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Camacho-Sanchez M, Camacho M, Redondo-Gómez S, Mateos-Naranjo E. Bacterial assemblage in Mediterranean salt marshes: Disentangling the relative importance of seasonality, zonation and halophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157514. [PMID: 35878855 DOI: 10.1016/j.scitotenv.2022.157514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Salt marshes gather a high diversity of prokaryotes across their environmental gradients. Most of this diversity and the factors determining their community assemblage are unknown. We massively sequenced a portion of the 16S gene to characterize the diversity of prokaryotes in soils from a salt marsh in Río Piedras, Southern Spain. We sampled in the four seasons, and in five plots dominated by a different halophyte (Spartina maritima, S. densiflora, Salicornia ramosissima, Arthrocaulon macrostachyum and Atriplex portulacoides) growing under different environmental conditions and representing different stages in the marsh ecological succession. Soil was sampled in their rhizosphere and adjacent bulk soil. We report the effects of different factors explaining prokaryotic beta diversity in the marsh: zonation (50 %), seasonality (14 %), and halophyte rhizosphere (7 %). Proteobacteria and Bacteroidota were the most abundant phyla. Firmicutes had a peak in winter and Desulfobacterota with other bacteria involved in sulfur cycling were abundant in the low marsh plots from S. maritima. Alpha diversity was highest in spring and decreased in winter. We detected a marked phylogenetic turnover between seasons and in rhizospheric soil respect to adjacent bulk soil for most pairwise comparisons. The effect of halophyte on its rhizosphere was species-specific, being S. maritima the species with more differentiated taxa between rhizosphere versus surrounding bulk soil. Our work highlights how the complex interaction between marsh zonation, seasonality and rhizosphere, onsets processes structuring bacterial community assemblage in salt marsh soils.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro Las Torres, 41200 Alcalá del Río, Sevilla, Spain.
| | - María Camacho
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Centro Las Torres, 41200 Alcalá del Río, Sevilla, Spain.
| | - Susana Redondo-Gómez
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain.
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Nomaki H, Bernhard JM, Ishida A, Tsuchiya M, Uematsu K, Tame A, Kitahashi T, Takahata N, Sano Y, Toyofuku T. Intracellular Isotope Localization in Ammonia sp. (Foraminifera) of Oxygen-Depleted Environments: Results of Nitrate and Sulfate Labeling Experiments. Front Microbiol 2016; 7:163. [PMID: 26925038 PMCID: PMC4759270 DOI: 10.3389/fmicb.2016.00163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much (15)N or (34)S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200-500 nm in diameter and co-occurred with possible endobionts, were labeled with (15)N originated from (15)N-labeled nitrate under anoxia and were labeled with both (15)N and (34)S under dysoxia. The labeling with (15)N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
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Affiliation(s)
- Hidetaka Nomaki
- Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Joan M Bernhard
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Akizumi Ishida
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Masashi Tsuchiya
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | | | | | - Tomo Kitahashi
- Project Team for Research and Development of Next-generation Technology for Ocean Resources Exploration, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Naoto Takahata
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Yuji Sano
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Takashi Toyofuku
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
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Stauffert M, Cravo-Laureau C, Duran R. Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15273-15284. [PMID: 25256587 DOI: 10.1007/s11356-014-3624-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Robert Duran
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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Lazar CS, Dinasquet J, L'Haridon S, Pignet P, Toffin L. Distribution of anaerobic methane-oxidizing and sulfate-reducing communities in the G11 Nyegga pockmark, Norwegian Sea. Antonie van Leeuwenhoek 2011; 100:639-53. [PMID: 21751028 DOI: 10.1007/s10482-011-9620-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/30/2011] [Indexed: 01/31/2023]
Abstract
Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well. The vertical distribution of the archaeal community assessed by PCR-DGGE highlighted the presence of ANME-2 in surface sediments, and ANME-1 in deeper sediments. Enrichments of methanogens showed the presence of hydrogenotrophic methanogens of the Methanogenium genus in surface sediment layers as well. The active fraction of the archaeal community was uniquely composed of ANME-2 in the shallow sulfate-rich sediments. Functional methyl coenzyme M reductase gene libraries showed that sequences affiliated with the ANME-1 and ANME-3 groups appeared in the deeper sediments but ANME-2 dominated both surface and deeper layers. Finally, dissimilatory sulfite reductase gene libraries revealed a high SRB diversity (i.e. Desulfobacteraceae, Desulfobulbaceae, Syntrophobacteraceae and Firmicutes) in the shallow sulfate-rich sediments. The SRB diversity was much lower in the deeper section. Overall, these results show that the microbial community in sediments associated with a pockmark harbour classical cold seep ANME and SRB communities.
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Affiliation(s)
- Cassandre Sara Lazar
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, IFREMER Centre de Brest, Département Etudes des Environnements Profonds, Université de Bretagne Occidentale, Plouzané, France.
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Abed RMM, Musat N, Musat F, Mussmann M. Structure of microbial communities and hydrocarbon-dependent sulfate reduction in the anoxic layer of a polluted microbial mat. MARINE POLLUTION BULLETIN 2011; 62:539-546. [PMID: 21194714 DOI: 10.1016/j.marpolbul.2010.11.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/27/2010] [Accepted: 11/30/2010] [Indexed: 05/30/2023]
Abstract
The bacterial communities in the anoxic layer of a heavily polluted microbial mat and their growth on hydrocarbons under sulfate-reducing conditions were investigated. Microbial communities were dominated by members of Alphaproteobacteria (27% of the total rRNA), Planctomycetes (21.1%) and sulfate-reducing bacteria (SRB: 17.5%). 16S rRNA cloning revealed sequences beloning to the same bacterial groups with SRB affiliated to the genera Desulfobulbus, Desulfocapsa, Desulfomicrobium, Desulfobacterium and Desulfosarcina/Desulfococcus. The derived enrichment cultures on crude oil, hexadecane and toluene were dominated by SRB. While most SRB sequences of the toluene and hexadecane cultures were related to the sequence of Desulfotignum toluolica, the crude oil enrichment showed a more diverse bacterial community with sequences from the genera Desulfotignum, Desulfobacter, Desulfatibacillus, Desulfosalina, and Desulfococcus. We conclude that the anoxic layer of the studied mats contains a diverse community of anaerobic bacteria, dominated by SRB, some of which are able to grow on hydrocarbons.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box 36, PC 123 Al Khoud, Oman.
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Davis DA, Gamble MD, Bagwell CE, Bergholz PW, Lovell CR. Responses of salt marsh plant rhizosphere diazotroph assemblages to changes in marsh elevation, edaphic conditions and plant host species. MICROBIAL ECOLOGY 2011; 61:386-398. [PMID: 20963583 DOI: 10.1007/s00248-010-9757-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 09/28/2010] [Indexed: 05/30/2023]
Abstract
An important source of new nitrogen in salt marsh ecosystems is microbial diazotrophy (nitrogen fixation). The diazotroph assemblages associated with the rhizospheres (sediment directly affected by the roots) of salt marsh plants are highly diverse, somewhat stable, and consist mainly of novel organisms. In Crab Haul Creek Basin, North Inlet, SC, the distribution of plant types into discrete zones is dictated by relatively minor differences in marsh elevation and it was hypothesized that the biotic and abiotic properties of the plant zones would also dictate the composition of the rhizosphere diazotroph assemblages. Over a period of 1 year, rhizosphere sediments were collected from monotypic stands of the black needlerush, Juncus roemerianus, the common pickleweed, Salicornia virginica, the short and tall growth forms of the smooth cordgrass Spartina alterniflora, and a mixed zone of co-occurring S. virginica and short form, S. alterniflora. DNA was extracted, purified and nifH sequences PCR amplified for denaturing gradient gel electrophoresis (DGGE) analysis to determine the composition of the diazotroph assemblages. The diazotroph assemblages were strongly influenced by season, abiotic environmental parameters and plant host. Sediment chemistry and nitrogen fixation activity were also significantly influenced by seasonal changes. DGGE bands that significantly affected seasonal and zone specific clustering were identified and most of these sequences were from novel diazotrophs, unaffiliated with any previously described organisms. At least one third of the recovered nifH sequences were from a diverse assemblage of Chlorobia, and γ-, α-, β- and δ-Proteobacteria. Diazotrophs that occurred throughout the growing season and among all zones (frequently detected) were also mostly novel. These significant sequences indicated that diazotrophs driving the structure of the assemblages were diverse, versatile, and some were ubiquitous while others were seasonally responsive. Several ubiquitous sequences were closely related to sequences of actively N(2) fixing diazotrophs previously recovered from this system. These sequences from ubiquitous and versatile organisms likely indicate the diazotrophs in these rhizosphere assemblages that significantly contribute to ecosystem function.
