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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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Comparative fragment recruitment for the PRT and GS00d metagenomes.Recruitment of the PRT metagenome compared to the GS00d metagenome to the Marine Microbial Genome Sequencing Project (MMGSP) genomes, Nitrosopumilus maritimus SCM1 [39], Candidatus Pelagibacter ubique HTCC1062 [40], and the four PRT single-cell genomes. Circles represent reference genomes. Reference genomes with greater normalized relative recruitment (sequence identity threshold 80%) to the PRT are below the zero line, while genomes above the zero are better recruiters for the GS00d dataset. In calculating the ratio of GS00d/PRT recruitment, the number of reads recruited from each metagenome was normalized to the size (in Mbp) of the reference genome as well as to the number of total reads in the metagenome. Similar results were observed for PRT and GS00c metagenome comparisons.
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pone-0020388-g006: Comparative fragment recruitment for the PRT and GS00d metagenomes.Recruitment of the PRT metagenome compared to the GS00d metagenome to the Marine Microbial Genome Sequencing Project (MMGSP) genomes, Nitrosopumilus maritimus SCM1 [39], Candidatus Pelagibacter ubique HTCC1062 [40], and the four PRT single-cell genomes. Circles represent reference genomes. Reference genomes with greater normalized relative recruitment (sequence identity threshold 80%) to the PRT are below the zero line, while genomes above the zero are better recruiters for the GS00d dataset. In calculating the ratio of GS00d/PRT recruitment, the number of reads recruited from each metagenome was normalized to the size (in Mbp) of the reference genome as well as to the number of total reads in the metagenome. Similar results were observed for PRT and GS00c metagenome comparisons.

Mentions: Fragment recruitment of the PRT raw metagenomic reads to the four single cells yielded extremely high recruitment compared to recruitment to 172 sequenced marine microbial genomes (Fig. 6). The majority of PRT reads which recruited to the single-cell genomes were matches to portions of the ribosomal operons, with percent identity ranging from 84.5 to 88.0%, as well as transfer-RNA sequences. The Planctomycetes bacterium JCVI-SC AAA004 was the only single cell to recruit fragments of the PRT metagenome to all contigs of the dataset, in addition to recruiting the most reads relative to the size of the genome for any of the genomes compared (45,373 hits/Mbp).


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)

Comparative fragment recruitment for the PRT and GS00d metagenomes.Recruitment of the PRT metagenome compared to the GS00d metagenome to the Marine Microbial Genome Sequencing Project (MMGSP) genomes, Nitrosopumilus maritimus SCM1 [39], Candidatus Pelagibacter ubique HTCC1062 [40], and the four PRT single-cell genomes. Circles represent reference genomes. Reference genomes with greater normalized relative recruitment (sequence identity threshold 80%) to the PRT are below the zero line, while genomes above the zero are better recruiters for the GS00d dataset. In calculating the ratio of GS00d/PRT recruitment, the number of reads recruited from each metagenome was normalized to the size (in Mbp) of the reference genome as well as to the number of total reads in the metagenome. Similar results were observed for PRT and GS00c metagenome comparisons.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020388-g006: Comparative fragment recruitment for the PRT and GS00d metagenomes.Recruitment of the PRT metagenome compared to the GS00d metagenome to the Marine Microbial Genome Sequencing Project (MMGSP) genomes, Nitrosopumilus maritimus SCM1 [39], Candidatus Pelagibacter ubique HTCC1062 [40], and the four PRT single-cell genomes. Circles represent reference genomes. Reference genomes with greater normalized relative recruitment (sequence identity threshold 80%) to the PRT are below the zero line, while genomes above the zero are better recruiters for the GS00d dataset. In calculating the ratio of GS00d/PRT recruitment, the number of reads recruited from each metagenome was normalized to the size (in Mbp) of the reference genome as well as to the number of total reads in the metagenome. Similar results were observed for PRT and GS00c metagenome comparisons.
Mentions: Fragment recruitment of the PRT raw metagenomic reads to the four single cells yielded extremely high recruitment compared to recruitment to 172 sequenced marine microbial genomes (Fig. 6). The majority of PRT reads which recruited to the single-cell genomes were matches to portions of the ribosomal operons, with percent identity ranging from 84.5 to 88.0%, as well as transfer-RNA sequences. The Planctomycetes bacterium JCVI-SC AAA004 was the only single cell to recruit fragments of the PRT metagenome to all contigs of the dataset, in addition to recruiting the most reads relative to the size of the genome for any of the genomes compared (45,373 hits/Mbp).

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