Microbial metatranscriptomics in a permanent marine oxygen minimum zone
Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial...
| Main Authors: | , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Society for Applied Microbiology and Blackwell Publishing Ltd
2012
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| Online Access: | http://hdl.handle.net/1721.1/69592 |
| _version_ | 1826208444801089536 |
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| author | Stewart, Frank J. Ulloa, Osvaldo DeLong, Edward |
| author2 | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Stewart, Frank J. Ulloa, Osvaldo DeLong, Edward |
| author_sort | Stewart, Frank J. |
| collection | MIT |
| description | Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline and into the upper OMZ. Shotgun pyrosequencing of cDNA yielded 180 000 to 550 000 transcript sequences per depth. Based on functional gene representation, transcriptome samples clustered apart from corresponding metagenome samples from the same depth, highlighting the discrepancies between metabolic potential and actual transcription. BLAST-based characterizations of non-ribosomal RNA sequences revealed a dominance of genes involved with both oxidative (nitrification) and reductive (anammox, denitrification) components of the marine nitrogen cycle. Using annotations of protein-coding genes as proxies for taxonomic affiliation, we observed depth-specific changes in gene expression by key functional taxonomic groups. Notably, transcripts most closely matching the genome of the ammonia-oxidizing archaeon Nitrosopumilus maritimus dominated the transcriptome in the upper three depths, representing one in five protein-coding transcripts at 85 m. In contrast, transcripts matching the anammox bacterium Kuenenia stuttgartiensis dominated at the core of the OMZ (200 m; 1 in 12 protein-coding transcripts). The distribution of N. maritimus-like transcripts paralleled that of transcripts matching ammonia monooxygenase genes, which, despite being represented by both bacterial and archaeal sequences in the community DNA, were dominated (> 99%) by archaeal sequences in the RNA, suggesting a substantial role for archaeal nitrification in the upper OMZ. These data, as well as those describing other key OMZ metabolic processes (e.g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling. |
| first_indexed | 2024-09-23T14:05:32Z |
| format | Article |
| id | mit-1721.1/69592 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:05:32Z |
| publishDate | 2012 |
| publisher | Society for Applied Microbiology and Blackwell Publishing Ltd |
| record_format | dspace |
| spelling | mit-1721.1/695922022-09-28T18:21:11Z Microbial metatranscriptomics in a permanent marine oxygen minimum zone Stewart, Frank J. Ulloa, Osvaldo DeLong, Edward Massachusetts Institute of Technology. Department of Civil and Environmental Engineering DeLong, Edward DeLong, Edward Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline and into the upper OMZ. Shotgun pyrosequencing of cDNA yielded 180 000 to 550 000 transcript sequences per depth. Based on functional gene representation, transcriptome samples clustered apart from corresponding metagenome samples from the same depth, highlighting the discrepancies between metabolic potential and actual transcription. BLAST-based characterizations of non-ribosomal RNA sequences revealed a dominance of genes involved with both oxidative (nitrification) and reductive (anammox, denitrification) components of the marine nitrogen cycle. Using annotations of protein-coding genes as proxies for taxonomic affiliation, we observed depth-specific changes in gene expression by key functional taxonomic groups. Notably, transcripts most closely matching the genome of the ammonia-oxidizing archaeon Nitrosopumilus maritimus dominated the transcriptome in the upper three depths, representing one in five protein-coding transcripts at 85 m. In contrast, transcripts matching the anammox bacterium Kuenenia stuttgartiensis dominated at the core of the OMZ (200 m; 1 in 12 protein-coding transcripts). The distribution of N. maritimus-like transcripts paralleled that of transcripts matching ammonia monooxygenase genes, which, despite being represented by both bacterial and archaeal sequences in the community DNA, were dominated (> 99%) by archaeal sequences in the RNA, suggesting a substantial role for archaeal nitrification in the upper OMZ. These data, as well as those describing other key OMZ metabolic processes (e.g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling. Agouron Institute Gordon and Betty Moore Foundation United States. Dept. of Energy (Office of Science) Comisión Nacional de Investigación Ciencia y Tecnología (Chile) (Program Fondap) 2012-03-08T15:44:19Z 2012-03-08T15:44:19Z 2012-01 2010-08 Article http://purl.org/eprint/type/JournalArticle 1462-2912 1462-2920 http://hdl.handle.net/1721.1/69592 Stewart, Frank J., Osvaldo Ulloa, and Edward F. DeLong. “Microbial Metatranscriptomics in a Permanent Marine Oxygen Minimum Zone.” Environmental Microbiology 14.1 (2012): 23–40. en_US http://dx.doi.org/10.1111/j.1462-2920.2010.02400.x Environmental Microbiology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Society for Applied Microbiology and Blackwell Publishing Ltd Delong via Anne Graham |
| spellingShingle | Stewart, Frank J. Ulloa, Osvaldo DeLong, Edward Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title | Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title_full | Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title_fullStr | Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title_full_unstemmed | Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title_short | Microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| title_sort | microbial metatranscriptomics in a permanent marine oxygen minimum zone |
| url | http://hdl.handle.net/1721.1/69592 |
| work_keys_str_mv | AT stewartfrankj microbialmetatranscriptomicsinapermanentmarineoxygenminimumzone AT ulloaosvaldo microbialmetatranscriptomicsinapermanentmarineoxygenminimumzone AT delongedward microbialmetatranscriptomicsinapermanentmarineoxygenminimumzone |