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Affiliation(s)
- Debra A Davis
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage. Appl Environ Microbiol 2010; 76:4819-28. [PMID: 20472728 DOI: 10.1128/aem.03006-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered dsrAB sequences from three sites sampled along an AMD flow path indicated the dominance of a single Desulfovibrio species. Other major sequence clades were related most closely to Desulfosarcina, Desulfococcus, Desulfobulbus, and Desulfosporosinus species. The presence of metal sulfides with low delta(34)S values relative to delta(34)S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of approximately 2), although possibly within less acidic microenvironments. Interestingly, delta(34)S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.
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Elboutahiri N, Thami-Alami I, Udupa SM. Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco. BMC Microbiol 2010; 10:15. [PMID: 20089174 PMCID: PMC2823721 DOI: 10.1186/1471-2180-10-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 01/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco. RESULTS RsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM), water stress (-1.5 MPa), high temperature (40 degrees C) and low pH (3.5), respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn) and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline). The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P < 0.01) genetic variation was distributed within regions (89%) than among regions (11%). CONCLUSION High degree of phenotypic and genotypic diversity is present in S. meliloti and S. medicae populations from marginal soils affected by salt and drought, in arid and semi-arid regions of Morocco. Some of the tolerant strains have a potential for exploitation in salt and drought affected areas for biological nitrogen fixation in alfalfa.
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Affiliation(s)
- Nadia Elboutahiri
- Institut National de la Recherche Agronomique (INRA), Centre Régional de la Recherche Agronomique de Rabat, B,P, 415, Rabat, Morocco
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Lasher C, Dyszynski G, Everett K, Edmonds J, Ye W, Sheldon W, Wang S, Joye SB, Moran MA, Whitman WB. The diverse bacterial community in intertidal, anaerobic sediments at Sapelo Island, Georgia. MICROBIAL ECOLOGY 2009; 58:244-61. [PMID: 19212699 PMCID: PMC2709879 DOI: 10.1007/s00248-008-9481-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 12/05/2008] [Indexed: 05/20/2023]
Abstract
The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the gamma-Proteobacteria. Other abundant groups included the delta-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa.
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Affiliation(s)
- Chris Lasher
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605 USA
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Glen Dyszynski
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605 USA
- 2521 Piedmont Rd NE #2427, Atlanta, GA 30324 USA
| | - Karin Everett
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605 USA
- 6006 172nd Place SW, Lynnwood, 98037 USA
| | - Jennifer Edmonds
- Department of Marine Sciences, University of Georgia, Athens, GA 30605 USA
- Department of Biological Sciences, University of Alabama, P.O. Box 870206, Tuscaloosa, AL 35487 USA
| | - Wenying Ye
- Department of Marine Sciences, University of Georgia, Athens, GA 30605 USA
- Synthetic Genomics, Inc., La Jolla, CA 92037 USA
| | - Wade Sheldon
- Department of Marine Sciences, University of Georgia, Athens, GA 30605 USA
| | - Shiyao Wang
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605 USA
| | - Samantha B. Joye
- Department of Marine Sciences, University of Georgia, Athens, GA 30605 USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA 30605 USA
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605 USA
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Guo Q, Blowes DW. Biogeochemistry of two types of permeable reactive barriers, organic carbon and iron-bearing organic carbon for mine drainage treatment: column experiments. JOURNAL OF CONTAMINANT HYDROLOGY 2009; 107:128-139. [PMID: 19467564 DOI: 10.1016/j.jconhyd.2009.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 04/18/2009] [Accepted: 04/24/2009] [Indexed: 05/27/2023]
Abstract
Permeable reactive barriers (PRBs) are an alternative technology to treat mine drainage containing sulfate and heavy metals. Two column experiments were conducted to assess the suitability of an organic carbon (OC) based reactive mixture and an Fe(0)-bearing organic carbon (FeOC) based reactive mixture, under controlled groundwater flow conditions. The organic carbon mixture contains about 30% (volume) organic carbon (composted leaf mulch) and 70% (volume) sand and gravel. The Fe(0)-bearing organic carbon mixture contains 10% (volume) zero-valent iron, 20% (volume) organic carbon, 10% (volume) limestone, and 60% (volume) sand and gravel. Simulated groundwater containing 380 ppm sulfate, 5 ppm As, and 0.5 ppm Sb was passed through the columns at flow rates of 64 (the OC column) and 62 (the FeOC column) ml d(-1), which are equivalent to 0.79 (the OC column) and 0.78 (the FeOC column) pore volumes (PVs) per week or 0.046 m d(-1) for both columns. The OC column showed an initial sulfate reduction rate of 0.4 micromol g (OC)(-1) d(-1) and exhausted its capacity to promote sulfate reduction after 30 PVs, or 9 months of flow. The FeOC column sustained a relatively constant sulfate reduction rate of 0.9 micromol g (OC)(-1) d(-1) for at least 65 PVs (17 months). In the FeOC column, the delta34S values increase with the decreasing sulfate concentration. The delta34S fractionation follows a Rayleigh fractionation model with an enrichment factor of 21.6 per thousand. The performance decline of the OC column was caused by the depletion of substrate or electron donor. The cathodic production of H2 by anaerobic corrosion of Fe probably sustained a higher level of SRB activity in the FeOC column. These results suggest that zero-valent iron can be used to provide an electron donor in sulfate reducing PRBs. A sharp increase in the delta(13)C value of the dissolved inorganic carbon and a decrease in the concentration of HCO3- indicate that hydrogenotrophic methanogenesis is occurring in the first 15 cm of the FeOC column.
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Affiliation(s)
- Qiang Guo
- Department of Earth Sciences, University of Waterloo, 200 Univ. Ave. W., Waterloo, Ontario N2L3G1, Canada.
