MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis
Abstract Ecological theory aids in understanding how disturbances affect ecosystems. However, experimental data are often complex, with multiple post‐disturbance theories potentially applying simultaneously to the same ecosystem. This emphasizes the need for tools to experimentally test these theore...
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| Format: | Article |
| Language: | English |
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Wiley
2025-07-01
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| Series: | Methods in Ecology and Evolution |
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| Online Access: | https://doi.org/10.1111/2041-210X.70047 |
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| author | Soheil A. Neshat Ezequiel Santillan Stefan Wuertz |
| author_facet | Soheil A. Neshat Ezequiel Santillan Stefan Wuertz |
| author_sort | Soheil A. Neshat |
| collection | DOAJ |
| description | Abstract Ecological theory aids in understanding how disturbances affect ecosystems. However, experimental data are often complex, with multiple post‐disturbance theories potentially applying simultaneously to the same ecosystem. This emphasizes the need for tools to experimentally test these theoretical predictions. We introduce MicroEcoTools, an R package designed to test ecological framework predictions using microbial community data. It assesses microbial diversity and evaluates the relative impacts of stochastic and deterministic assembly mechanisms through a taxa‐based null model approach for replicated designs. Furthermore, the package allows application of Grime's trait‐based life‐history categories—competitor, stress‐tolerant and ruderal (CSR)—to taxa, functional traits and ecosystem functions within microbial communities. MicroEcoTools also includes relevant statistical tests, numeric simulations and publicly available datasets for demonstration. To demonstrate MicroEcoTools' functionality, we applied the package to experimental data from microcosm‐scale perturbation experiments on an activated sludge microbial ecosystem (included in the R package). This enabled us to assess assembly mechanisms and assign CSR categories. Results generated by MicroEcoTools closely aligned with previous findings from manual analysis. In conclusion, MicroEcoTools facilitates the application of ecological frameworks, including community assembly mechanisms, diversity analysis, and life‐history strategies, to microbial ecosystems under disturbance. This R package, along with its source code, can be freely accessed on GitHub at https://www.github.com/Soheil‐A‐Neshat/MicroEcoTools. |
| format | Article |
| id | doaj-art-94736752c79f4e59872780a5f57f725e |
| institution | Kabale University |
| issn | 2041-210X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-94736752c79f4e59872780a5f57f725e2025-08-20T03:31:02ZengWileyMethods in Ecology and Evolution2041-210X2025-07-011671369137710.1111/2041-210X.70047MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysisSoheil A. Neshat0Ezequiel Santillan1Stefan Wuertz2Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore Singapore SingaporeSingapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore Singapore SingaporeSingapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore Singapore SingaporeAbstract Ecological theory aids in understanding how disturbances affect ecosystems. However, experimental data are often complex, with multiple post‐disturbance theories potentially applying simultaneously to the same ecosystem. This emphasizes the need for tools to experimentally test these theoretical predictions. We introduce MicroEcoTools, an R package designed to test ecological framework predictions using microbial community data. It assesses microbial diversity and evaluates the relative impacts of stochastic and deterministic assembly mechanisms through a taxa‐based null model approach for replicated designs. Furthermore, the package allows application of Grime's trait‐based life‐history categories—competitor, stress‐tolerant and ruderal (CSR)—to taxa, functional traits and ecosystem functions within microbial communities. MicroEcoTools also includes relevant statistical tests, numeric simulations and publicly available datasets for demonstration. To demonstrate MicroEcoTools' functionality, we applied the package to experimental data from microcosm‐scale perturbation experiments on an activated sludge microbial ecosystem (included in the R package). This enabled us to assess assembly mechanisms and assign CSR categories. Results generated by MicroEcoTools closely aligned with previous findings from manual analysis. In conclusion, MicroEcoTools facilitates the application of ecological frameworks, including community assembly mechanisms, diversity analysis, and life‐history strategies, to microbial ecosystems under disturbance. This R package, along with its source code, can be freely accessed on GitHub at https://www.github.com/Soheil‐A‐Neshat/MicroEcoTools.https://doi.org/10.1111/2041-210X.70047community assemblyCSR‐frameworkdeterministic assemblydiversityecological theorynull model analysis |
| spellingShingle | Soheil A. Neshat Ezequiel Santillan Stefan Wuertz MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis Methods in Ecology and Evolution community assembly CSR‐framework deterministic assembly diversity ecological theory null model analysis |
| title | MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis |
| title_full | MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis |
| title_fullStr | MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis |
| title_full_unstemmed | MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis |
| title_short | MicroEcoTools: An R package for comprehensive theoretical microbial ecology analysis |
| title_sort | microecotools an r package for comprehensive theoretical microbial ecology analysis |
| topic | community assembly CSR‐framework deterministic assembly diversity ecological theory null model analysis |
| url | https://doi.org/10.1111/2041-210X.70047 |
| work_keys_str_mv | AT soheilaneshat microecotoolsanrpackageforcomprehensivetheoreticalmicrobialecologyanalysis AT ezequielsantillan microecotoolsanrpackageforcomprehensivetheoreticalmicrobialecologyanalysis AT stefanwuertz microecotoolsanrpackageforcomprehensivetheoreticalmicrobialecologyanalysis |