENVIRONM SCI RES CTR, POB 999/RICHLAND//WA/99352 (REPRINT)o?) o Fredrickson, James K.
Zachara, John M.
Kukkadapu, Ravi K.
Gorby, Yuri A.
Smith, Steven C.
Brown, Christopher F. 2001Y Biotransformation of Ni-substituted hydrous ferric oxide by an Fe(III)-reducing bacterium 703-712." Environmental Science & Technology 35 4A The reductive biotransformation of a Ni2plus-minussubstituted (5 mol %) hydrous ferric oxide (NiHFO) by Shewanella putrefaciens, strain CN32, was investigated under anoxic conditions at circumneutral pH. Our objectives were to define the influence of Ni2+ substitution on the bioreducibility of the HFO and the biomineralization products formed and to identify biogeochemical factors controlling the phase distribution of Ni2+ during bioreduction. Incubations with CN32 and NiHFO were sampled after 14 and 32 d, and both aqueous chemistry and solid phases were characterized. By comparison of these results with a previous study (Fredrickson, J. K.; Zachara, J. M.; Kennedy, D. W.; Dong, H.; Onstott, T. C.; Hinman, N. W.; Li, S. W. Geochim. Cosmochim. Acta 1998, 62, 3239-3257), it was concluded that coprecipitated/sorbed Ni2+ inhibited the bioreduction of HFO through an undefined chemical mechanism. Mossbauer spectroscopy allowed analysis of the residual HFO phase and the identity and approximate mass percent of biogenic mineral phases. The presence of AQDS, a soluble electron shuttle that obviates need for cell-oxide contact, was found to counteract the inhibiting effect of Ni2+. Nickel was generally mobilized during bioreduction in a trend that correlated with final pH, except in cases where PO43- was present and vivianite precipitation occurred. CN32 promoted the formation of Ni2plus-minussubstituted magnetite (Fe2IIIFe(1-x)IINixIIO4) in media with AQDS but without PO43-. The formation of this biogenic coprecipitate, however, had little discernible impact on final aqueous Ni2+ concentrations. These results demonstrate that coprecipitated Ni can inhibit dissimilatory microbial reduction of amorphous iron oxide, but the presence of humic acids may facilitate the immobilization of Ni within the crystal structure of biogenic magnetite. Journal article ?* j S John, Seth G.
Ruggiero, Christy E.
Hersman, Larry E.
Tung, Chang-Shung
Neu, Mary P. 2001O Siderophore mediated plutonium accumulation by Microbacterium flavescens (JG-9)
2942-2948." Environmental Science & Technology 35 14 Uptake of plutonium and uranium mediated by the siderophore desferrioxamine-B (DFOB) has been studied for the common soil aerobe Microbacterium flavescens (JG-9). M. flavescens does not bind or take up nitrilotriacetic acid (NTA) complexes of U(VI), Fe(III), or Pu(IV) or U(VI)-DFOB but does take up Fe(III)-DFOB and Pu(IV)-DFOB. Pu(IV)-DFOB and Fe(III)-DFOB accumulations are similar: only living and metabolically active bacteria take up these metal-siderophore complexes. The Fe(III)-DFOB and Pu(IV)-DFOB complexes mutually inhibit uptake of the other, indicating that they compete for shared binding sites or uptake proteins. However, Pu uptake is much slower than Fe uptake, and cumulative Pu uptake is less than Fe, 1.0 nmol of Fe vs 0.25 nmol of Pu per mg of dry weight bacteria. The Pu(IV)-DFOB interactions with M. flavescens suggest that Pu-siderophore complexes could generally be recognized by Fe-siderophore uptake systems of many bacteria, fungi, or plants, thereby affecting Pu environmental mobility and distribution. The results also suggest that the siderophore complexes of tetravalent metals can be recognized by Fe-siderophore uptake proteins. Journal article]?+ Liu, Chongxuan
Zachara, John M. 2001V Uncertainties of Monod kinetic parameters nonlinearly estimated from batch experiments 133-141." Environmental Science & Technology 35 1 Monod kinetic parameters (Ks, mumax, and Y) that are estimated from batch experimental data can have large uncertainties due to linear correlations between them. The degree of correlation and the resulting uncertainties of the Monod parameters are functions of the initial experimental conditions, the values of the parameters, the type and magnitude of measurement errors, and the sampling number. Careful manipulation of experimental conditions can reduce the correlations between Monod parameters allowing for the estimation of Monod kinetic parameters with the lowest degree of uncertainty. By dimensionless analysis, the correlation and relative standard deviations of Monod parameters were found to be functions of a few dimensionless variables involving the initial substrate (S0) and cell (X0) concentrations. Quantitative relationships were analyzed between the dimensionless variables and the correlation and the uncertainties of the Monod parameters. This analysis allowed for identification of the optimal experimental conditions for estimating Monod parameters under both no growth and growth conditions coupled with two kinds of measurement errors: those with constant absolute standard deviation and those with constant relative standard deviation. Examples involving the microbial reduction of iron(III) as an electron acceptor are used to illustrate the application of the developed technique. Journal article?, Nevin, Kelly P.