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Gough HL, Dahl AL, Tribou E, Noble PA, Gaillard JF, Stahl DA. Elevated sulfate reduction in metal-contaminated freshwater lake sediments. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2008jg000738] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Heidi L. Gough
- Department of Civil and Environmental Engineering; Northwestern University; Evanston Illinois USA
- Department of Civil and Environmental Engineering; University of Washington; Seattle Washington USA
| | - Amy L. Dahl
- Department of Civil and Environmental Engineering; Northwestern University; Evanston Illinois USA
| | - Erik Tribou
- Department of Civil and Environmental Engineering; University of Washington; Seattle Washington USA
| | - Peter A. Noble
- Department of Civil and Environmental Engineering; University of Washington; Seattle Washington USA
| | - Jean-François Gaillard
- Department of Civil and Environmental Engineering; Northwestern University; Evanston Illinois USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering; University of Washington; Seattle Washington USA
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Liu Y, Nikolausz M, Jin P. Abundance and diversity of sulphate-reducing bacteria within a crude oil gathering and transferring system in China. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Vladár P, Rusznyák A, Márialigeti K, Borsodi AK. Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach. MICROBIAL ECOLOGY 2008; 56:64-75. [PMID: 18066486 DOI: 10.1007/s00248-007-9324-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
The community structure of sulfate-reducing bacteria (SRB) associated with reed (Phragmites australis) rhizosphere in Lake Velencei (Hungary) was investigated by using cultivation-based and molecular methods. The cultivation methods were restricted to recover lactate-utilizing species with the exclusion of Desulfobacter and some Desulfobacterium species presumably not being dominant members of the examined community. The most-probable-number (MPN) estimations of lactate-utilizing SRB showed that the cell counts in reed rhizosphere were at least one order of magnitude higher than that in the bulk sediment. The number of endospores was low compared to the total SRB counts. From the highest positive dilution of MPN series, 47 strains were isolated and grouped by restriction fragment length polymorphism (RFLP) analysis of the amplified 16S ribosomal RNA (rRNA) and dsrAB (dissimilatory sulfite reductase) genes. Contrary to the physiological diversity of the isolates, the combined results of RFLP analysis revealed higher diversity at species as well as at subspecies level. Based on the partial 16S rRNA sequences, the representative strains were closely affiliated with the genera Desulfovibrio and Desulfotomaculum. The partial dsrAB sequences of the clones, recovered after isolation and PCR amplification of the community DNA, were related to hitherto uncultured species of the genera Desulfovibrio and Desulfobulbus. Nevertheless, the representative of the second largest clone group was shown to be closely affiliated with the sequenced dsrAB gene of a strain isolated from the same environment and identified as Desulfovibrio alcoholivorans. Another clone sequence was closely related to a possible novel species also isolated within the scope of this work.
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Affiliation(s)
- Péter Vladár
- Department of Microbiology, Eötvös Loránd University, Pázmány P sétány 1/C, Budapest, Hungary
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Hamdan LJ, Gillevet PM, Sikaroodi M, Pohlman JW, Plummer RE, Coffin RB. Geomicrobial characterization of gas hydrate-bearing sediments along the mid-Chilean margin. FEMS Microbiol Ecol 2008; 65:15-30. [DOI: 10.1111/j.1574-6941.2008.00507.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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15
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Isolation of surfactant-resistant bacteria from natural, surfactant-rich marine habitats. Appl Environ Microbiol 2008; 74:5093-9. [PMID: 18586977 DOI: 10.1128/aem.02734-07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental remediation efforts often utilize either biodegradative microbes or surfactants, but not in combination. Coupling both strategies holds the potential to dramatically increase the rate and extent of remediation because surfactants can enhance the bioavailability of contaminants to microbes. However, many surfactants permeabilize bacterial cell membranes and are effective disinfectants. An important goal then is to find or genetically modify microorganisms that possess both desirable degradative capabilities and the ability to thrive in the presence of surfactants. The guts of some marine invertebrates, particularly deposit feeders, have previously been shown to contain high levels of biosurfactants. Our primary aim was to mine these natural, surfactant-rich habitats for surfactant-resistant bacteria. Relative to sediment porewaters, the gut contents of two polychaete deposit feeders, Nereis succinea and Amphitrite ornata, exhibited a significantly higher ratio of bacteria resistant to both cationic and anionic surfactants. In contrast, bacteria in the gut fluids of a holothuroid, Leptosynapta tenuis, showed surfactant susceptibility similar to that of bacteria from sediments. Analyses of 16S rRNA gene sequences revealed that the majority of surfactant-resistant isolates were previously undescribed species of the genus Vibrio or were of a group most closely related to Spongiobacter spp. We also tested a subset of resistant bacteria for the production of biosurfactants. The majority did produce biosurfactants, as demonstrated via the oil-spreading method, but in all cases, production was relatively weak under the culture conditions employed. Novel surfactant-resistant, biosurfactant-producing bacteria, and the habitats from which they were isolated, provide a new source pool for potential microorganisms to be exploited in the in situ bioremediation of marine sediments.
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16
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Suntornvongsagul K, Burke DJ, Hamerlynck EP, Hahn D. Fate and effects of heavy metals in salt marsh sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2007; 149:79-91. [PMID: 17291650 DOI: 10.1016/j.envpol.2006.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 12/11/2006] [Accepted: 12/15/2006] [Indexed: 05/13/2023]
Abstract
The fate and effects of selected heavy metals were examined in sediment from a restored salt marsh. Sediment cores densely covered with Spartina patens were collected and kept either un-amended or artificially amended with nickel (Ni) under standardized greenhouse conditions. Ni-amendment had no significant effect on the fate of other metals in sediments, however, it increased root uptake of the metals. Metal translocation into the shoots was small for all metals. Higher Ni concentrations in plants from amended cores were accompanied by seasonal reductions in plant biomass, photosynthetic capacity and transfer efficiency of open photosystem II reaction centers; these effects, however, were no longer significant at the end of the growing season. Root colonization by arbuscular mycorrhizal fungi (AMF) resembled that of natural salt marshes with up to 20% root length colonized. Although Ni-amendment increased AMF colonization, especially during vegetative growth, in general AMF were largely unaffected.
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Affiliation(s)
- Kallaya Suntornvongsagul
- Department of Chemical Engineering, New Jersey Institute of Technology (NJIT), University Heights, Newark, NJ 07102, USA
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17
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Simmons SL, Edwards KJ. Unexpected diversity in populations of the many-celled magnetotactic prokaryote. Environ Microbiol 2007; 9:206-15. [PMID: 17227425 DOI: 10.1111/j.1462-2920.2006.01129.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The many-celled magnetotactic prokaryote (MMP) is an uncultivated, highly motile aggregate of 10-30 cells containing numerous chains of greigite (Fe(3)S(4)) magnetosomes. It is unique to marine environments and is abundant in slightly sulfidic sediments of the Little Sippewissett salt marsh (Falmouth, MA). We sequenced 16s rDNA genes from a natural population of MMP and found five lineages separated by at least 5% sequence divergence. Fluorescent in situ hybridization probes for three of these lineages showed significant variation in their relative abundances across a seasonal cycle in marsh productivity. The MMP should therefore be considered a separate genus in the delta-proteobacteria rather than a single species as previously thought. All cells in each aggregate express identical SSU rRNAs, suggesting that the aggregates are composed of a single MMP phylotype. This observation supports a model of the MMP as comprised of clonal cells which reproduce by binary fission of the aggregate.
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Affiliation(s)
- Sheri L Simmons
- Geomicrobiology Group, Department of Marine Chemistry and Geochemistry, MS 52, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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18
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Hoshino T, Furukawa K, Tsuneda S, Inamori Y. RNA microarray for estimating relative abundance of 16S rRNA in microbial communities. J Microbiol Methods 2007; 69:406-10. [PMID: 17320226 DOI: 10.1016/j.mimet.2007.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 11/22/2022]
Abstract
We developed an RNA microarray protocol in which total RNA from a microbial community was attached to a slide glass, and rRNA was detected by fluorescently labeled oligonucleotide probes. The RNA microarray requires only 4 h for hybridization and enables double staining and estimating relative abundance of rRNA.
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Affiliation(s)
- Tatsuhiko Hoshino
- Department of Chemical Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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19
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Hines ME. Microbially Mediated Redox Cycling at the Oxic–Anoxic Boundary in Sediments: Comparison of Animal and Plants Habitats. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11267-006-9036-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Macalady JL, Lyon EH, Koffman B, Albertson LK, Meyer K, Galdenzi S, Mariani S. Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl Environ Microbiol 2006; 72:5596-609. [PMID: 16885314 PMCID: PMC1538711 DOI: 10.1128/aem.00715-06] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. beta-, gamma-, delta-, and epsilon-proteobacteria in sulfur-cycling clades accounted for > or = 75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating delta-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous gamma-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of epsilon-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks.
