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Going deeper: metagenome of a hadopelagic microbial community.

Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH - PLoS ONE (2011)

Bottom Line: A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea.The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes.Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.

View Article: PubMed Central - PubMed

Affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.

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Transporter family distribution.Outer circle moving inwards: PRT, HOT4000, DeepMed, GS00d, GS00c. Log abundance profiles for (A) the Resistance-nodulation-cell division (RND) superfamily and (B) the ATP-binding cassette (ABC) superfamily are shown for the PRT compared to the GS00c. Positive values in the bar chart denote greater abundances in the PRT, while negative values are greater abundances in the GS00c for the given transporter family member. Similar results were observed for PRT and GS00d metagenome comparisons. Transporter classification details are included in the Supplementary Materials.
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pone-0020388-g005: Transporter family distribution.Outer circle moving inwards: PRT, HOT4000, DeepMed, GS00d, GS00c. Log abundance profiles for (A) the Resistance-nodulation-cell division (RND) superfamily and (B) the ATP-binding cassette (ABC) superfamily are shown for the PRT compared to the GS00c. Positive values in the bar chart denote greater abundances in the PRT, while negative values are greater abundances in the GS00c for the given transporter family member. Similar results were observed for PRT and GS00d metagenome comparisons. Transporter classification details are included in the Supplementary Materials.

Mentions: Transport mechanisms are one of the major cellular processes differentially influenced by hydrostatic pressure changes in transcriptomic analyses in the piezophilic bacterium P. profundum strain SS9 [60]. Additionally, the most pressure-regulated proteins produced by this bacterium are outer membrane porin proteins [61], [62]. Since high hydrostatic pressure acts to reduce the system volume, and consequently modifies the cellular membrane, the structural diversity, specificity, and variety of transporters would presumably be distinct in deep ocean microbial assemblages compared to surface seawater counterparts. To address this question, the nonredundant protein sets were classified using the Transporter Classification Database (TCDB) [30]. The overall diversity of transporter families identified was comparable across the metagenomes, generally with an even distribution and representation (Fig. 5). However, comparisons of the deep and surface seawater metagenomes revealed that 281 transporter classifications (TC IDs) within 116 transporter families (out of a total of 610 transporter families) were significantly different (p<0.05), and 155 of the 281 TC IDs were enriched in the deep-sea compared to the shallow-water datasets. These included the general secretory and outer membrane protein secreting pathways, many outer membrane proteins (most are members of the outer membrane receptor family, the outer membrane porin family, the OmpA-OmpF porin family, and the FadL outer membrane family), diverse cation transporters (sodium symporters, monovalent cation antiporters, cation diffusion facilitators, ferrous iron and magnesium transporters), including many associated with heavy metals (chromate, arsenical resistance family, resistance-nodulation-cell division, arsenite-antimonite efflux, iron lead transporters, mercuric ion permeases, P-type ATPases). Also enriched were peptide transporters, including those linked with carbon starvation, mono, di- and tri-carboxylate transporters, mechanosensitive ion channels, members of the major facilitator superfamily, tripartite ATP-independent periplasmic transporters and ATP-binding cassette superfamily transporters (Supplementary Table S2).


Going deeper: metagenome of a hadopelagic microbial community.

Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH - PLoS ONE (2011)

Transporter family distribution.Outer circle moving inwards: PRT, HOT4000, DeepMed, GS00d, GS00c. Log abundance profiles for (A) the Resistance-nodulation-cell division (RND) superfamily and (B) the ATP-binding cassette (ABC) superfamily are shown for the PRT compared to the GS00c. Positive values in the bar chart denote greater abundances in the PRT, while negative values are greater abundances in the GS00c for the given transporter family member. Similar results were observed for PRT and GS00d metagenome comparisons. Transporter classification details are included in the Supplementary Materials.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101246&req=5

pone-0020388-g005: Transporter family distribution.Outer circle moving inwards: PRT, HOT4000, DeepMed, GS00d, GS00c. Log abundance profiles for (A) the Resistance-nodulation-cell division (RND) superfamily and (B) the ATP-binding cassette (ABC) superfamily are shown for the PRT compared to the GS00c. Positive values in the bar chart denote greater abundances in the PRT, while negative values are greater abundances in the GS00c for the given transporter family member. Similar results were observed for PRT and GS00d metagenome comparisons. Transporter classification details are included in the Supplementary Materials.
Mentions: Transport mechanisms are one of the major cellular processes differentially influenced by hydrostatic pressure changes in transcriptomic analyses in the piezophilic bacterium P. profundum strain SS9 [60]. Additionally, the most pressure-regulated proteins produced by this bacterium are outer membrane porin proteins [61], [62]. Since high hydrostatic pressure acts to reduce the system volume, and consequently modifies the cellular membrane, the structural diversity, specificity, and variety of transporters would presumably be distinct in deep ocean microbial assemblages compared to surface seawater counterparts. To address this question, the nonredundant protein sets were classified using the Transporter Classification Database (TCDB) [30]. The overall diversity of transporter families identified was comparable across the metagenomes, generally with an even distribution and representation (Fig. 5). However, comparisons of the deep and surface seawater metagenomes revealed that 281 transporter classifications (TC IDs) within 116 transporter families (out of a total of 610 transporter families) were significantly different (p<0.05), and 155 of the 281 TC IDs were enriched in the deep-sea compared to the shallow-water datasets. These included the general secretory and outer membrane protein secreting pathways, many outer membrane proteins (most are members of the outer membrane receptor family, the outer membrane porin family, the OmpA-OmpF porin family, and the FadL outer membrane family), diverse cation transporters (sodium symporters, monovalent cation antiporters, cation diffusion facilitators, ferrous iron and magnesium transporters), including many associated with heavy metals (chromate, arsenical resistance family, resistance-nodulation-cell division, arsenite-antimonite efflux, iron lead transporters, mercuric ion permeases, P-type ATPases). Also enriched were peptide transporters, including those linked with carbon starvation, mono, di- and tri-carboxylate transporters, mechanosensitive ion channels, members of the major facilitator superfamily, tripartite ATP-independent periplasmic transporters and ATP-binding cassette superfamily transporters (Supplementary Table S2).

Bottom Line: A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea.The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes.Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.

View Article: PubMed Central - PubMed

Affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.

ABSTRACT
The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.

Show MeSH