Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments

Purdy, Kevin J.

doi:10.1016/s0168-6496(01)00128-3

Cited by 17 publications

(34 citation statements)

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“…All our isolates were incompletely-oxidizing SRBs, and we could not isolate any completely-oxidizing SRBs. It has been reported that Desulfobacter species, a group of the completely-oxidizing SRBs, are one of the dominant SRBs in estuarine sediments of Japan based on hybridization analysis for the 16S rRNA gene (Purdy et al, 2001(Purdy et al, , 2002. Although we could enrich acetate-oxidizing SRBs from the same sediment sample used in this study, we did not succeed in isolating pure cultures of SRBs from the enrichment by colony isolation using the anaerobic roll tube method.…”

Section: Discussionmentioning

confidence: 99%

“…It has been shown that diverse SRBs are present in natural environments including marine sediments by using cultivation-independent molecular techniques Dhillon et al, 2003;Joulian et al, 2001;Minz et al, 1999;Purdy et al, 2001Purdy et al, , 2002Voordouw et al, 1996;Wagner et al, 1998). In this study, we could really isolate phylogenetically diverse SRBs including novel lineages from an estuarine sediment using different isolation methods.…”

Section: Values In Parentheses Indicate Growth Rate (H ϫ1mentioning

confidence: 99%

“…Many studies on the diversity of SRBs in natural environments have been performed using cultivation-independent molecular techniques based on PCR amplification of the 16S rRNA gene or dissimilatory sulfite reductase gene Dhillon et al, 2003;Hines et al, 1999;Joulian et al, 2001;Minz et al, 1999;Purdy et al, 2001Purdy et al, , 2002Voordouw et al, 1996;Wagner et al, 1998). These studies have revealed that phylogenetically diverse uncultivated SRBs are present in natural ecosystems.…”

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confidence: 99%

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Diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in Japan

Suzuki

Ueki

Amaishi

et al. 2007

J. Gen. Appl. Microbiol.

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Section: Discussionmentioning

confidence: 99%

Section: Values In Parentheses Indicate Growth Rate (H ϫ1mentioning

confidence: 99%

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confidence: 99%

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Diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in Japan

Suzuki

Ueki

Amaishi

et al. 2007

J. Gen. Appl. Microbiol.

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“…However, it is currently uncertain if these benthic sediments, which do not undergo significant seasonal changes in their geochemical and microbial composition, host specific microbial communities. Although the sediment microbial community has been shown to be dominated by members of the Planctomycetes, the Cytophaga/ Flavobacterium group, Gammaproteobacteria and bacteria of the Desulfosarcina/Desulfococcus group, the role and importance of anaerobes such as sulfatereducing bacteria (SRB) and methanogenic archaea have been well documented (Purdy et al, 2001(Purdy et al, , 2003Loy et al, 2002;Dalsgaard et al, 2005;Musat et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida

Brück

Self

et al. 2010

The ISME Journal

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Marine sediments and sponges may show steep variations in redox potential, providing niches for both aerobic and anaerobic microorganisms. Geodia spp. and sediment specimens from the Straits of Florida were fixed using paraformaldehyde and 95% ethanol (v/v) for fluorescence in situ hybridization (FISH). In addition, homogenates of sponge and sediment samples were incubated anaerobically on various cysteine supplemented agars. FISH analysis showed a prominent similarity of microbiota in sediments and Geodia spp. samples. Furthermore, the presence of sulfate-reducing and annamox bacteria as well as other obligate anaerobic microorganisms in both Geodia spp. and sediment samples were also confirmed. Anaerobic cultures obtained from the homogenates allowed the isolation of a variety of facultative anaerobes, primarily Bacillus spp. and Vibrio spp. Obligate anaerobes such as Desulfovibrio spp. and Clostridium spp. were also found. We also provide the first evidence for a culturable marine member of the Chloroflexi, which may enter into symbiotic relationships with deep-water sponges such as Geodia spp. Resuspended sediment particles, may provide a source of microorganisms able to associate or form a symbiotic relationship with sponges.

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“…In sediment slurry microcosms from the River Colne estuary, sulphate-dependent acetate utilisation was linked to Desulfobacter at both the mouth of the estuary and the freshwater-dominated East Hill Bridge 33) . Desulfobacter has been reported to be the predominant active SRB genus in marine-dominated estuarine sediments from Japan 35) . Thus, it would appear that SRB related to complete oxidizers of the Desulfobacteraceae family are present and play an important role in anaerobic mineralisation along the length of the Colne estuary.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Spatial Dynamics of Sulphate-reducing Bacterial Compositions in Sediment along a Salinity Gradient in a UK Estuary

et al. 2007

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The diversity of sulphate-reducing bacteria (SRB) was investigated in sediments along environmental gradients in the River Colne estuary, Essex, UK. DNA samples were collected from four sites; marine-dominated (Alresford Creek), brackish (the Hythe), predominantly freshwater (East Hill Bridge) and freshwater (the Weir) between September 2001 and May 2002. SRB community composition was assessed by PCR amplification, cloning and sequencing of part of the α subunit of dissimilatory sulphite reductase (dsrA) using directly extracted sediment DNA. The majority of the dsrA sequences were associated with members of the Desulfobacteraceae family, the Desulfobulbaceae family and a deeply branched group in the dsrA tree with no cultured representatives. There was some evidence of a salinity-related distribution within both the Desulfobacteraceae and Desulfobulbaceae groups. Clones related to Desulfotomaculum of the xenologues Firmicutes and a phylogenetically distinct Colne group 3 were detected only at the freshwater East Hill Bridge and Weir sites. Conversely, clones related to an uncultured group (Colne group 1) were found only at the marine and brackish sites. A statistical analysis of composition revealed that dsrA sequences from the marine-dominated Alresford Creek and the brackish site at the Hythe were not significantly different from each other (P>0.05), but were significantly different from those of the freshwater-dominated East Hill Bridge and the Weir (P<0.05). The sequences from East Hill Bridge and the Weir were not significantly different from each other (P>0.05). The data presented show a complex distribution of SRB along the estuary with some evidence to support the idea that salinity and sulphate concentrations are an important factor in determining SRB community structure.Key words: dissimilatory sulphite reductase gene, environmental gradients, estuarine sediment, sulphate reduction Sulphate reduction is an important process involved in both the global carbon and sulphur cycles. This process can dominate anaerobic terminal mineralisation of organic matter in high-sulphate sediments, degrading up to 50% of all organic matter in coastal marine sediments 12) and plays a minor but still important role in low-sulphate sediments 26,38) . Rates of sulphate reduction vary in relation to temperature and electron donor and acceptor concentrations with the availability of sulphate an important factor in the control of the rate of sulphate reduction. Sulphate concentrations range from approximately 25 mM in full-strength seawater to <0.2 mM in freshwater 7) . Freshwater-adapted sulphatereducing bacteria (SRB) have a greater affinity for sulphate (K m =5-68 µM) than marine-adapted SRB (K m =200 µM) 8,37) , allowing them to continue sulphate reduction at much lower sulphate concentrations than marine SRB. Physiological differences between freshwater-and marine-adapted SRB may be reflected in differences in species or phylogenetic compositions of SRB communities.The Colne estuary is a small, muddy, macrotidal (3 to 5...

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Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments

Cited by 17 publications

References 13 publications

Diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in Japan

Diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in Japan

Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida

Spatial Dynamics of Sulphate-reducing Bacterial Compositions in Sediment along a Salinity Gradient in a UK Estuary

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