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Affiliation(s)
- Jennifer L Macalady
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA.
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21
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Yang C, Mills D, Mathee K, Wang Y, Jayachandran K, Sikaroodi M, Gillevet P, Entry J, Narasimhan G. An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA. J Microbiol Methods 2006; 65:49-62. [PMID: 16054254 DOI: 10.1016/j.mimet.2005.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 04/22/2005] [Accepted: 06/24/2005] [Indexed: 01/08/2023]
Abstract
Support vector machines (SVM) and K-nearest neighbors (KNN) are two computational machine learning tools that perform supervised classification. This paper presents a novel application of such supervised analytical tools for microbial community profiling and to distinguish patterning among ecosystems. Amplicon length heterogeneity (ALH) profiles from several hypervariable regions of 16S rRNA gene of eubacterial communities from Idaho agricultural soil samples and from Chesapeake Bay marsh sediments were separately analyzed. The profiles from all available hypervariable regions were concatenated to obtain a combined profile, which was then provided to the SVM and KNN classifiers. Each profile was labeled with information about the location or time of its sampling. We hypothesized that after a learning phase using feature vectors from labeled ALH profiles, both these classifiers would have the capacity to predict the labels of previously unseen samples. The resulting classifiers were able to predict the labels of the Idaho soil samples with high accuracy. The classifiers were less accurate for the classification of the Chesapeake Bay sediments suggesting greater similarity within the Bay's microbial community patterns in the sampled sites. The profiles obtained from the V1+V2 region were more informative than that obtained from any other single region. However, combining them with profiles from the V1 region (with or without the profiles from the V3 region) resulted in the most accurate classification of the samples. The addition of profiles from the V 9 region appeared to confound the classifiers. Our results show that SVM and KNN classifiers can be effectively applied to distinguish between eubacterial community patterns from different ecosystems based only on their ALH profiles.
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Affiliation(s)
- Chengyong Yang
- Bioinformatics Research Group (BioRG), School of Computer Science, Florida International University, Miami, Florida, 33199, USA
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22
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Achá D, Iñiguez V, Roulet M, Guimarães JRD, Luna R, Alanoca L, Sanchez S. Sulfate-reducing bacteria in floating macrophyte rhizospheres from an Amazonian floodplain lake in Bolivia and their association with Hg methylation. Appl Environ Microbiol 2005; 71:7531-5. [PMID: 16269796 PMCID: PMC1287671 DOI: 10.1128/aem.71.11.7531-7535.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five subgroups of sulfate-reducing bacteria (SRB) were detected by PCR in three macrophyte rhizospheres (Polygonum densiflorum, Hymenachne donacifolia, and Ludwigia helminthorriza) and three subgroups in Eichhornia crassipes from La Granja, a floodplain lake from the upper Madeira basin. The SRB community varied according to the macrophyte species but with different degrees of association with their roots. The rhizosphere of the C4 plant Polygonum densiflorum had higher frequencies of SRB subgroups as well as higher mercury methylation potentials (27.5 to 36.1%) and carbon (16.06 +/- 5.40%), nitrogen (2.03 +/- 0.64%), Hg (94.50 +/- 6.86 ng Hg g(-1)), and methylmercury (8.25 +/- 1.45 ng Hg g(-1)) contents than the rhizosphere of the C3 plant Eichhornia crassipes. Mercury methylation in Polygonum densiflorum and Eichhornia crassipes was reduced when SRB metabolism was inhibited by sodium molybdate.
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Affiliation(s)
- Darío Achá
- Instituto de Biología Molecular y Biotecnología, Facultad de Ciencias Puras, Universidad Mayor de San Andrés, La Paz, Bolivia.
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23
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Lovell CR, Leaphart AB. Community-level analysis: key genes of CO2-reductive acetogenesis. Methods Enzymol 2005; 397:454-69. [PMID: 16260309 DOI: 10.1016/s0076-6879(05)97028-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
CO2-reductive acetogenic bacteria are ubiquitous in anaerobic habitats and are physiologically and phylogenetically diverse. The latter characteristics have rendered their diversity in natural environments, their distributions, and their ecological function(s) difficult to assess. Recently introduced polymerase chain reaction (PCR) primers for specific amplification of the structural gene encoding formyltetrahydrofolate synthetase (FTHFS, EC 6.3.4.3), a key enzyme in the acetyl-CoA pathway of acetogenesis, have facilitated studies of acetogen diversity and ecology. These primers amplify an approximately 1100-bp segment of the FTHFS gene. FTHFS sequences have been recovered from authentic acetogens, from sulfate reducing bacteria, and from a variety of other nonacetogenic bacteria. Phylogenetic analyses segregated these sequences into distinct clusters, only one of which contained sequences from known acetogens. This chapter describes the PCR primers, defines conditions for successful amplification of FTHFS sequences, and details the phylogenetic analysis of the FTHFS sequences. Information on the types of sequences that have been recovered from natural acetogen habitats and how they have been interpreted is also included.
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Affiliation(s)
- Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
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24
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Leloup J, Petit F, Boust D, Deloffre J, Bally G, Clarisse O, Quillet L. Dynamics of sulfate-reducing microorganisms (dsrAB genes) in two contrasting mudflats of the Seine estuary (France). MICROBIAL ECOLOGY 2005; 50:307-14. [PMID: 16308673 DOI: 10.1007/s00248-004-0034-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Accepted: 10/29/2004] [Indexed: 05/05/2023]
Abstract
By combining molecular biology and biochemical approaches, the dynamics of sulfate-reducing microorganisms (SRM) was investigated in the sediments of the Seine estuary (France). Both intertidal mixing-zone and freshwater mudflats were sampled during a 1-year period; the quantification of SRM was realized by using competitive polymerase chain reaction (PCR) based on dsrAB gene amplification, previously described by Leloup et al. (2004), and sulfate reduction rate (SRR) was determined via the SO4(2-) radiotracer method. Throughout the year, abundance of dsrAB genes and SRR were predominantly high in the top 15 cm of the sediment. A seasonal dynamic was observed; a predominance of activity was noted during the early summer, and seems to be mainly controlled by physical-chemical parameters (temperature and dissolved organic carbon concentration) and topographic evolution of the mudflat (erosion/deposit erosion).
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Affiliation(s)
- J Leloup
- Max-Planck Institute for Marine Microbiology, Bremen, Germany.
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25
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Bahr M, Crump BC, Klepac-Ceraj V, Teske A, Sogin ML, Hobbie JE. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 2005; 7:1175-85. [PMID: 16011754 DOI: 10.1111/j.1462-2920.2005.00796.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfate reduction, mediated by sulfate-reducing bacteria (SRB), is the dominant remineralization pathway in sediments of New England salt marshes. High sulfate reduction rates are associated with the rhizosphere of Spartina alterniflora when plants elongate aboveground. The growth process concurrently produces significant amounts of new rhizome material belowground and the plants leak dissolved organic compounds. This study investigated the diversity of SRB in a salt marsh over an annual growth cycle of S. alterniflora by exploring the diversity of a functional gene, dissimilatory sulfite reductase (dsrAB). Because the dsrAB gene is a key gene in the anaerobic sulfate-respiration pathway, it allows the identification of microorganisms responsible for sulfate reduction. Conserved dsrAB primers in polymerase chain reaction (PCR) generated full-length dsrAB amplicons for cloning and DNA sequence analysis. Nearly 80% of 380 clone sequences were similar to genes from Desulfosarcina and Desulfobacterium species within Desulfobacteraceae. This reinforces the hypothesis that complete oxidizers with high substrate versatility dominate the marsh. However, the phylotypes formed several clades that were distinct from cultured representatives, indicating a greater diversity of SRB than previously appreciated. Several dsrAB sequences were related to homologues from gram-positive, thermophilic and non-thermophilic Desulfotomaculum species. One dsrAB lineage formed a sister group to cultured members of the delta-proteobacterial group Syntrophobacteraceae. A deeply branching dsrAB lineage was not affiliated with genes from any cultured SRB. The sequence data from this study will allow for the design of probes or primers that can quantitatively assess the diverse range of sulfate reducers present in the environment.
