Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land us...

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Autores principales:	Gourvendu Saxena, Suparna Mitra, Ezequiel M. Marzinelli, Chao Xie, Toh Jun Wei, Peter D. Steinberg, Rohan B. H. Williams, Staffan Kjelleberg, Federico M. Lauro, Sanjay Swarup
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	benthic microbial communities community composition and functions land use rain perturbations urban environment Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c4f977acc06545c1b825156042fb5006
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spelling	oai:doaj.org-article:c4f977acc06545c1b825156042fb50062021-12-02T18:15:44ZMetagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway10.1128/mSystems.00136-172379-5077https://doaj.org/article/c4f977acc06545c1b825156042fb50062018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00136-17https://doaj.org/toc/2379-5077ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.Gourvendu SaxenaSuparna MitraEzequiel M. MarzinelliChao XieToh Jun WeiPeter D. SteinbergRohan B. H. WilliamsStaffan KjellebergFederico M. LauroSanjay SwarupAmerican Society for Microbiologyarticlebenthic microbial communitiescommunity composition and functionsland userain perturbationsurban environmentMicrobiologyQR1-502ENmSystems, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	benthic microbial communities community composition and functions land use rain perturbations urban environment Microbiology QR1-502
spellingShingle	benthic microbial communities community composition and functions land use rain perturbations urban environment Microbiology QR1-502 Gourvendu Saxena Suparna Mitra Ezequiel M. Marzinelli Chao Xie Toh Jun Wei Peter D. Steinberg Rohan B. H. Williams Staffan Kjelleberg Federico M. Lauro Sanjay Swarup Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
description	ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.
format	article
author	Gourvendu Saxena Suparna Mitra Ezequiel M. Marzinelli Chao Xie Toh Jun Wei Peter D. Steinberg Rohan B. H. Williams Staffan Kjelleberg Federico M. Lauro Sanjay Swarup
author_facet	Gourvendu Saxena Suparna Mitra Ezequiel M. Marzinelli Chao Xie Toh Jun Wei Peter D. Steinberg Rohan B. H. Williams Staffan Kjelleberg Federico M. Lauro Sanjay Swarup
author_sort	Gourvendu Saxena
title	Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
title_short	Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
title_full	Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
title_fullStr	Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
title_full_unstemmed	Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway
title_sort	metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/c4f977acc06545c1b825156042fb5006
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Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

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