Potential interactions between syntrophic bacteria and methanogens via type IV pili and quorum-sensing systems

Yin, Qidong; Gu, Mengqi; Hermanowicz, Slawomir W.; Hu, Hong-Ying; Wu, Guangxue

doi:10.1016/j.envint.2020.105650

Cited by 48 publications

(12 citation statements)

References 61 publications

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“…All of these MAGs were novel to at least the species level and include representatives of new genera from each of the four phyla. Genomes from Muirbacteria, Wallbacteria and Riflebacteria phyla were mostly derived from industrial(Yin et al 2018, 2020; Cheng et al 2019; Ma et al 2021) or environmental communities. Recovered Fusobacteria were associated with non-human eukaryotic hosts including insects(Laviad-Shitrit et al 2020), birds(Cao et al 2020), monkeys(Rhoades et al 2021), and fish(Le Doujet et al 2019; Riiser et al 2020; Collins et al 2021; Pratte et al 2022).…”

Section: Resultsmentioning

confidence: 99%

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

Woodcroft,

Aroney,

Zhao

et al. 2024

Preprint

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Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem in microbial ecology. To address the limitations of existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities of known microbial species, and is the only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency, we applied it to 248,559 publicly available metagenomes and show that the vast majority of samples from marine, freshwater, sediment and soil environments are dominated by novel species lacking genomic representation (median relative abundance 75.0%). SingleM also provides a way to identify metagenomes for the recovery of novel metagenome-assembled genomes from lineages of interest, and can incorporate user-recovered genomes into its reference database to improve profiling resolution. Quantifying the full diversity of Bacteria and Archaea in metagenomic data shows that microbial genome databases are far from saturated.

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Section: Resultsmentioning

confidence: 99%

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

Woodcroft,

Aroney,

Zhao

et al. 2024

Preprint

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“…Through microbial nanowires, electrons generated by the intracellular metabolism of microorganisms could be transported over long distances to the extracellular receptors, altering the recognition of electron transfer as being restricted to the intracellular compartment [38,39]. Conductive pili-mediated DIET had been broadly reported in wastewater treatment, bioremediation, and methanogenesis [40][41][42]. Li et al revealed that Pseudomonas and Sporanaerobacter, which were enriched in pilA, were capable of DIET-based syntrophic metabolism by the utilization of In this paper, we introduced the evolution of DIET and sorted out the application of biochar to facilitate DIET for alleviating antibiotic inhibition and enhancing methanogenesis over the years.…”

Section: The Evolution Of the Dietmentioning

confidence: 99%

“…Li et al revealed that Pseudomonas and Sporanaerobacter, which were enriched in pilA, were capable of DIET-based syntrophic metabolism by the utilization of complex organic compounds as electron donors directly [40]. Yin et al reported a remarkably high abundance of pilA in the syntrophic coculture of Geobacter, Methanosaeta, and Methanosarcina, implying the potential involvement of conductive pili-mediated DIET in methane production [41].…”

Section: The Evolution Of the Dietmentioning

confidence: 99%

“…DIET-associated genes of microorganisms might notably be upregulated in AD amended with biochar, which was commonly provided as proof to demonstrate the occurrence of DIET among syntrophic methanogenesis [37,58]. Yin et al found that conductive material facilitated the improvement of diffusible signal factor (DSF) and 3 -5 cyclic guanosine monophosphate (c-di-GMP)-associated gene abundance in microorganisms, and the signal molecule encoded by these genes probably co-regulated the biosynthesis of type IV pili, which affected the syntrophic metabolism for methanogenesis [41] (Figure 3). Li et al found that the abundance of gene pilA, encoding type IV pili, was significantly improved 3.75 times over 20 days in AD amended with biochar, which suggested that the DIET process between syntrophic microbes was probably conducted through type IV pili [110].…”

Section: Regulated Diet-associated Gene Expressionmentioning

confidence: 99%

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Biochar Facilitated Direct Interspecies Electron Transfer in Anaerobic Digestion to Alleviate Antibiotics Inhibition and Enhance Methanogenesis: A Review