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Affiliation(s)
- Michele Bahr
- Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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26
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Mussmann M, Ishii K, Rabus R, Amann R. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol 2005; 7:405-18. [PMID: 15683401 DOI: 10.1111/j.1462-2920.2005.00708.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity and distribution of Deltaproteobacteria in an intertidal mud flat of the German Wadden Sea was characterized by molecular biological techniques and cultivation. A 16S rRNA gene library generated with general primers (303 clones) suggested that sulfate-reducing bacteria (SRB) related to Desulfobulbaceae and Desulfosarcina were abundant. Fluorescence in situ hybridization (FISH) with probes targeting these groups was used to characterize their vertical distribution. The combination of FISH with catalysed reporter deposition (CARD-FISH) significantly enhanced the detection of selected subgroups of Deltaproteobacteria, particularly in deeper sediment layers. Up to 11% of all cells were assigned to SRB. Organisms related to Desulfosarcina and Desulfobulbaceae were the dominant SRB in the surface sediments. Two abundant subpopulations of Desulfosarcina-related bacteria were identified by FISH. The SRB community differed between the sampling site and a sandy intertidal flat chosen as a reference. Enrichments and MPN cultures inoculated with surface sediment were monitored by FISH. Nine strains of Deltaproteobacteria were isolated. Four strains were related to Desulfobulbaceae, such as Desulfobacterium catecholicum and Desulfocapsa spp. A subgroup including clone sequences and strains related to D. catecholicum could be detected in situ by a specific FISH probe. The first physiological experiments suggested specific functional roles for the isolates. Two strains utilized environmentally relevant compounds in coastal areas such as catechol and nitrate. One strain related to Desulfocapsa spp. disproportionated thiosulfate and might thus contribute to the sulfur isotope fractionation at the study site. A Fe(III)-reducing strain was obtained that affiliated with the Pelobacter-Desulphuromonas group. This group accounted for up to 6% of total cell numbers and even exceeded SRB numbers in upper sediment layers. These bacteria might substantially contribute to carbon mineralization via dissimilatory reduction of, e.g. Fe(III).
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Affiliation(s)
- Marc Mussmann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany.
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27
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Matsui GY, Ringelberg DB, Lovell CR. Sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea. Appl Environ Microbiol 2005; 70:7053-65. [PMID: 15574900 PMCID: PMC535212 DOI: 10.1128/aem.70.12.7053-7065.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.
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Affiliation(s)
- George Y Matsui
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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28
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Lovell CR. Belowground interactions among salt marsh plants and microorganisms. COASTAL AND ESTUARINE STUDIES 2005. [DOI: 10.1029/ce060p0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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29
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Feris KP, Ramsey PW, Frazar C, Rillig M, Moore JN, Gannon JE, Holben WE. Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl Environ Microbiol 2004; 70:2323-31. [PMID: 15066828 PMCID: PMC383024 DOI: 10.1128/aem.70.4.2323-2331.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R(2) = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R(2) = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the alpha, beta, and gamma-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.
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Affiliation(s)
- Kevin P Feris
- Microbial Ecology Program, Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
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30
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Plante CJ, Wilde SB. Biotic disturbance, recolonization, and early succession of bacterial assemblages in intertidal sediments. MICROBIAL ECOLOGY 2004; 48:154-166. [PMID: 15116280 DOI: 10.1007/s00248-003-1031-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 06/24/2003] [Indexed: 05/24/2023]
Abstract
The role of disturbance in structuring natural microbial communities has been largely unexplored. Disturbance associated with invertebrate ingestion can reduce bacterial biomass and alter metabolic activities and compositions of bacterial assemblages in marine sediments. The primary objectives of the research presented here were to test whether ingestion by a taxonomically diverse group of deposit feeders constituted a disturbance, and to determine the mechanisms by which bacterial assemblages recover following deposit-feeder ingestion. To test the question of disturbance, we compared fresh egesta vs surficial sediments with respect to bacterial assemblage structure. In emersed intertidal sediments, microbial recovery could be due to regrowth of bacterial populations surviving gut passage or to immigration from adjacent sediments. To differentiate between these modes of recolonization we used field manipulative experiments to exclude migration by isolating freshly extruded fecal coils of three deposit-feeding species from surrounding sediments. We then followed the quantitative and qualitative recovery in egesta and sediments through time using epifluorescence microscopy and PCR-DGGE analysis of 16S rDNA. Our findings indicate that (1) the degree and nature of the disturbance to bacterial assemblages from deposit feeding varies among invertebrate taxa, (2) recovery was significant but incomplete over 3 h, and (3) recolonization of biotically disturbed sediments is dominated by immigration.
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Affiliation(s)
- C J Plante
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, USA.
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31
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Klepac-Ceraj V, Bahr M, Crump BC, Teske AP, Hobbie JE, Polz MF. High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ Microbiol 2004; 6:686-98. [PMID: 15186347 DOI: 10.1111/j.1462-2920.2004.00600.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biogeochemistry of North Atlantic salt marshes is characterized by the interplay between the marsh grass Spartina and sulphate-reducing bacteria (SRB), which mineralize the diverse carbon substrates provided by the plants. It was hypothesized that SRB populations display high diversity within the sediment as a result of the rich spatial and chemical structuring provided by Spartina roots. A 2000-member 16S rRNA gene library, prepared with delta-proteobacterial SRB-selective primers, was analysed for diversity patterns and phylogenetic relationships. Sequence clustering detected 348 16S rRNA sequence types (ribotypes) related to delta-proteobacterial SRB, and it was estimated that a total of 623 ribotypes were present in the library. Similarity clustering showed that approximately 46% of these sequences fell into groups with < 1% divergence; thus, microheterogeneity accounts for a large portion of the observable genetic diversity. Phylogenetic comparison revealed that sequences most frequently recovered were associated with the Desulfobacteriaceae and Desulfobulbaceae families. Sequences from the Desulfovibrionaceae family were also observed, but were infrequent. Over 80% of the delta-proteobacterial ribotypes clustered with cultured representatives of Desulfosarcina, Desulfococcus and Desulfobacterium genera, suggesting that complete oxidizers with high substrate versatility dominate. The large-scale approach demonstrates the co-existence of numerous SRB-like sequences and reveals an unexpected amount of microdiversity.
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Affiliation(s)
- Vanja Klepac-Ceraj
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Bldg 48-421, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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32
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Liu X, Bagwell CE, Wu L, Devol AH, Zhou J. Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats. Appl Environ Microbiol 2004; 69:6073-81. [PMID: 14532064 PMCID: PMC201208 DOI: 10.1128/aem.69.10.6073-6081.2003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability.
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Affiliation(s)
- Xueduan Liu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Feris KP, Ramsey PW, Frazar C, Rillig MC, Gannon JE, Holben WE. Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western United States. MICROBIAL ECOLOGY 2003; 46:200-15. [PMID: 14708745 DOI: 10.1007/bf03036883] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6-96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.
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Affiliation(s)
- K P Feris
- Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, MT 59812-1002, USA
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Brown MM, Friez MJ, Lovell CR. Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora. FEMS Microbiol Ecol 2003; 43:411-7. [DOI: 10.1111/j.1574-6941.2003.tb01081.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Leaphart AB, Friez MJ, Lovell CR. Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Appl Environ Microbiol 2003; 69:693-6. [PMID: 12514064 PMCID: PMC152474 DOI: 10.1128/aem.69.1.693-696.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sixty-two partial formyltetrahydrofolate synthetase (FTHFS) structural gene sequences were recovered from roots of salt marsh plants, including Spartina alterniflora, Salicornia virginica, and Juncus roemerianus. Only S. alterniflora roots yielded sequences grouping with FTHFS sequences from known acetogens. Most other FTHFS or FTHFS-like sequences grouped with those from sulfate-reducing bacteria. Several sequences that grouped with Sphingomonas paucimobilis ligH were also recovered.
