The deepest chemosynthesis-based community yet discovered from the hadal zone, 7326 m deep, in the Japan Trench

The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel, Bathymodiolus sp., and the seep vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50 cbbL clones and 50 cbbM clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded from the 250 total cbbM clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that the Thiobacillus-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.Phylogenetic information on deep-sea microorganisms that has been accumulated relates mainly to the 16S ribosomal DNA (rDNA) sequences (9,33,53). In understanding the microbial contribution to deep-sea primary production, the 16S rDNA-based phylogeny will be better complemented by knowledge of the genes encoding the enzymes relevant to carbon fixation. The genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) represent such an enzyme that is involved in autotrophy. RuBisCO is the most abundant enzyme on the globe and has attracted much phylogenetic attention (5). RuBisCO catalyzes the assimilation of carbon dioxide to organic carbon via the Calvin-Benson cycle. The enzyme consists of large and small subunits (42). The site responsible for carbon fixation is in the large subunit (42). More than 20% of the amino acid residues in the large subunit are conserved among the higher plants (32). Generally, RuBisCO has two forms. Form I consists of large and small subunits (L n S n , typically L 8 S 8 ), and form II contains only large subunits (L n ) with 25 to 30% amino acid sequence identity with those of form I (32). The large subunits of form I and form II are coded by genes designated cbbL and cbbM, respectively (37). Some organisms have two genes en...

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“…The anoxic nature of these habitats may account for the divergence of the genes for anaerobic RuBisCO form II (15,45).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Elsaied

Naganuma

2001

Appl Environ Microbiol

124

132

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“…Conchocele disjuncta is a thyasirid clam found at seeps in Japanese waters (Fujikura et al 1999) and in the Sea of Okhotsk (Zonenshayn et al 1987). It is also well documented in the fossil cold-seep record (Callender & Powell 1999).…”

Section: Conchocele Spmentioning

confidence: 99%

16S rDNA-based phylogeny of sulphur-oxidising bacterial endosymbionts in marine bivalves from cold-seep habitats

Imhoff

Sahling²,

Süling³

et al. 2003

Mar. Ecol. Prog. Ser.

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The phylogenetic relationship of sulphur-oxidising endosymbiotic bacteria from bivalves of the families Vesicomyidae (Calyptogena sp. C1, Calyptogena sp. C3), Solemyidae (Acharax sp.) and Thyasiridae (Conchocele sp.) from cold-seep habitats were determined by 16S rDNA nucleotide sequence analyses. The endosymbiotic bacteria form distinct groups within the gamma-Proteobacteria and are well separated from each other and from free-living sulphuroxidising bacteria of the genera Beggiatoa, Halothiobacillus and Thiomicrospira. The endosymbiotic bacteria of Acharax sp. from cold seeps off Oregon, Indonesia and Pakistan have sequences highly similar to each other but quite distinct from other thiotrophic endosymbionts. This includes endosymbionts from Solemya spp., to which they are distantly related. Symbiotic bacteria of Conchocele sp. from a cold seep in the Sea of Okhotsk are similar to those of Bathymodiolus thermophilus and related species, as shown by their overall sequence similarity and by signature sequences. The endosymbiotic bacteria of Calyptogena spp. from cold seeps off Oregon and Pakistan are closely related to those of other vesicomyids. Endosymbiont species found off Oregon corresponded to 2 different clusters of Calyptogena spp. symbionts in the same samples. The results corroborate the hypothesis of a monophyletic origin of the symbionts in vesicomyid clams, and support the existence of deeply branching groups in solemyid symbionts and of divergent lines and distribution for thyasirid symbionts. The results also indicate that certain symbiont species cluster according to the depth distribution of their hosts, and that in consequence host species together with their symbionts may have undergone depth-specific adaptation and evolution.

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“…Hovland, 1992;Fujikura et al, 1999;Domack et al, 2005;Dando, 2010). High concentration of reduced compounds causes seeps to host dense communities of invertebrates relying on chemosynthetic primary production, unlike the 'normal' marine benthic faunas which in great majority depend on organic matter produced due to photosynthesis (Sibuet and Olu, 1998;Levin 2005).…”

Section: Introductionmentioning

confidence: 99%

Paleocene methane seep and wood-fall marine environments from Spitsbergen, Svalbard

Hryniewicz

Bitner

Durska

et al. 2016

Palaeogeography, Palaeoclimatology, Palaeoecology

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The deepest chemosynthesis-based community yet discovered from the hadal zone, 7326 m deep, in the Japan Trench

Abstract: ties exists throughout deep-sea trenches. Additionally, the thyasind species discussed here differs from other thyasinds by having drcular symbionts which appear to exist intracellularly, and by living exposed above the sediment snuiace.

Cited by 98 publications

References 26 publications

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms

16S rDNA-based phylogeny of sulphur-oxidising bacterial endosymbionts in marine bivalves from cold-seep habitats

Paleocene methane seep and wood-fall marine environments from Spitsbergen, Svalbard

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