Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)

Mavromatis, Konstantinos; Abt, Birte; Brambilla, Evelyne; Lapidus, Alla; Copeland, Alex; Deshpande, Shweta; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan‐Fang; Han, Cliff; Detter, John C.; Woyke, Tanja; Goodwin, Lynne; Pitluck, Sam; Held, Brittany; Brettin, Thomas; Tapia, Roxanne; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Liolios, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia D.; Rohde, Manfred; Göker, Markus; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans Peter; Kyrpides, Nikos C.

doi:10.4056/sigs.952166

Cited by 21 publications

(18 citation statements)

References 31 publications

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“…Other investigators have taken advantage of early access to the GEBA-I genomes and discovered prominent member species in their samples, for example, Treponema succinifaciens 36 and Treponema brennaborense in the gut microbiomes of non-human primates and traditional hunter-gatherers 37 , Ktedonobacter racemifer in an enrichment to identify rare soil microbes 38 , Coraliomargarita akajimensis 39 in an Amazon river plume 40 , Sphaerobacter thermophiles 41 in thermophilic switchgrass-adapted compost 42 .…”

Section: Improved Taxonomic Assignment Of Metagenomic Sequencesmentioning

confidence: 99%

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

et al. 2017

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We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

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Section: Improved Taxonomic Assignment Of Metagenomic Sequencesmentioning

confidence: 99%

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

et al. 2017

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“…Coraliomargarita accounted for 197 reads in this data set (1.6% of all MYI reads), split among 14 lineages. This genus has no psychrophilic members in culture and, despite a sequenced genome for C. akajimensis (Mavromatis et al, 2010), there is little in the natural history of this genus to suggest why it should be associated with MYI. Like many sea ice-associated microbes C. akajimensis is copiotrophic, a feature that might favor its persistence within organic-rich horizons of MYI.…”

Section: Discussionmentioning

confidence: 99%

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

et al. 2011

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Dramatic decreases in the extent of Arctic multiyear ice (MYI) suggest this environment may disappear as early as 2100, replaced by ecologically different first-year ice. To better understand the implications of this loss on microbial biodiversity, we undertook a detailed census of the microbial community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than in underlying surface water, we found diversity to be comparable using the Simpson and Shannon's indices (for Simpson t=0.65, P=0.56; for Shannon t=0.25, P=0.84 for a Student's t-test of mean values). Cyanobacteria, comprising 6.8% of reads obtained from MYI, were observed for the first time in Arctic sea ice. In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within MYI.

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“…Most of the isolated and reconstructed genomes of marine Verrucomicrobia came from surface samples 450 (Yoon et al, 2007;Mavromatis et al, 2010;Hugerth et al, 2015). For the phylogenomic classification of the bins we have included representatives of reconstructed genomes from the Baltic Sea (Hugerth et al, 2015), single cell genomes, and genomes from the family Opitutaceae.…”

Section: Verrucomicrobiamentioning

confidence: 99%

Fine stratification of microbial communities through a metagenomic profile of the photic zone

López‐Pérez

Torre

et al. 2017

Preprint

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Most marine metagenomic studies of the marine photic zone analyze only samples taken at one or two depths. However, when the water column is stratified, physicochemical parameters change dramatically 25 over relatively short depth intervals. We sampled the photic water column every 15m depth at a single point of an off-shore Mediterranean site during a period of strong stratification (early autumn) to evaluate the effects of small depth increases on the microbiome. Using genomic assembly and metagenomic read recruitment, we found major shifts in the community structure over small variations of depth, with most microbes showing a distribution limited to layers approximately 30 meters thick (stenobathic). Only some 30 representatives of the SAR11 clade and the Sphingomonadaceae appeared to be eurybathic, spanning a greater range of depths. These results were confirmed by studying a single gene (rhodopsin) for which we also found narrow depth distributions. Our results highlight the importance of considering vertical distribution as a major element when analyzing the presence of marine clades and species or comparing the microbiome present at different locations. 35

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Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)

Cited by 21 publications

References 31 publications

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

Fine stratification of microbial communities through a metagenomic profile of the photic zone

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