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Affiliation(s)
- A B Leaphart
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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Tanaka Y, Sogabe M, Okumura K, Kurane R. A highly selective direct method of detecting sulphate-reducing bacteria in crude oil. Lett Appl Microbiol 2002; 35:242-6. [PMID: 12180949 DOI: 10.1046/j.1472-765x.2002.01175.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The aim of this work was to develop a highly selective method of detecting sulphate-reducing bacteria (SRB) in crude oil. METHODS A pair of PCR primers was designed based on an alignment of the nucleotide sequence of the 16S rRNA genes from the Desulfovibrionaceae family. DNA extraction from crude oil was performed by the method using zirconia beads and a stool kit. RESULTS The PCR specifically detected Desulfovibrio and Desulfomicrobium in a sediment sample. When nucleic acids extracted directly from crude oil were used for the PCR, 16S rRNA genes of Desulfovibrio and Thermodesulforhabdus norvegicus were detected. IMPACT OF STUDY: A simple direct method for detection of the SRB in crude oil using PCR was established.
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Affiliation(s)
- Y Tanaka
- Research Institute of Biological Resources, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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Kleikemper J, Pelz O, Schroth MH, Zeyer J. Sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms. FEMS Microbiol Ecol 2002; 42:109-18. [DOI: 10.1111/j.1574-6941.2002.tb01000.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Burke DJ, Hamerlynck EP, Hahn D. Interactions among plant species and microorganisms in salt marsh sediments. Appl Environ Microbiol 2002; 68:1157-64. [PMID: 11872463 PMCID: PMC123761 DOI: 10.1128/aem.68.3.1157-1164.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2001] [Accepted: 12/07/2001] [Indexed: 11/20/2022] Open
Abstract
The interactions among Spartina patens and sediment microbial populations and the interactions among Phragmites australis and sediment microbial populations were studied at monotypic sites in Piermont Marsh, a salt marsh of the Hudson River north of New York, N.Y., at key times during the growing season. Arbuscular mycorrhizal fungi (AMF) effectively colonized S. patens but not P. australis, and there were seasonal increases and decreases that coincided with plant growth and senescence (17 and 6% of the S. patens root length were colonized, respectively). In sediment samples from the Spartina site, the microbial community and specific bacterial populations were at least twice as large in terms of number and biomass as the microbial community and specific bacterial populations in sediment samples from the Phragmites site, and peak values occurred during reproduction. Members of the domain Bacteria, especially members of the alpha-, gamma-, and delta-subdivisions of the Proteobacteria, were the most abundant organisms at both sites throughout the growing season. The populations were generally more dynamic in samples from the Spartina site than in samples from the Phragmites site. No differences between the two sites and no differences during the growing season were observed when restriction fragment length polymorphism analyses of nifH amplicons were performed in an attempt to detect shifts in the diversity of nitrogen-fixing bacteria. Differences were observed only in the patterns generated by PCR or reverse transcription-PCR for samples from the Spartina site, suggesting that there were differences in the overall and active populations of nitrogen-fixing bacteria. Regression analyses indicated that there was a positive interaction between members of the delta-subdivision of the Proteobacteria and root biomass but not between members of the delta-subdivision of the Proteobacteria and macroorganic matter at both sites. In samples from the Spartina site, there were indications that there were bacterium-fungus interactions since populations of members of the alpha-subdivision of the Proteobacteria were negatively associated with AMF colonization and populations of members of the gamma-subdivision of the Proteobacteria were positively associated with AMF colonization.
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Affiliation(s)
- David J Burke
- Department of Biological Sciences, Rutgers University, 101 Warren Street, Newark, New Jersey 07102-1811, USA
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King JK, Harmon SM, Fu TT, Gladden JB. Mercury removal, methylmercury formation, and sulfate-reducing bacteria profiles in wetland mesocosms. CHEMOSPHERE 2002; 46:859-870. [PMID: 11922066 DOI: 10.1016/s0045-6535(01)00135-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A pilot-scale model was constructed to determine if a wetland treatment system (WTS) could effectively remove low-level mercury from an outfall located at the Department of Energy's Savannah River Site. Site-specific hydrosoil was planted with giant bulrush, Scirpus californicus, and surface amended with gypsum (CaSO4) prior to investigating the biogeochemical dynamics of sediment-based sulfur and mercury speciation. On average, the pilot WTS decreased total mercury concentrations in the outfall stream by 50%. Transformation of mercury to a more "bioavailable" species, methylmercury, was also observed in the wetland treatment system. Methylmercury formation in the wetland was ascertained with respect to sediment biogeochemistry and S. californicus influences. Differences in sulfate-reduction rates (SRRs) were observed between mesocosms that received additional decomposing Scirpus matter and mesocosms that were permitted growth of the submerged macrophyte, Potamogeton pusillus. Relative abundance measurements of sulfate-reducing bacteria (SRB) as characterized using oligonucleotide probes were also noticeably different between the two mesocosms. A positive correlation between increased sulfide, dissolved total mercury, and dissolved methylmercury concentrations was also observed in porewater. The data suggest that soluble mercury-sulfide complexes were formed and contributed, in part, to a slight increase in mercury solubility. Observed increases in methylmercury concentration also suggest that soluble mercury-sulfide complexes represent a significant source of mercury that is "available" for methylation. Finally, a volunteer macrophyte, Potamogeton pusillus, is implicated as having contributed additional suspended particulate matter in surface water that subsequently reduced the pool of dissolved mercury while also providing an environment suitable for demethylation.
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Affiliation(s)
- Jeffrey K King
- Westinghouse Savannah River Company, Aiken, SC 29808, USA.
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Wieland G, Neumann R, Backhaus H. Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 2001; 67:5849-54. [PMID: 11722945 PMCID: PMC93382 DOI: 10.1128/aem.67.12.5849-5854.2001] [Citation(s) in RCA: 254] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the influence of plant species, soil type, and plant development time on the shaping of microbial communities in soil and in association with roots. The sample group consisted of a total of 32 microcosms in three habitats: soil, rhizosphere, and rhizoplane. Communities were represented by the patterns of a sequence-specific separation of rRNA target sequences. Effects of experimental parameters were classified by a cluster analysis of pattern similarities. The type of plant species (clover, bean, or alfalfa) had the greatest effect in plant-associated habitats and also affected soil patterns. Plant development had a minor habitat-dependent effect that was partly obscured by replicate variation. The results stress the applicability of biased community representations in an analysis of induced variation.
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Affiliation(s)
- G Wieland
- Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Braunschweig, Germany
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Joulian C, Ramsing NB, Ingvorsen K. Congruent phylogenies of most common small-subunit rRNA and dissimilatory sulfite reductase gene sequences retrieved from estuarine sediments. Appl Environ Microbiol 2001; 67:3314-8. [PMID: 11425760 PMCID: PMC93019 DOI: 10.1128/aem.67.7.3314-3318.2001] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of sulfate-reducing bacteria (SRB) in brackish sediment was investigated using small-subunit rRNA and dissimilatory sulfite reductase (DSR) gene clone libraries and cultivation. The phylogenetic affiliation of the most commonly retrieved clones for both genes was strikingly similar and produced Desulfosarcina variabilis-like sequences from the inoculum but Desulfomicrobium baculatum-like sequences from a high dilution in natural media. Related organisms were subsequently cultivated from the site. PCR bias appear to be limited (or very similar) for the two primersets and target genes. However, the DSR primers showed a much higher phylogenetic specificity. DSR gene analysis is thus a promising and specific approach for investigating SRB diversity in complex habitats.
