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Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks
Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the s...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649028/ https://www.ncbi.nlm.nih.gov/pubmed/26635741 http://dx.doi.org/10.3389/fmicb.2015.01269 |
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author | Uksa, Marie Schloter, Michael Endesfelder, David Kublik, Susanne Engel, Marion Kautz, Timo Köpke, Ulrich Fischer, Doreen |
author_facet | Uksa, Marie Schloter, Michael Endesfelder, David Kublik, Susanne Engel, Marion Kautz, Timo Köpke, Ulrich Fischer, Doreen |
author_sort | Uksa, Marie |
collection | PubMed |
description | Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments. |
format | Online Article Text |
id | pubmed-4649028 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-46490282015-12-03 Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks Uksa, Marie Schloter, Michael Endesfelder, David Kublik, Susanne Engel, Marion Kautz, Timo Köpke, Ulrich Fischer, Doreen Front Microbiol Microbiology Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments. Frontiers Media S.A. 2015-11-18 /pmc/articles/PMC4649028/ /pubmed/26635741 http://dx.doi.org/10.3389/fmicb.2015.01269 Text en Copyright © 2015 Uksa, Schloter, Endesfelder, Kublik, Engel, Kautz, Köpke and Fischer. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Uksa, Marie Schloter, Michael Endesfelder, David Kublik, Susanne Engel, Marion Kautz, Timo Köpke, Ulrich Fischer, Doreen Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title | Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title_full | Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title_fullStr | Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title_full_unstemmed | Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title_short | Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks |
title_sort | prokaryotes in subsoil—evidence for a strong spatial separation of different phyla by analysing co-occurrence networks |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649028/ https://www.ncbi.nlm.nih.gov/pubmed/26635741 http://dx.doi.org/10.3389/fmicb.2015.01269 |
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