Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep

Smedile, Francesco; Messina, Enzo; Cono, Violetta La; Tsoy, Olga; Monticelli, Luis Salvador; Borghini, Mireno; Giuliano, Laura; Golyshin, Peter N.; Mushegian, Arcady; Yakimov, Michail M.

doi:10.1111/j.1462-2920.2012.02827.x

Cited by 58 publications

(87 citation statements)

References 79 publications

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“…Figure S5). The Sea of Marmara (MARM) dataset showed similar distributions between subclade Ia (predominantly HTCC1062 type) and Ic (Supplementary Figure S6), and although the Matapan-Vavilov Deep (MATA) dataset had very little recruitment to any SAR11 genome (Supplementary Figure S7), consistent with the previous analysis (Smedile et al, 2013), those sequences that did recruit to SAR11 genomes were predominantly Ic-like. Longer Sanger shotgunsequencing reads from 4000 m at Station ALOHA (Konstantinidis et al, 2009) also demonstrated increased recruitment to the SAGs relative to other genomes in deeper water (Supplementary Figure S8).…”

Section: Comparative Genomicssupporting

confidence: 75%

“…Metagenomes from ALOHA were previously described in Shi et al (2011). Data were also analyzed from 454 metagenomic sequences collected from Eastern Tropical South Pacific Oxygen Minimum Zone (Stewart et al, 2012), the Puerto Rico Trench (Eloe et al, 2011a), the Sea of Marmara (Quaiser et al, 2010) and the Matapan-Vavilov Deep in the Mediterranean Sea (Smedile et al, 2013). All raw data were trimmed of low-quality end sequences using Lucy (Chou and Holmes, 2001) and de-replicated using CDHIT-454 (Fu et al, 2012).…”

Section: Comparative Genomicsmentioning

confidence: 99%

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Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

et al. 2014

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Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

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Section: Comparative Genomicssupporting

confidence: 75%

Section: Comparative Genomicsmentioning

confidence: 99%

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

et al. 2014

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“…To compare the results among the different data sets, the number of reads was normalized considering the size of the contig and of the collection (number of reads per kilobase per gigabase of the collection). The meso and bathypelagic metagenome collections screened were: Marmara Sea-1000 m (Quaiser et al, 2011), Matapan-Vavilov Deep in the Mediterranean Sea-4900 m (Smedile et al, 2012), North Pacific subtropical gyre-ALOHA station-4000 m (Konstantinidis et al, 2009), Guaymas Basin hydrothermal vent in the Gulf of California (Lesniewski et al, 2012) and a metagenome obtained at 800 m in the South Atlantic Gyre (Swan et al, 2014).…”

Section: Metagenomic Recruitmentmentioning

confidence: 99%

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

et al. 2014

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We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

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“…Yet, current knowledge of the pelagic microbial community structure of the dark ocean, the largest biome in the biosphere, is based on a pool of samples collected at specific locations (DeLong et al, 2006;Martín-Cuadrado et al, 2007;Brown et al, 2009;Galand et al, 2010;Agogué et al, 2011;Eloe et al, 2011;Quaiser et al, 2011;Smedile et al, 2012;Wang et al, 2013;Wilkins et al, 2013;Ganesh et al, 2014) (Supplementary Figure S1) and thus are dwarf in comparison with the analyses of upper ocean microbial communities, which have indeed been assessed at global scales Yooseph et al, 2007;Zinger et al, 2011;Sunagawa et al, 2015). Whereas the deep ocean is often considered to be a rather uniform environment, the connectivity of pelagic microbial communities may be reduced by the limited mixing between water masses (Agogué et al, 2011;Hamdan et al, 2013) or modulated by advection (Wilkins et al, 2013) imposing limitations on the dispersion of marine microbes in this low-turbulence environment.…”

Section: Introductionmentioning

confidence: 99%

Global diversity and biogeography of deep-sea pelagic prokaryotes

Salazar¹,

et al. 2015

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The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.

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Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep

Cited by 58 publications

References 79 publications

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

Global diversity and biogeography of deep-sea pelagic prokaryotes

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