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Affiliation(s)
- C Joulian
- Institute of Biological Sciences, Department of Microbial Ecology, Aarhus University, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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King JK, Kostka JE, Frischer ME, Saunders FM, Jahnke RA. A quantitative relationship that demonstrates mercury methylation rates in marine sediments are based on the community composition and activity of sulfate-reducing bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2001; 35:2491-6. [PMID: 11432553 DOI: 10.1021/es001813q] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A quantitative framework was developed which estimates mercury methylation rates (MMR) in sediment cores based on measured sulfate reduction rates (SRR) and the community composition sulfate-reducing bacterial consortia. MMR and SRR as well as group-specific 16S rRNA concentrations (as quantified by probe signal) associated with sulfate-reducing bacteria (SRB) were measured in triplicate cores of saltmarsh sediments. Utilizing previously documented conversion factors in conjunction with field observations of sulfate reduction, MMR were calculated, and the results were compared to experimentally derived measurements of MMR. Using our novel field data collected in saltmarsh sediment where sulfate reduction activity is high, calculated and independently measured MMR results were consistently within an order of magnitude and displayed similar trends with sediment depth. In an estuarine sediment where sulfate reduction activity was low, calculated and observed MMR diverged by greater than an order of magnitude, but again trends with depth were similar. We have expanded the small database generated to date on mercury methylation in sulfur-rich marine sediments. The quantitative frameworkwe have developed further elucidates the coupling of mercury methylation to sulfate reduction by basing calculated rates of mercury methylation on the activity and community composition of sulfate-reducing bacteria. The quantitative framework may also provide a promising alternative to the difficult and hazardous determination of MMR using radiolabeled mercury.
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Affiliation(s)
- J K King
- Skidaway Institute of Oceanography, Savannah, Georgia 31411, USA.
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Madrid VM, Taylor GT, Scranton MI, Chistoserdov AY. Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Appl Environ Microbiol 2001; 67:1663-74. [PMID: 11282619 PMCID: PMC92783 DOI: 10.1128/aem.67.4.1663-1674.2001] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial community samples were collected from the anoxic zone of the Cariaco Basin at depths of 320, 500, and 1,310 m on a November 1996 cruise and were used to construct 16S ribosomal DNA libraries. Of 60 nonchimeric sequences in the 320-m library, 56 belonged to the epsilon subdivision of the Proteobacteria (epsilon-Proteobacteria) and 53 were closely related to ectosymbionts of Rimicaris exoculata and Alvinella pompejana, which are referred to here as epsilon symbiont relatives (ESR). The 500-m library contained sequences affiliated with the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the division Verrucomicrobia, the division Proteobacteria, and the OP3 candidate division. The Proteobacteria included members of the gamma, delta, epsilon and new candidate subdivisions, and gamma-proteobacterial sequences were dominant (25.6%) among the proteobacterial sequences. As in the 320-m library, the majority of the epsilon-proteobacteria belonged to the ESR group. The genus Fibrobacter and its relatives were the second largest group in the library (23.6%), followed by the delta-proteobacteria and the epsilon-proteobacteria. The 1,310-m library had the greatest diversity; 59 nonchimeric clones in the library contained 30 unique sequences belonging to the planctomycetes, the fibrobacteria, the Flexibacter-Cytophaga-Bacteroides division, the Proteobacteria, and the OP3 and OP8 candidate divisions. The proteobacteria included members of new candidate subdivisions and the beta, gamma, delta, and epsilon-subdivisions. ESR sequences were still present in the 1,310-m library but in a much lower proportion (8.5%). One archaeal sequence was present in the 500-m library (2% of all microorganisms in the library), and eight archaeal sequences were present in the 1,310-m library (13.6%). All archaeal sequences fell into two groups; two clones in the 1,310-m library belonged to the kingdom Crenarchaeota and the remaining sequences in both libraries belonged to the kingdom Euryarchaeota. The latter group appears to be related to the Eel-TA1f2 sequence, which belongs to an archaeon suggested to be able to oxidize methane anaerobically. Based on phylogenetic inferences and measurements of dark CO(2) fixation, we hypothesized that (i) the ESR are autotrophic anaerobic sulfide oxidizers, (ii) sulfate reduction and fermentative metabolism may be carried out by a large number of bacteria in the 500- and 1,310-m libraries, and (iii) members of the Euryarchaeota found in relatively large numbers in the 1,310-m library may be involved in anaerobic methane oxidation. Overall, the composition of microbial communities from the Cariaco Basin resembles the compositions of communities from several anaerobic sediments, supporting the hypothesis that the Cariaco Basin water column is similar to anaerobic sediments.
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Affiliation(s)
- V M Madrid
- Marine Sciences Research Center, State University of New York at Stony Brook, Stony Brook, NY 11794-5000, USA
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Boschker HT, de Graaf W, Köster M, Meyer-Reil LA, Cappenberg TE. Bacterial populations and processes involved in acetate and propionate consumption in anoxic brackish sediment. FEMS Microbiol Ecol 2001; 35:97-103. [PMID: 11248394 DOI: 10.1111/j.1574-6941.2001.tb00792.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bacterial populations and pathways involved in acetate and propionate consumption were studied in anoxic brackish sediment from the Grosser Jasmunder Bodden, German Baltic Sea. Uptake of acetate and propionate from the porewater was studied using stable carbon isotope-labeled compounds. Labeled acetate was not produced as an intermediate during propionate uptake experiments, and propionate consumption was not affected by the addition of acetate. In parallel, incorporation of labeled acetate and propionate into phospholipid-derived fatty acids (PLFA) was studied to indicate bacterial populations involved in the consumption of these substrates. The (13)C-acetate label was mainly recovered in even-numbered PLFA (16:1omega7c, 16:0 and 18:1omega7c). In contrast, primarily odd-numbered PLFA (a15:0, 15:0, 17:1omega6 and 17:0) and the even-numbered i16:0 were labeled after incubation with (13)C-propionate. Although single PLFA labeled with propionate are commonly found in sulfate reducers, the complete PLFA-labeling pattern does not resemble any of the know strains. However, the acetate-labeling pattern is similar to Desulfotomaculum acetoxidans and Desulfofrigus spp., two acetate-consuming, sulfate reducers. In conclusion, our data suggest that acetate and propionate were predominantly consumed by different, specialized groups of sulfate-reducing bacteria.
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Abstract
Throughout the first 90 years after their discovery, sulfate-reducing bacteria were thought to be strict anaerobes. During the last 15 years, however, it has turned out that they have manifold properties that enable them to cope with oxygen. Sulfate-reducing bacteria not only survive oxygen exposure for at least days, but many of them even reduce oxygen to water. This process can be a true respiration process when it is coupled to energy conservation. Various oxygen-reducing systems are present in Desulfovibrio species. In Desulfovibrio vulgaris and Desulfovibrio desulfuricans, oxygen reduction was coupled to proton translocation and ATP conservation. In these species, the periplasmic fraction, which contains hydrogenase and cytochrome c3, was found to catalyze oxygen reduction with high rates. In Desulfovibrio gigas, a cytoplasmic rubredoxin oxidase was identified as an oxygen-reducing terminal oxidase. Generally, the same substrates as with sulfate are oxidized with oxygen. As additional electron donors, reduced sulfur compounds can be oxidized to sulfate. Sulfate-reducing bacteria are thus able to catalyze all reactions of a complete sulfur cycle. Despite a high respiration rate and energy coupling, aerobic growth of pure cultures is poor or absent. Instead, the respiration capacity appears to have a protective function. High numbers of sulfate-reducing bacteria are present in the oxic zones and near the oxic-anoxic boundaries of sediments and in stratified water bodies, microbial mats and termite guts. Community structure analyses and microbiological studies have shown that the populations in those zones are especially adapted to oxygen. How dissimilatory sulfate reduction can occur in the presence of oxygen is still enigmatic, because in pure culture oxygen blocks sulfate reduction. Behavioral responses to oxygen include aggregation, migration to anoxic zones, and aerotaxis. The latter leads to band formation in oxygen-containing zones at concentrations of </=20% air saturation.