Lovley, Derek R. 2000^ Potential for nonenzymatic reduction of Fe(III) via electron shuttling in subsurface sediments
2472-2478." Environmental Science & Technology 34 12 The potential for various substances to serve as electron shuttles between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides in aquifer sediments was evaluated in order to determine whether abiological mechanisms might play a role in the apparent microbial reduction of Fe(III) in subsurface sediments. Humic substances (humics) and the humics analogue, anthraquinone-2,6-disulfonate (AQDS), which were previously found to stimulate microbial reduction of synthetic poorly crystalline Fe(III) oxide under laboratory conditions, were found to also stimulate the reduction of aquifer Fe(III) oxides by indigenous microorganisms. Electron shuttling via biological reduction of U(VI) or Sdegree followed by abiological reduction of Fe(III) by U(IV) or sulfide enhanced the reduction of synthetic Fe(III) oxide in cell suspensions, but these potential electron shuttles did not stimulate Fe(III) reduction when they were added to aquifer sediments. These results emphasize the importance of evaluating potential mechanisms for Fe(III) reduction with natural Fe(III) oxides, under environmentally relevant conditions. The finding that humics and other extracellular quinones can serve as electron shuttles to the Fe(III) oxides found in subsurface environments suggests that some Fe(III) reduction which was previously considered to be the result of direct enzymatic reduction of Fe(III) oxides may instead result from abiotic reduction of Fe(III) by microbially reduced humics or other microbially generated hydroquinones. Journal article ?- w Tokunaga, Tetsu K.
Wan, Jiamin
Firestone, Mary K.
Hazen, Terry C.
Schwartz, Egbert
Sutton, Stephen R.
Newville, Matthew 20013 Chromium diffusion and reduction in soil aggregates
3169-3174." Environmental Science & Technology 35 15 The distribution of metal contaminants such as chromium in soils can be strongly localized by transport limitations and redox gradients within soil aggregates. Measurements of Cr(VI) diffusion and reduction to Cr(III) were obtained in soil columns representing transects into soil aggregates in order to quantify influences of organic carbon (OC) and redox potentials on Cr transport distances and microbial community composition. Shifts in characteristic redox potentials, and the extent of Cr(VI) reduction to Cr(III) were related to OC availability. Depth profiles of Cr(VI, III) obtained with micro X-ray absorption near edge structure (micro-XANES) spectroscopy reflected interdependent effects of diffusion and spatially dependent redox potentials on reduction kinetics and microbial community composition. Shallow diffusion depths (2-10 mm) and very sharply terminated diffusion fronts in columns amended with OC (80 and 800 ppm) reflected rapid increases in Cr reduction kinetics over very short (mm) distances. These results suggest that Cr contamination in soils can be restricted to the outsides of soil aggregates due to localized transport and rapid reduction and that bulk sample characterization is inadequate for understanding the controlling biogeochemical processes. Journal article v?. X B Vanbriesen, J. M.
Rittmann, B. E.
Xun, L.
Girvin, D. C.
Bolton, H. 2000` The rate-controlling substrate of nitrilotriacetate for biodegradation by Chelatobacter heintzii
3346-3353." Environmental Science & Technology 34 16 Codisoposal of anthropogenic chelating agents such as nitrilotriacetate (NTA) with radioactive and heavy metals can enhance environmental transport of the metals, extending subsurface contamination and threatening groundwater sources. The biodegradation of the chelating agent can lead to the immobilization of the chelated metal and radionuclide contaminants. The rate of biodegradation of the organic complexing agent may depend on the concentration of a specific, biologically available form of the chelate. In mixtures of metals and chelating agents, the relative distribution of different chemical forms of the chelate at equilibrium is controlled by the total concentrations of organic and inorganic constituents and thermodynamic stability constants for the aqueous complexes that form. In this paper, we evaluate experimental results for biodegradation of NTA by Chelatobacter heintzii in different metal/NTA systems in order to identify the chelate form controlling the rate of degradation. The CaNTA- is the only species that can control the rate of NTA degradation in our systems. Our analysis of the potentially rate-limiting reactions in the biodegradation of NTA indicates that kinetically controlled complexation in the NTA system is not affecting the biodegradation of the chelate. The rate of transport of CaNTA- into the cell appears to control the overall rate of NTA degradation. Thus, we expect enhanced rates of biological degradation of the chelate and immobilization of codisposed metals when CaNTA- is available to C. heintzii. Journal article q?/ 2 Weber, Karrie A.
Picardal, Flynn W.
Roden, Eric E. 2001Z Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds
1644-1650." Environmental Science & Technology 35 8} The potential for microbially catalyzed NO3--dependent oxidation of solid-phase Fe(II) compounds was examined using a previously described autotrophic, denitrifying, Fe-(II)-oxidizing enrichment culture. The following solid-phase Fe(II)-bearing minerals were considered: microbially reduced synthetic goethite, two different end products of microbially hydrous ferric oxide (HFO) reduction (biogenic Fe3O4 and biogenic FeCO3), chemically precipitated FeCO3, and two microbially reduced iron(III) oxide-rich subsoils. The microbially reduced goethite, subsoils, and chemically precipitated FeCO3 were subject to rapid NO3--dependent Fe(II) oxidation. Significant oxidation of biogenic Fe3O4 was observed. Very little biogenic FeCO3 was oxidized. No reduction of NO3- or oxidation of Fe(II) occurred in pasteurized cultures. The molar ratio of NO3- reduced to Fe(II) oxidized in cultures containing chemically precipitated FeCO3, and one of the microbially reduced subsoils approximated the theoretical stoichiometry of 0.2:1. However, molar ratios obtained for oxidation of microbially reduced goethite, the other subsoil, and the HFO reduction en