Active Bacterial Flora Surrounding Foraminifera (Xenophyophorea) Living on the Deep-Sea Floor

Hori, Shigeru; Tsuchiya, Masashi; Nishi, Shinro; Arai, Wataru; Yoshida, Takao; Takami, Hideto

doi:10.1271/bbb.120663

Cited by 16 publications

(11 citation statements)

References 12 publications

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“…members of that family, as recently confirmed by analysis of deep-sea assembled genomes (Hoffmann et al in revision). Closest related sequences of Subgroup have been reported in deep-sea sediments (Schauer et al 2010) and across Pacific nodule fields (Wu et al, 2013), but also in association with deep-sea benthic giant foraminifera (Xenophyophores) and in surrounding sediments (Hori et al, 2013). The subgroup 21-like OTU was also one of the 10 most abundant OTUs retrieved from nodules (0.9 %).…”

Section: Microbial Diversity Of Nodule Fields Is Distinct From Other mentioning

confidence: 82%

“…The presence of a large proportion of bacterial community with low abundance in the sediments, but enriched by the nodule environment at the level of genera (35 %) and OTUs (24 %) (Table 4 and Mason et al, 2009;Lee et al, 2015), sulfide and carbonate hydrothermal deposits (e.g. Sylvan et al, 2012;Kato et al, 2015), and giant foraminifera (Hori et al, 2013; Table 5b and Figure 5). There are currently no cultivated representatives and metabolic information for these members of the Bacteria, and it is not known whether they have metal tolerance mechanisms or they are actively involved in metal cycling.…”

Section: Potential Functions Of Microbial Communities Associated To Nmentioning

confidence: 99%

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Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

Molari¹,

Janßen²,

Vonnahme³

et al. 2020

Preprint

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Abstract. Industrial-scale mining of deep-sea polymetallic nodules will need to remove nodules in large areas of the seafloor. The regrowth of the nodules by metal precipitation is estimated to take millions of years. Thus for future mining impact studies, it is crucial to understand the role of nodules in shaping microbial diversity and function in deep-sea environments. Here we investigated microbial community composition based on 16S rRNA gene sequences retrieved from sediments and nodules of the Peru Basin (> 4100 m water depth). The nodule field of the Peru Basin showed a typical deep-sea microbiome, with dominance of the classes Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Acidimicrobiia. Nodules and sediments host distinct bacterial and archaeal communities, with nodules showing lower diversity and a higher proportion of sequences related to potential metal-cycling bacteria (i.e. Magnetospiraceae, Hyphomicrobiaceae), bacterial and archaeal nitrifiers (i.e. AqS1, unclassified Nitrosomonadaceae, Nitrosopumilus, Nitrospina, Nitrospira), and bacterial sequences found in ocean crust, nodules, hydrothermal deposits and sessile fauna. Sediment and nodule communities overall shared a low proportion of Operational Taxonomic Units (OTU; 21 % for Bacteria and 19 % for Archaea). Our results show that nodules represent a specific ecological niche (i.e. hard substrate, high metal concentrations and sessile fauna), with a potentially relevant role in organic carbon degradation. Differences in nodule community composition (e.g. Mn-cycling bacteria, nitrifiers) between the Clarion-Clipperton Fracture Zone (CCZ) and the Peru Basin suggest that changes in environmental setting (i.e. sedimentation rates) play also a significant role in structuring the nodule microbiome.

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Section: Microbial Diversity Of Nodule Fields Is Distinct From Other mentioning

confidence: 82%

Section: Potential Functions Of Microbial Communities Associated To Nmentioning

confidence: 99%

Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

Molari¹,

Janßen²,

Vonnahme³

et al. 2020

Preprint

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“…On the other hand, both Rhodospirillales and Radiolaria were less abundant in SE M. Ivanov and Porto MVs. The BLAST analysis appears to support an association between Rhodospiralles and members of the Rhizaria phylum; two of the most abundant Rhodospirillales OTUs (19 and 22) were highly similar (sequences similarity = 99%) to OTUs from deep-sea sediment surrounding colonies of giant foraminifera at the Pacific Ocean ( Xenophyophorea ) 67 .…”

Section: Discussionmentioning

confidence: 83%

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

Coelho

Louvado

Domingues

et al. 2016

Sci Rep

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The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

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“…Homology to known 16S rRNA genes was generally low, with the only 97% identity score matching a deep-sea sediment sample obtained at a water column depth greater than 5000 m (DSC2, Schauer et al, 2010). Four of the SAG 16S rRNA genes are most closely related to sequences obtained from deep-sea sediments in the South Atlantic, Guinea Basin [DSC2 (97% similarity), 6 (89%), 7 (88%), and 9 (92%); Schauer et al, 2010; > 5000 m], two others are closely related to samples from sub-seafloor sediment of the South China Sea [DSC 8 (87%) and 10 (84%); Tao et al, 2008; 3697 m below the sea surface and 0.1m below the seafloor], DSC1 is related to samples recovered from a canyon slope in the Eastern Mediterranean Sea at 3603 m (93%; Polymenakou et al, 2009) and DSC4 (93%) and 5 (96%) are closely related to sediments within the Japan Trench at depths of 7111 and 6379 m respectively (Li et al, 1999;Hori et al, 2013). No previous suggestion of deep sea relatedness across Parcubacteria has been noted, yet these new sequences from the Mariana Trench clearly show significant relationships to deep sea relatives.…”

Section: Phylogenetic Relationshipsmentioning

confidence: 99%

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)

León-Zayas

Peoples

Biddle

et al. 2017

Environmental Microbiology

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Summary Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential, and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason we analyzed twelve Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification, and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.

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Active Bacterial Flora Surrounding Foraminifera (Xenophyophorea) Living on the Deep-Sea Floor

Cited by 16 publications

References 12 publications

Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)

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