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Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly
Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ec...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8894727/ https://www.ncbi.nlm.nih.gov/pubmed/35250925 http://dx.doi.org/10.3389/fmicb.2022.803420 |
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author | Danczak, Robert E. Sengupta, Aditi Fansler, Sarah J. Chu, Rosalie K. Garayburu-Caruso, Vanessa A. Renteria, Lupita Toyoda, Jason Wells, Jacqueline Stegen, James C. |
author_facet | Danczak, Robert E. Sengupta, Aditi Fansler, Sarah J. Chu, Rosalie K. Garayburu-Caruso, Vanessa A. Renteria, Lupita Toyoda, Jason Wells, Jacqueline Stegen, James C. |
author_sort | Danczak, Robert E. |
collection | PubMed |
description | Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI(feat)), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI(feat), we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI(feat) can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI(feat) values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI(feat) offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types. |
format | Online Article Text |
id | pubmed-8894727 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88947272022-03-05 Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly Danczak, Robert E. Sengupta, Aditi Fansler, Sarah J. Chu, Rosalie K. Garayburu-Caruso, Vanessa A. Renteria, Lupita Toyoda, Jason Wells, Jacqueline Stegen, James C. Front Microbiol Microbiology Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI(feat)), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI(feat), we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI(feat) can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI(feat) values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI(feat) offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types. Frontiers Media S.A. 2022-02-18 /pmc/articles/PMC8894727/ /pubmed/35250925 http://dx.doi.org/10.3389/fmicb.2022.803420 Text en Copyright © 2022 Danczak, Sengupta, Fansler, Chu, Garayburu-Caruso, Renteria, Toyoda, Wells and Stegen. https://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) and the copyright owner(s) 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 Danczak, Robert E. Sengupta, Aditi Fansler, Sarah J. Chu, Rosalie K. Garayburu-Caruso, Vanessa A. Renteria, Lupita Toyoda, Jason Wells, Jacqueline Stegen, James C. Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title | Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title_full | Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title_fullStr | Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title_full_unstemmed | Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title_short | Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly |
title_sort | inferring the contribution of microbial taxa and organic matter molecular formulas to ecological assembly |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8894727/ https://www.ncbi.nlm.nih.gov/pubmed/35250925 http://dx.doi.org/10.3389/fmicb.2022.803420 |
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