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Affiliation(s)
- H Cypionka
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, D-26111 Oldenburg, Germany.
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Carelli M, Gnocchi S, Fancelli S, Mengoni A, Paffetti D, Scotti C, Bazzicalupo M. Genetic diversity and dynamics of Sinorhizobium meliloti populations nodulating different alfalfa cultivars in Italian soils. Appl Environ Microbiol 2000; 66:4785-9. [PMID: 11055924 PMCID: PMC92380 DOI: 10.1128/aem.66.11.4785-4789.2000] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the genetic diversity of 531 Sinorhizobium meliloti strains isolated from nodules of Medicago sativa cultivars in two different Italian soils during 4 years of plant growth. The isolates were analyzed for DNA polymorphism with the random amplified polymorphic DNA method. The populations showed a high level of genetic polymorphism distributed throughout all the isolates, with 440 different haplotypes. Analysis of molecular variance allowed us to relate the genetic structure of the symbiotic population to various factors, including soil type, alfalfa cultivar, individual plants within a cultivar, and time. Some of these factors significantly affected the genetic structure of the population, and their relative influence changed with time. At the beginning of the experiment, the soil of origin and, even more, the cultivar significantly influenced the distribution of genetic variability of S. meliloti. After 3 years, the rhizobium population was altered; it showed a genetic structure based mainly on differences among plants, while the effects of soil and cultivar were not significant.
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Affiliation(s)
- M Carelli
- Istituto Sperimentale Colture Foraggere, 200075 Lodi, Italy
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Bagwell CE, Lovell CR. Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability. Appl Environ Microbiol 2000; 66:4625-33. [PMID: 11055903 PMCID: PMC92359 DOI: 10.1128/aem.66.11.4625-4633.2000] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rhizoplane-rhizosphere nitrogen-fixing microorganisms (diazotrophs) are thought to provide a major source of biologically available nitrogen in salt marshes dominated by Spartina alterniflora. Compositional and functional stability has been demonstrated for this important functional group; however, the quantitative responses of specific diazotroph populations to environmental variability have not been assessed. Changes in the relative abundances of selected rhizoplane diazotrophs in response to long-term fertilization were monitored quantitatively by reverse sample genome probing. Fertilization stimulated Spartina, with plant height nearly tripling after 1 year. Fertilization also resulted in significant changes in interstitial porewater parameters. Diazotrophic activity (acetylene reduction assay) was sensitive to the fertilization treatments and was inhibited in some plots on several sampling dates. However, inhibition was never consistent across all of the replicates within a treatment and activity always recovered. The rhizoplane diazotrophs were quite responsive to environmental variability and to experimental treatments, but none were displaced by either environmental variability or experimental treatments. All strains were detected consistently throughout this study, and extensive spatial heterogeneity in the distribution patterns of these organisms was observed. The physiological traits that differentiate the diazotroph populations presumably support competitiveness and niche specialization, resulting in the observed resilience of the diazotroph populations in the rhizosphere.
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Affiliation(s)
- C E Bagwell
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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Ravenschlag K, Sahm K, Knoblauch C, Jørgensen BB, Amann R. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl Environ Microbiol 2000; 66:3592-602. [PMID: 10919825 PMCID: PMC92189 DOI: 10.1128/aem.66.8.3592-3602.2000] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54. 8% of the total SRB detected. A comparison of the two methods used for quantification showed that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5 mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface. Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell(-1) day(-1)), decreased by a factor of 3 within the first 2 cm, and were relatively constant in deeper layers.
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MESH Headings
- Arctic Regions
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Ecosystem
- Fermentation
- Genes, rRNA
- Geologic Sediments/microbiology
- In Situ Hybridization, Fluorescence
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Oxidation-Reduction
- Phylogeny
- Polymerase Chain Reaction
- RNA, Bacterial/analysis
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- Sulfates/metabolism
- Sulfur-Reducing Bacteria/chemistry
- Sulfur-Reducing Bacteria/genetics
- Sulfur-Reducing Bacteria/isolation & purification
- Sulfur-Reducing Bacteria/metabolism
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Affiliation(s)
- K Ravenschlag
- Molecular Ecology Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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49
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Daly K, Sharp RJ, McCarthy AJ. Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 7):1693-1705. [PMID: 10878133 DOI: 10.1099/00221287-146-7-1693] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PCR primer sets for the 16S rRNA gene of six phylogenetic groups of sulfate-reducing bacteria (SRB) were designed. Their application in conjunction with group-specific internal oligonucleotide probes was used to detect SRB DNA in samples of landfill leachate. Six generic/suprageneric groups could be differentiated: DESULFOTOMACULUM:; DESULFOBULBUS:; DESULFOBACTERIUM:; DESULFOBACTER:; DESULFOCOCCUS:-DESULFONEMA:-DESULFOSARCINA:; DESULFOVIBRIO:-DESULFOMICROBIUM: The predicted specificities of the PCR primer and oligonucleotide probe combinations were confirmed with DNA from reference strains. In all cases, the PCR primers and probes were specific, the only exception being that the Desulfococcus-Desulfonema-Desulfosarcina (group 5) PCR primers were able to amplify DNA from DESULFOBACTERIUM: (group 3) reference strains but these groups could nevertheless be differentiated with the internal oligonucleotide probes. The proliferation of SRB in landfill sites interferes with methanogenesis and waste stabilization, but relatively little is known about the composition of SRB populations in this environment. DNA was extracted from samples of landfill leachate from several municipal waste landfill sites and used as template in PCR reactions with SRB group-specific primer sets. Group-specific oligonucleotide probes were then used to confirm that the PCR products obtained contained the target SRB 16S rDNA. Both 'direct' and 'nested' PCR protocols were used to amplify SRB 16S rDNA from landfill leachates. Three of the six SRB groups could be detected using the 'direct' PCR approach (DESULFOTOMACULUM:, DESULFOBACTER: and Desulfococcus-Desulfonema-Desulfosarcina). When 'nested' PCR was applied, an additional two groups could be detected (DESULFOBULBUS: and DESULFOVIBRIO:-DESULFOMICROBIUM:). Only DESULFOBACTERIUM: could not be detected in any leachate samples using either direct or nested PCR. The SRB-specific 16S rDNA primers and probes described here can be applied to investigations of SRB molecular ecology in general, and can be further developed for examining SRB population composition in relation to landfill site performance.
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Affiliation(s)
- Kristian Daly
- School of Biological Sciences, Life Sciences Building, University of Liverpool, Liverpool L69 7ZB, UK1
| | - Richard J Sharp
- Centre for Applied Microbiology and Research, Porton Down, Salisbury, Wiltshire SP4 0JG, UK2
| | - Alan J McCarthy
- School of Biological Sciences, Life Sciences Building, University of Liverpool, Liverpool L69 7ZB, UK1
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50
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Frischer ME, Danforth JM, Newton Healy MA, Saunders FM. Whole-cell versus total RNA extraction for analysis of microbial community structure with 16S rRNA-targeted oligonucleotide probes in salt marsh sediments. Appl Environ Microbiol 2000; 66:3037-43. [PMID: 10877803 PMCID: PMC92108 DOI: 10.1128/aem.66.7.3037-3043.2000] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% +/- 3.7% [mean +/- standard deviation]) relative to direct DAPI (4',6'-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r(2) = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.
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Affiliation(s)
- M E Frischer
- Skidaway Institute of Oceanography, Savannah, Georgia 31411, USA.
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