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Functional conservation of microbial communities determines composition predictability in anaerobic digestion

The ISME Journal volume 17, pages 1920–1930 (2023)Cite this article

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Abstract

A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.

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Fig. 1: Microbial community response and the response predictability.
Fig. 2: Experimental design.
Fig. 3: The characteristics of response consortia.
Fig. 4: The generic characteristics of immediate response consortia (the assemblages of immediate response microorganisms) at different taxonomic levels, based on the comparison between 100 simulated communities generalizing community features before feedstock addition, and 100 simulated communities generalizing community features on the first day after feedstock addition.
Fig. 5: Microbial transcriptional profiles.
Fig. 6: Variability and functional profiles of the response OTUs.

Data availability

The original amplicon sequencing data are deposited at the European Nucleotide Archive by accession number PRJEB59216. The original metatranscriptomic sequencing data are deposited in the project “mgp80358” at MG-RAST.

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Acknowledgements

Thank all people who work against COVID-19 pandemic and appreciate the support from our families for our works.

Funding

This study was supported by the Open Found of Key Laboratory of Environmental and Applied Microbiology CAS (11050004GB), and China Biodiversity Observation Networks (Sino BON).

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Author notes

  1. These authors contributed equally: Qiang Lin, Lingjuan Li.

Authors and Affiliations

  1. Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China

    Qiang Lin, Chaonan Li, Xiaoyu Fang & Xiangzhen Li

  2. Department of Biology, University of Antwerp, 2610, Wilrijk, Belgium

    Lingjuan Li

  3. Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, 9000, Belgium

    Jo De Vrieze

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  1. Qiang Lin
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Contributions

QL conceived this study, conducted the experiment, analyzed data, and wrote and revised the manuscript. LJL analyzed data and revised the manuscript. JDV, CNL, and XZL revised the manuscript. XYF conducted the experiment.

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Correspondence to Xiangzhen Li.

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Lin, Q., Li, L., De Vrieze, J. et al. Functional conservation of microbial communities determines composition predictability in anaerobic digestion. ISME J 17, 1920–1930 (2023). https://doi.org/10.1038/s41396-023-01505-x

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