The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

Abstract

29Background 30 Microorganisms in biogas reactors are essential for degradation of organic matter and methane 31 production through anaerobic digestion process. However, a comprehensive genome-centric 32 comparison, including relevant metadata for each sample, is still needed to identify the globally 33 distributed biogas community members and serve as a reliable repository. 34 Results 35Here, 134 publicly available datasets derived from different biogas reactors were used to recover 36 1,635 metagenome-assembled genomes (MAGs) representing different bacterial and archaeal 37 species. All genomes were estimated to be >50% complete and nearly half were ≥90% complete 38 with ≤5% contamination. In most samples, specialized microbial communities were established, 39 while only a few taxa were widespread among the different reactor systems. Metabolic 40 reconstruction of the MAGs enabled the prediction of functional traits related to biomass 41 degradation and methane production from waste biomass. An extensive evaluation of the replication 42 index provided an estimation of the growth rate for microbes involved in different steps of the food 43 chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other 44 underexplored taxa suggests their specific involvement in the anaerobic degradation of organic 45 matter. 46 Conclusions 47 The outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic 48 composition and adaptability to the environmental conditions, including temperatures and a wide 49 range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of 50 anaerobic digestion microbiome and substantially extend the existing repository of genomes. The 51 established database represents a relevant resource for future studies related to this engineered 52 ecosystem. 53 3 54Background 55 Anaerobic environments are ubiquitous in the biosphere, some examples are the digestive tract of 56 animals, paddy fields and aquatic sediments. These environments play crucial roles in the 57 degradation of organic matter and in the global carbon cycle [1,2]. The anaerobic digestion (AD) 58 process is also an example of such an environment, having great societal importance since it 59 reduces our dependence on fossil fuels via its ability to generate methane within engineered 60 bioreactors [3]. For these reasons, the AD process has been widely acknowledged as an efficient 61 biochemical route allowing the conversion of organic wastes into energy and other valuable 62 products, and has been posited as a sustainable solution for resource recovery and renewable energy 63 production underpinning the circular economy concept [4]. Apart from biowaste valorization, this 64 process is also of great importance for nutrient recycling, since it stabilizes the nitrogen compounds 65 making them more easily assimilable by plants, reducing nitrogen leakage to soil and groundwater. 66 Methane is one of the most relevant end-products generated during the meth...

Abundance tracking by long-read nanopore sequencing of complex microbial communities in samples from 20 different biogas/wastewater plants

“…In general, the phylum-level estimates obtained in this work are in line with findings in 16S rRNA studies and MAG studies pointing to Firmicutes and Bacteroidetes as the main phyla for most AD processes [5,18,23]. They are also in line with Campanaro et al, who identified 790 Firmicutes MAGs among 1600 public available MAGs from ADs [3]. Sun et al identified mainly Bacteroidetes (17-70%), followed by Firmicutes (5-10%), in five samples from WWTP [24].…”

“…In AD, many microorganisms form complex consortia to link and combine metabolic activities, and each member has different requirements for nutrients and physical conditions. However, the majority of the microorganisms involved are unknown [3], because isolation and characterisation of these microorganisms is time-consuming and many are not cultivable.…”

Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)

“…In total, MUFFIN retrieved 654 MAGs with genome completeness of over 90 %, of which 456 have less than 2% contamination out of the 20 datasets. For comparison, a recent study was using 134 publicly available datasets from different biogas reactors and retrieved 1,635 metagenome-assembled genomes with genome completeness of over 50% 46 .…”

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

“…For this propose, the integration of different -omics approaches (integrated or poly-omics), as example, the combination of metagenome with metatranscriptome datasets, is indispensable to distinguish between metabolically active and less active microbial species. Genomecentered biogas microbiome analyses already disclosed and prospectively will disclose further functionalities and interactions of keystone microbiome members [14][15][16][17][18][19][20][21].…”