Zhang

Deng

Liu

et al. 2023

IJERPH

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Efficient conversion of organic waste into low-carbon biofuels such as methane through anaerobic digestion (AD) is a promising technology to alleviate energy shortages. However, issues such as inefficient methane production and poor system stability remain for AD technology. Biochar-facilitated direct interspecies electron transfer (DIET) has recently been recognized as an important strategy to improve AD performance. Nonetheless, the underlying mechanisms of biochar-facilitated DIET are still largely unknown. For this reason, this review evaluated the role of biochar-facilitated DIET mechanism in enhancing AD performance. First, the evolution of DIET was introduced. Then, applications of biochar-facilitated DIET for alleviating antibiotic inhibition and enhancing methanogenesis were summarized. Next, the electrochemical mechanism of biochar-facilitated DIET including electrical conductivity, redox-active characteristics, and electron transfer system activity was discussed. It can be concluded that biochar increased the abundance of potential DIET microorganisms, facilitated microbial aggregation, and regulated DIET-associated gene expression as a microbial mechanism. Finally, we also discussed the challenges of biochar in practical application. This review elucidated the role of DIET facilitated by biochar in the AD system, which would advance our understanding of the DIET mechanism underpinning the interaction of biochar and anaerobic microorganisms. However, direct evidence for the occurrence of biochar-facilitated DIET still requires further investigation.

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“…In anaerobic digestion (AD), especially hydrogenotrophic and some mixotrophic methanogens consume H 2 that is produced during acido- and aceto-genesis, hence providing a natural hydrogen sink that facilitates anaerobic degradation of organic compounds to acetate and other volatile fatty acids (VFA; Kouzuma et al, 2015 ; Camacho and Ruggeri, 2018 ). The reduction of CO 2 to CH 4 during methanogenesis can take place either (1) via mediated interspecies electron transfer (MIET), in which methanogens use endogenous (H 2 ) or exogenous mediators (redox-active compounds such as neutral red) as electron carriers ( Park et al, 1999 ; Rotaru et al, 2014b ; Mayer et al, 2019 ), or (2) direct interspecies electron transfer (DIET), in which, e.g., members of the Methanosarcinaceae and Methanosaetaceae , establish physical cell-to-cell contact with electroactive bacteria (EAB) to directly receive electrons released by the latter during oxidation of mainly acetate ( Rotaru et al, 2014a ; Yee and Rotaru, 2020 ; Yin et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

A unified and simple medium for growing model methanogens

Ngoumelah

Sulheim²,

Heggeset³

et al. 2023

Front. Microbiol.

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Apart from their archetypic use in anaerobic digestion (AD) methanogenic archaea are targeted for a wide range of applications. Using different methanogenic archaea for one specific application requires the optimization of culture media to enable the growth of different strains under identical environmental conditions, e.g., in microbial electrochemical technologies (MET) for (bio)electromethanation. Here we present a new culture medium (BFS01) adapted from the DSM-120 medium by omitting resazurin, yeast extract, casitone, and using a low salt concentration, that was optimized for Methanosarcina barkeri, Methanobacterium formicicum, and Methanothrix soehngenii. The aim was to provide a medium for follow-up co-culture studies using specific methanogens and Geobacter spp. dominated biofilm anodes. All three methanogens showed growth and activity in the BFS01 medium. This was demonstrated by estimating the specific growth rates (μ) and doubling times (td) of each methanogen. The μ and td based on methane accumulation in the headspace showed values consistent with literature values for M. barkeri and M. soehngenii. However, μ and td based on methane accumulation in the headspace differed from literature data for M. formicicum but still allowed sufficient growth. The lowered salt concentration and the omission of chemically complex organic components in the medium may have led to the observed deviation from μ and td for M. formicicum as well as the changed morphology. 16S rRNA gene-based amplicon sequencing and whole genome nanopore sequencing further confirmed purity and species identity.

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Potential interactions between syntrophic bacteria and methanogens via type IV pili and quorum-sensing systems

Cited by 48 publications

References 61 publications

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

Biochar Facilitated Direct Interspecies Electron Transfer in Anaerobic Digestion to Alleviate Antibiotics Inhibition and Enhance Methanogenesis: A Review

A unified and simple medium for growing model methanogens

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