Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors

Abstract

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

Steering the product spectrum in high-pressure anaerobic processes: CO2 partial pressure as a novel tool in biorefinery concepts

“…as observed in this research (Additional file 1 : Fig. S1) and other anaerobic reactors [ 84 , 87 ]. These findings encourage further exploration of this presumed syntrophic relation in atmospheric and pressurized anaerobic systems.…”

“…On one side, since these microorganisms were highly abundant in the original inoculum (Fig. 5 A), they could be considered part of the core anaerobic microbiome as other close relatives in the Chloroflexi phylum [ 84 ]. On the other side, the observed fluctuations in absolute abundances throughout experiment II (Additional file 1 : Fig.…”

Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice

“…KNHs209 (species); Clostridium symbiosum (species) Lachnospiraceae family is proven to have fibrolytic specialization, and possesses a large number of cellulose degradation pathways 25 . Members of Marvinbryantia and Blautia are acetogens 29 PIB Firmicutes Ruminococcaceae (family) Angelakisella (genus) , Angelakisella massiliensis (species) ; Ruthenibacterium (genus) , Ruthenibacterium lactatiformans (species) ; Provencibacterium (genus) , Provencibacterium massiliense (species) ; Ruminococcaceae bacterium D16 [unclassified Ruminococcaceae ] Ruminococcaceae family is proven to have fibrolytic specialization, and possesses a large number of cellulose degradation pathways 25 PIB Chloroflexi Anaerolineae (class) Most of the isolated strains of Anaerolineae has the potential to degrade cellulose, carbohydrates, and/or proteins anaerobically, playing an important role as primary and secondary fermenters 30 PIB Proteobacteria Deltaproteobacteria (class); Desulfovibrionales (order); Desulfovibrionaceae (family); Desulfovibrio (genus), Desulfovibrio piger (species); Mailhella (genus), Mailhella massiliensis (genus) To remove access H 2 gas produced during the fiber metabolization, Desulfovibrio probably performs dissimilatory sulphate reduction 15 . M. massiliensis have sulfate reducing ability 31 GB Firmicutes Bacilli (class); Lactobacillales (order); Lactobacillaceae (family); Lactobacillus (genus); L. crispatus, L. taiwannesis, L.gasseri, L. johnsoniii, L. fermentum and L.reuteri (species) Rapidly grow upon soluble fiber GB Firmicutes Lachnospiraceae bacterium V9D3004 (member of unclassified Lachnospiraceae ) …”

Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles

“…As shown in previous studies (De Vrieze et al, 2016;Heyer et al, 2013;Kirkegaard et al, 2017;Repinc et al, 2018), microbial fingerprints enable monitoring of the AD process' stability, and also single features of the fingerprinting methods correlate with process parameters. For example, the phylum Chloroflexi prefers the conditions in anaerobic digesters treating sewage sludge as feedstock (Bovio-Winkler et al, 2021;Speirs et al, 2019). Several correlations could be identified between TAN, temperature, feedstock composition, and digester types with taxa and metaproteins identified in previous studies (De Vrieze et al, 2015;Heyer et al, 2016;Zhang et al, 2014).…”