Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis

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Abstract

Background

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure.

Results

The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors.

Conclusions

The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

Electronic supplementary material

The online version of this article (doi:10.1186/s13068-016-0465-6) contains supplementary material, which is available to authorized users.

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Most cited references 54

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Standard Methods for the Examination of Water and Wastewater

American Public Health Association (2005)

"The Twenty-First Edition has continued the trend to revise methods as issues are identified and contains further refined quality assurance requirements in a number of Parts [sic] and new data on precision and bias. New methods have been added in Parts 2000, 4000, 5000, 6000, 7000, 8000, and 9000, and numerous methods have been revised. Details of these changes appear on the reverse of the title page for each part."--Pref. p. iv.

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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

N Fierer, J W Leff, B. J. Adams … (2012)

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

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Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Noah Fierer, Christian L Lauber, Kelly Ramirez … (2012)

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

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Author and article information

Contributors

Gang Luo: gangl@fudan.edu.cn

Ioannis A. Fotidis: ioanf@env.dtu.dk

Irini Angelidaki: iria@env.dtu.dk

Journal

Journal ID (nlm-ta): Biotechnol Biofuels

Journal ID (iso-abbrev): Biotechnol Biofuels

Title: Biotechnology for Biofuels

Publisher: BioMed Central (London )

ISSN (Electronic): 1754-6834

Publication date (Electronic): 2 March 2016

Publication date PMC-release: 2 March 2016

Publication date Collection: 2016

Volume: 9

Electronic Location Identifier: 51

Affiliations

[ ]Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China

[ ]Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark

Article

Publisher ID: 465

DOI: 10.1186/s13068-016-0465-6

PMC ID: 4776419

PubMed ID: 26941838

SO-VID: 4cfad202-2955-4901-ad5f-7a6a9dfd8c1f

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 9 December 2015

Date accepted : 19 February 2016

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100008394, Natur og Univers, Det Frie Forskningsråd (DK);

Award ID: (12-126632)

Award Recipient : Gang Luo

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ScienceOpen disciplines: Biotechnology

Keywords: biogas reactors,metagenomic sequencing,taxonomic patterns,functional patterns,methanogenic pathway

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ScienceOpen disciplines: Biotechnology

Keywords: biogas reactors, metagenomic sequencing, taxonomic patterns, functional patterns, methanogenic pathway

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis

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Abstract

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Genome Engineering using CRISPR

Most cited references 54

Standard Methods for the Examination of Water and Wastewater

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

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