Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
Highlights
Anaerobic digestion (AD) is a biological process where complex polymers are converted to small molecules and mineralized to methane and carbon dioxide
Among 20 short-term enrichment cultures degrading individual amino acid (AA) established in our previous study (Mei et al, 2020), 14 were further selected for metagenomic sequencing (Supplementary Table 1)
After merging bins closely clustered with each other based on phylogenomic analysis, 56 final bins were obtained. These 56 final bins showed good representativeness of the populations in the enrichment cultures as majority of the metagenomic (67.4% on average) and metatranscriptomic reads (86.2% on average) in each culture could be mapped to them (Supplementary Figure 2)
Summary
Anaerobic digestion (AD) is a biological process where complex polymers are converted to small molecules and mineralized to methane and carbon dioxide. There are still more than 20 uncultured family-level lineages in this order based on the most recent SILVA database (release 138) (Yilmaz et al, 2013), including Bacteroidetes vadinHA17, Bacteroidetes BD2-2, and Bacteroidales RF16, suggesting the metabolic diversity of this order is not fully uncovered Some of those uncharacterized Bacteroidales are likely capable of protein and amino acids degradation given their high abundances observed in anaerobic reactors treating protein-rich substrates such as bovine serum albumin (Tang et al, 2005) and casein (Ley et al, 2006). Their ecological prevalence in full-scale ADs and sediment environments was evaluated
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