Assessing mechanisms for microbial taxa and community dynamics using process models
Abstract Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, par...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-09-01
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| Series: | mLife |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/mlf2.12076 |
| _version_ | 1797671749111775232 |
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| author | Linwei Wu Yunfeng Yang Daliang Ning Qun Gao Huaqun Yin Naija Xiao Benjamin Y. Zhou Si Chen Qiang He Jizhong Zhou |
| author_facet | Linwei Wu Yunfeng Yang Daliang Ning Qun Gao Huaqun Yin Naija Xiao Benjamin Y. Zhou Si Chen Qiang He Jizhong Zhou |
| author_sort | Linwei Wu |
| collection | DOAJ |
| description | Abstract Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time‐series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology. |
| first_indexed | 2024-03-11T21:20:03Z |
| format | Article |
| id | doaj.art-91f3eeeeec7c443ba2a82a52babf0ab8 |
| institution | Directory Open Access Journal |
| issn | 2770-100X |
| language | English |
| last_indexed | 2024-03-11T21:20:03Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | mLife |
| spelling | doaj.art-91f3eeeeec7c443ba2a82a52babf0ab82023-09-28T10:25:52ZengWileymLife2770-100X2023-09-012323925210.1002/mlf2.12076Assessing mechanisms for microbial taxa and community dynamics using process modelsLinwei Wu0Yunfeng Yang1Daliang Ning2Qun Gao3Huaqun Yin4Naija Xiao5Benjamin Y. Zhou6Si Chen7Qiang He8Jizhong Zhou9Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences Peking University Beijing ChinaState Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing ChinaInstitute for Environmental Genomics University of Oklahoma Norman OK USAState Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing ChinaSchool of Minerals Processing and Bioengineering Central South University Changsha ChinaInstitute for Environmental Genomics University of Oklahoma Norman OK USADepartment of Mathematics, Lunt Hall Northwestern University Evanston Illinois USADepartment of Civil and Environmental Engineering The University of Tennessee Knoxville Tennessee USADepartment of Civil and Environmental Engineering The University of Tennessee Knoxville Tennessee USAInstitute for Environmental Genomics University of Oklahoma Norman OK USAAbstract Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time‐series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.https://doi.org/10.1002/mlf2.12076community assembly mechanismsconsumer–resource modelneutral modelspecies dynamics |
| spellingShingle | Linwei Wu Yunfeng Yang Daliang Ning Qun Gao Huaqun Yin Naija Xiao Benjamin Y. Zhou Si Chen Qiang He Jizhong Zhou Assessing mechanisms for microbial taxa and community dynamics using process models mLife community assembly mechanisms consumer–resource model neutral model species dynamics |
| title | Assessing mechanisms for microbial taxa and community dynamics using process models |
| title_full | Assessing mechanisms for microbial taxa and community dynamics using process models |
| title_fullStr | Assessing mechanisms for microbial taxa and community dynamics using process models |
| title_full_unstemmed | Assessing mechanisms for microbial taxa and community dynamics using process models |
| title_short | Assessing mechanisms for microbial taxa and community dynamics using process models |
| title_sort | assessing mechanisms for microbial taxa and community dynamics using process models |
| topic | community assembly mechanisms consumer–resource model neutral model species dynamics |
| url | https://doi.org/10.1002/mlf2.12076 |
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