Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments

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108

111

To evaluate possible compositional changes in archaeal communities at a deep-sea hydrothermal vent field scale, we examined five different samples obtained after deploying in situ collectors for different times on three spatially separated venting sulphide structures on the East Pacific Rise (13 degrees N). Direct cell counts and whole-cell hybridizations with fluorescently labelled 16S rRNA-based oligonucleotide probes revealed that the relative abundance of archaeal populations represented from 14 to 33% of the prokaryotic community. 16S rDNA sequence analysis of the archaeal clone libraries indicated that a large percentage of clones were closely related to known archaeal isolates recovered from similar habitats. Among the 24 different phylotypes identified, Thermococcales-related sequences were dominant in all the libraries that also included representative genera of orders Methanopyrales, Methanococcales, Archaeoglobales and Desulfurococcales. The presence of most of these phylogenetic groups was confirmed in enrichment cultures performed at temperatures from 60 to 90 degrees C. Additional sequences with no known cultivated relatives grouped with the Marine group I Crenarchaeota, Korarchaeota and Deep-sea Hydrothermal Vent Euryarchaeota (DHVE) within which a novel lineage was identified. Furthermore, the archaeal community composition was distinct from vent to vent within the same vent field and varied within short time scales. This study provides new insights into microbial diversity and distribution at deep-sea hydrothermal vents.

Section: (Ii) Sequences Related To Uncultured Organismsmentioning

confidence: 80%

Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13°N)

Nercessian

Reysenbach

Prieur

et al. 2003

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108

111

“…Nankai 1 (n = 15) grouped with clones from abyssal plain sediments from the north-western Atlantic Ocean previously assigned to Marine Benthic Group B (CRA8-27 cm; APA3-11 cm; Vetriani et al, 1999). Nankai 2 clones (n = 5) were phylogenetically similar to several other deep-sea sediment clones.…”

Section: Diversity Of Archaeamentioning

confidence: 88%

“…Nankai 2 clones (n = 5) were phylogenetically similar to several other deep-sea sediment clones. For example, from the Atlantic (ACA4-0 cm; Vetriani et al, 1999), the Cascadia Margin (ODPB-A; Bidle et al 1999) and the Juan de Fuca ridge (33-F120A00, not included; Huber et al, 2002). This cluster has been designated Marine Group 1 (Vetriani et al, 1999), but has previously been called Group 1.1a (DeLong, 1998).…”

Section: Diversity Of Archaeamentioning

confidence: 99%

“…This group has been called Group 1.2 (DeLong, 1998;Jurgens et al, 2000). More clones (n = 7) fell into Nankai 4 which was within a grouping called Marine Benthic Group C (Vetriani et al, 1999), also called Group 1.3 (DeLong, 1998;Jurgens et al, 2000;Pesaro and Widmer, 2002). This cluster included clones JTB173 (Li et al, 1999b) from 6400 m deep Japan Trench surface sediment, 19c-51 from Aegean Sea sediment (unpublished) and CRA9-17 cm from Atlantic Ocean deep-sea sediments (Vetriani et al, 1999;not included).…”

Section: Diversity Of Archaeamentioning

confidence: 99%

See 1 more Smart Citation

Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Newberry

Webster

Cragg

et al. 2004

183

172

Diversity of Bacteria and Archaea was studied in deep marine sediments by PCR amplification and sequence analysis of 16S rRNA and methyl co-enzyme M reductase (mcrA) genes. Samples analysed were from Ocean Drilling Program (ODP) Leg 190 deep subsurface sediments at three sites spanning the Nankai Trough in the Pacific Ocean off Shikoku Island, Japan. DNA was amplified, from three depths at site 1173 (4.15, 98.29 and 193.29 mbsf; metres below the sea floor), and phylogenetic analysis of clone libraries showed a wide variety of uncultured Bacteria and Archaea. Sequences of Bacteria were dominated by an uncultured and deeply branching 'deep sediment group' (53% of sequences). Archaeal 16S rRNA gene sequences were mainly within the uncultured clades of the Crenarchaeota. There was good agreement between sequences obtained independently by cloning and by denaturing gradient gel electrophoresis. These sequences were similar to others retrieved from marine sediment and other anoxic habitats, and so probably represent important indigenous bacteria. The mcrA gene analysis suggested limited methanogen diversity with only three gene clusters identified within the Methanosarcinales and Methanobacteriales. The cultivated members of the Methanobacteriales and some of the Methanosarcinales can use CO2 and H2 for methanogenesis. These substrates also gave the highest rates in 14C-radiotracer estimates of methanogenic activity, with rates comparable to those from other deep marine sediments. Thus, this research demonstrates the importance of the 'deep sediment group' of uncultured Bacteria and links limited diversity of methanogens to the dominance of CO2/H2 based methanogenesis in deep sub-seafloor sediments.

“…Recent progress in culture-independent molecular phylogenetic surveys using PCR-mediated rDNA sequence has revealed a great diversity of naturally occurring microbial habitats (Giovannoni et al, 1990;DeLong, 1992;Fuhrman et al, 1992;Pace, 1997). The molecular ecological approach facilitates detection and identification of microbial components even in deep-sea extreme environments (Kato et al, 1997;Hinrichs et al, 1999;Takai and Horikoshi, 1999;Vetriani et al, 1999;Inagaki et al, 2001;Takai et al, 2001;Inagaki et al, 2002). Some explorations of the deep sea floor have focused on the 'cold seep' area where the hydrocarbon-rich reductive cold water seeps along the fault from the subseafloor zone (Ohta and Laubier, 1987).…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments

Inagaki

Sakihama

Inoue

et al. 2002

A depth profile of naturally occurring bacterial community structures associated with the deep-sea cold seep push-core sediment in the Japan Trench at a depth of 5343 m were evaluated using molecular phylogenetic analyses of RNA reverse transcription-PCR (RT-PCR) amplified 16S crDNA fragments. A total of 137 clones of bacterial crDNA (complimentary rDNA) phylotypes (phylogenetic types) obtained at three different depths (2-4, 8-10 and 14-16 cm) were identified in partial crDNA sequencings. crDNA phylotypes from the cold seep sediment were dominantly composed of delta- and epsilon-Proteobacteria (36% and 42% respectively). Phylotype analysis of crDNA clone libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the majority of bacterial components shifted from delta- Proteobacteria to epsilon-Proteobacteria with increasing depth. Among the delta-proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant. Almost all sequences of crDNA belonging to epsilon-Proteobacteria were affiliated with the same cluster (epsilon-CSG: epsilon-proteobacterial cold seep group), and were closely related with rDNA sequences from deep-sea hydrothermal vent environments.