Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly
Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biologic...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011269/full |
| _version_ | 1828105708811321344 |
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| author | Kai Ma Qichao Tu Qichao Tu |
| author_facet | Kai Ma Qichao Tu Qichao Tu |
| author_sort | Kai Ma |
| collection | DOAJ |
| description | Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined. |
| first_indexed | 2024-04-11T10:06:42Z |
| format | Article |
| id | doaj.art-d6bc2cf5df4c4b838a08bffbae6fe375 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T10:06:42Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-d6bc2cf5df4c4b838a08bffbae6fe3752022-12-22T04:30:12ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-10-011310.3389/fmicb.2022.10112691011269Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assemblyKai Ma0Qichao Tu1Qichao Tu2Institute of Marine Science and Technology, Shandong University, Qingdao, ChinaInstitute of Marine Science and Technology, Shandong University, Qingdao, ChinaJoint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, ChinaRevealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011269/fullrandom samplingβ-diversitymicrobial communitystochasticitynull modelsRaup–Crick metric |
| spellingShingle | Kai Ma Qichao Tu Qichao Tu Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly Frontiers in Microbiology random sampling β-diversity microbial community stochasticity null models Raup–Crick metric |
| title | Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| title_full | Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| title_fullStr | Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| title_full_unstemmed | Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| title_short | Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| title_sort | random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly |
| topic | random sampling β-diversity microbial community stochasticity null models Raup–Crick metric |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011269/full |
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