New insights into the r/K selection theory achieved in methanogenic systems through continuous-flow and sequencing batch operational modes

Guo, Qiannan; Yin, Qidong; Du, Jin; Zuo, Jiane; Wu, Guangxue

doi:10.1016/j.scitotenv.2021.150732

Cited by 24 publications

(5 citation statements)

References 57 publications

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“…In contrast, studies on oil-polluted soil samples suggest a predominance of K-strategists, especially in the harsh conditions (High concentration of HC, soil dryness, etc.) commonly seen in many such soil environments [54][55][56]. Hosting multiple copies of genes coding for HC degrading enzymes seems to be a shared feature in both r-and K-strategists with small and large genome sizes alike and appears to be a universal evolutionary strategy for HC degradation.…”

Section: Ecological Strategy Of Hc Degrading Bacteriamentioning

confidence: 99%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

BMC Genomics

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Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

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Section: Ecological Strategy Of Hc Degrading Bacteriamentioning

confidence: 99%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

BMC Genomics

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show abstract

“…In contrast, reports of oil-polluted soil samples suggest a predominance of k-strategists, especially in the harsh conditions (High concentration of HC, soil dryness, etc.) commonly seen in many such soil environments [39][40][41]. Hosting multiple copies of genes coding for HC degrading enzymes seems to be a shared feature in both r-and kstrategists with small and large genome sizes alike and appears to be a universal evolutionary strategy for HC degradation.…”

Section: Resultsmentioning

confidence: 99%

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee

Amoozegar

Dastgheib³

et al. 2022

Preprint

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Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen. They mainly accumulate in oil reservoirs, but aromatic HCs can also have other sources and are widely distributed in the biosphere. Our perception of pathways for biotic degradation of major HCs and genetic information of key enzymes in these bioconversion processes have mainly been based on cultured microbes and are biased by uneven taxonomic representation. Here we use Annotree to provide a gene-centric view of aerobic degradation of aliphatic and aromatic HCs in a total of 23446 genomes from 123 bacterial and 14 archaeal phyla. Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. While genomes containing full pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota, other lineages capable of mediating such key steps could partner with representatives with truncated HC degradation pathways and collaboratively drive the process. Phylogeny reconstruction shows that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

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“…Hydrogenotrophic methanogens are suggested to grow faster than acetoclastic methanogens. 50 Besides, H 2 -utilizing methanogens might be more tolerant than the other methanogens even at pH 5.0. 51 Therefore, unlike SBR 25-A which acclimated Methanosarcina, a high concentration of acetate in SBR 10-E still fails to enrich acetoclastic methanogens due to the short SRT and low pH.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Methanogenesis was partially recovered on also day 60, suggesting the successful establishment of syntrophic cooperation between Methanobacterium and Desulfovibrio in SBR 10-E . Hydrogenotrophic methanogens are suggested to grow faster than acetoclastic methanogens . Besides, H 2 -utilizing methanogens might be more tolerant than the other methanogens even at pH 5.0 .…”

Section: Discussionmentioning

confidence: 99%

Solids Retention Times Shift Methanogenic Ethanol Oxidation: Novel Insights into Metabolic Pathways, Microbial Community Dynamics, and Energy Metabolisms

Xing

Yin

et al. 2021

ACS Sustainable Chem. Eng.

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Solids retention time (SRT) is a key parameter affecting the performance of anaerobic digestion. Nevertheless, the knowledge of how SRT impacts the anaerobic ecosystem is still insufficient. In this study, the shifts in system performance, microbial population, metabolic pathway, and energy metabolism induced by different SRTs (25 and 10 days) in anaerobic reactors with ethanol as the substrate were systematically investigated. Ethanol was oxidized to acetate and propionate, and methane was generated via mixotrophic pathways at SRT of 25 days due to the enrichment of ethanol oxidizers Geobacter and Pelobacter, propionate oxidizers Smithella, and methanogens Methanothrix. However, ethanol was metabolized to only acetate by Desulfovibrio which outcompeted other ethanol oxidizers and established interspecies H 2 transfer with H 2 -utilizing methanogen Methanobacterium at a SRT of 10 days. Under short SRT conditions, acetoclastic methanogens were eliminated, resulting in the accumulation of acetate and low CH 4 yield. Additionally, the major ATPase-gene owners were shifted from bacteria (F-type ATPase) to methanogens (V/A-type ATPase) with decreasing SRT and pH, suggesting the energy-metabolism turnover of anaerobic microbes when encountering different SRTs.

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New insights into the r/K selection theory achieved in methanogenic systems through continuous-flow and sequencing batch operational modes

Cited by 24 publications

References 57 publications

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Solids Retention Times Shift Methanogenic Ethanol Oxidation: Novel Insights into Metabolic Pathways, Microbial Community Dynamics, and Energy Metabolisms

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