Effect of ammonia on the active microbiome and metagenome from stable full-scale digesters

Ruiz-Sánchez, J.; Campanaro, Stefano; Guivernau, Miriam; Fernández, Belén; Prenafeta-Boldú, Francesc X.

doi:10.1016/j.biortech.2017.11.068

Cited by 62 publications

(17 citation statements)

References 47 publications

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“…Together, these results suggest syntrophic acetate oxidation (SAO) via reverse WLP was not a major acetate metabolic pathway in these cultures. Most of the genes encoding the key enzymes in the alternative acetate oxidation pathway via the pyruvate–serine–glycine cleavage system [ 9 , 13 ] were either absent in the PGs or negligibly transcribed, indicating insignificant acetate oxidation via this pathway. Genes for propionate metabolism via the methylmalonyl-CoA pathway and butanoic acid metabolism via the butyryl-CoA:acetate CoA-transferase (But) or butyrate kinase (Buk) were also negligibly transcribed (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Jia

et al. 2018

Biotechnol Biofuels

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BackgroundAlthough anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions.ResultsMetagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum-related and Ruminococcus-related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum-related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions.ConclusionsOverall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1121-0) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Jia

et al. 2018

Biotechnol Biofuels

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“…Average Nucleotide Identity (ANI) values were calculated as previously described (Campanaro et al, 2017) considering genomes deposited in the NCBI microbial database representative for all the microbial species. ANI was also calculated with the MAGs identified in previous binning projects (Campanaro et al, 2016;Jing et al, 2017;Mosbaek et al, 2016;Ruiz-Sánchez et al, 2017;Stolze et al, 2016;Treu et al, 2016b;Vanwonterghem et al, 2016). Two genomes were considered as belonging to the same species if ANI was higher than 95% and they have at least 70% of genes in (Varghese et al, 2015).…”

Section: Metagenomic Sequencing and Binning Analysismentioning

confidence: 99%

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

et al. 2018

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The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.

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“…Among the microbiota, methanogens are the most sensitive to ammonia. In addition, a study about isotopic fractionation of biogas also demonstrated that aceticlastic methanogens (AM) were prevalent in reactors operated at TAN below 3.0 g•N•L −1 while hydrogenotrophic methanogens (HM) were predominant at TAN above 6.0 g•N•L −1 [15]. The frail AM that were easily affected by TAN raises a further challenge of achieving the desired efficiency of methanogenesis via HSAD, because AM are generally responsible for as much as 70% of the methane production in an AD reactor [16].…”

Section: Introductionmentioning

confidence: 99%

Biochemical Conversion and Microbial Community in Response to Ternary pH Buffer System during Anaerobic Digestion of Swine Manure

et al. 2018

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The ternary pH buffer system with ammonia-carbonates-volatile fatty acids (VFAs) is essential to anaerobes for bioenergy recovery via anaerobic digestion (AD). However, ammonia and VFAs are recognized as potential inhibitors that depress methanogenesis. In this study, biochemical conversion and the microbial community in batch AD at total solid (TS) from 4% to 14% were investigated to reveal their response to the ternary pH buffer system. The rapid ammonia release, probably promoted by Anaerosphaera and Eubacterium inferred from the concurrent peak of their relative abundance, triggered total ammonia (TAN) inhibition with the accumulation of VFAs in the start-up stage of high solid AD (HSAD, TS ≥ 8%). Along with evolution of the microbial community to resist high TAN and VFAs, methanogenesis recovered with improved degradation of VFAs and reduction of COD. When exposed to 3500 mg·N·L−1 TAN at 8% TS, aceticlastic Methanosarcina became dominant first and then together with hydrogenotrophic Methanoculleus, achieved the optimal biochemical conversion. While in HSAD at 11–14% TS, the main pathway of methanogenesis appeared to have shifted from the aceticlastic pathway to the hydrogenotrophic pathway, as inferred by changes in the relative abundance of methanogens, and this could have been induced by the increasing concentration of high free ammonia (FAN, ≥588 mg·N·L−1). Although the anaerobes had acclimatized to high TAN, the propionate-oxidizing bacteria and acetate-oxidizing bacteria might have again been inhibited by high FAN, frustrating the H2 supply for FAN-tolerant Methanoculleus and causing an 8.2–11.3% depression of COD reduction (mainly propionate residual).

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Effect of ammonia on the active microbiome and metagenome from stable full-scale digesters

Cited by 62 publications

References 47 publications

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

Biochemical Conversion and Microbial Community in Response to Ternary pH Buffer System during Anaerobic Digestion of Swine Manure

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