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Loza A, García-Guevara F, Segovia L, Escobar-Zepeda A, Sanchez-Olmos MDC, Merino E, Sanchez-Flores A, Pardo-Lopez L, Juarez K, Gutierrez-Rios RM. Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide. Front Microbiol 2022; 12:781497. [PMID: 35178038 PMCID: PMC8846951 DOI: 10.3389/fmicb.2021.781497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site.
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Larkin AA, Garcia CA, Garcia N, Brock ML, Lee JA, Ustick LJ, Barbero L, Carter BR, Sonnerup RE, Talley LD, Tarran GA, Volkov DL, Martiny AC. High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects. Sci Data 2021; 8:107. [PMID: 33863919 PMCID: PMC8052323 DOI: 10.1038/s41597-021-00889-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/12/2021] [Indexed: 11/09/2022] Open
Abstract
Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California at Irvine, Irvine, CA, USA
| | - Catherine A Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, USA
| | - Nathan Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, USA
| | - Melissa L Brock
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA
| | - Jenna A Lee
- Department of Earth System Science, University of California at Irvine, Irvine, CA, USA
| | - Lucas J Ustick
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA
| | - Leticia Barbero
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA.,Cooperative Institute for Marine & Atmospheric Studies, University of Miami, Miami, FL, USA
| | - Brendan R Carter
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA.,Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, USA
| | - Rolf E Sonnerup
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA.,Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, USA
| | - Lynne D Talley
- Climate, Atmospheric Sciences, and Physical Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | | | - Denis L Volkov
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA.,Cooperative Institute for Marine & Atmospheric Studies, University of Miami, Miami, FL, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California at Irvine, Irvine, CA, USA. .,Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA, USA.
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