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Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470...

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Autores principales: Tran, Patricia Q., Bachand, Samantha C., McIntyre, Peter B., Kraemer, Benjamin M., Vadeboncoeur, Yvonne, Kimirei, Ismael A., Tamatamah, Rashid, McMahon, Katherine D., Anantharaman, Karthik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245535/
https://www.ncbi.nlm.nih.gov/pubmed/33564113
http://dx.doi.org/10.1038/s41396-021-00898-x
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author Tran, Patricia Q.
Bachand, Samantha C.
McIntyre, Peter B.
Kraemer, Benjamin M.
Vadeboncoeur, Yvonne
Kimirei, Ismael A.
Tamatamah, Rashid
McMahon, Katherine D.
Anantharaman, Karthik
author_facet Tran, Patricia Q.
Bachand, Samantha C.
McIntyre, Peter B.
Kraemer, Benjamin M.
Vadeboncoeur, Yvonne
Kimirei, Ismael A.
Tamatamah, Rashid
McMahon, Katherine D.
Anantharaman, Karthik
author_sort Tran, Patricia Q.
collection PubMed
description Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.
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spelling pubmed-82455352021-07-20 Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika Tran, Patricia Q. Bachand, Samantha C. McIntyre, Peter B. Kraemer, Benjamin M. Vadeboncoeur, Yvonne Kimirei, Ismael A. Tamatamah, Rashid McMahon, Katherine D. Anantharaman, Karthik ISME J Article Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes. Nature Publishing Group UK 2021-02-09 2021-07 /pmc/articles/PMC8245535/ /pubmed/33564113 http://dx.doi.org/10.1038/s41396-021-00898-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Tran, Patricia Q.
Bachand, Samantha C.
McIntyre, Peter B.
Kraemer, Benjamin M.
Vadeboncoeur, Yvonne
Kimirei, Ismael A.
Tamatamah, Rashid
McMahon, Katherine D.
Anantharaman, Karthik
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title_full Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title_fullStr Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title_full_unstemmed Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title_short Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
title_sort depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater lake tanganyika
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245535/
https://www.ncbi.nlm.nih.gov/pubmed/33564113
http://dx.doi.org/10.1038/s41396-021-00898-x
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