Methanogenesis on Early Stages of Life: Ancient but Not Primordial

Muñoz-Velasco, Israel; García-Ferris, Carlos; Hernández-Morales, Ricardo; Lazcano, Antonio; Peretó, Juli; Becerra, Arturo

doi:10.1007/s11084-018-9570-9

Cited by 17 publications

(11 citation statements)

References 70 publications

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“…Methane metabolic pathway genes detected in our archaeal MAGs distinguished by pathway 32, 111, 132, 133 .…”

Section: Resultsmentioning

confidence: 87%

“…Only three (Ar-2, Ar-3, and Ar-4) out of the five Methanomassiliicoccales archaea-MAGs contained a complete genetic pathway associated with monomethylamine ( mtmBC ) and dimethylamine ( mtbBC ) utilization 32, 111 . Moreover, only two Methanomassiliicoccales populations (Ar-2 and Ar-4) contained mttBC , associated with trimethylamine (TMA) utilization 32, 111 . TMA has been associated with increased cardiovascular disease, so TMA metabolism is beneficial for the host 4, 5 .…”

Section: Resultsmentioning

confidence: 99%

“…Original trees are in Supplementary Figure S1. 32,111,966 We utilized the 'anvi-run-workflow' program to run a combined bioinformatics workflow in anvi'o v.7.1 (https://anvio.org/install/) 135,137 , with a co-assembling strategy. The workflow used Snakemake to implement numerous tasks including: short-read quality filtering, assembly, gene calling, functional annotation, hidden Markov model search, metagenomic read-recruitment and binning 138 .…”

Section: Discussionmentioning

confidence: 99%

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Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Feehan

Ran

Dorman

et al. 2022

Preprint

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Background: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focussing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea detection and methanogenic functions while assessing global and host distribution of our novel archaeal metagenome assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, and MAG taxonomic assignment and functional annotation. Results: We generated 1,130 non-redundant MAGs with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in monogastric archaea which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further our understanding of microbiome development and functions.

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“…Methane metabolic pathway genes detected in our archaeal MAGs distinguished by pathway 32, 111, 132, 133 .…”

Section: Resultsmentioning

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Feehan

Ran

Dorman

et al. 2022

Preprint

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“…An exhaustive homology search was conducted for each enzyme (and for each subunit of multimeric enzymes) of the hydrogenotrophic, acetoclastic and methylotrophic methanogenesis pathways, using HMM profiles that were constructed with HMMER 92 ⁠. These profiles were used to scan the local database, following the approach of Muñoz-Velasco et al 93 . Using this strategy, we also searched the enzymes of the biosynthetic pathways of the main coenzymes involved in biological methane production and the enzymes present in the Wood-Ljungdahl pathway (homoacetogenesis).…”

Section: Methodsmentioning

confidence: 99%

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Moguel

Pérez

Alcaraz

et al. 2021

Sci Rep

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Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

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“…The distribution of methyltransferases among a current set of TACK superphylum genomes indicate methanol-MT system is unique feature of Brockarchaeota within the TACK superphylum ( Figure 1). Prior to this, methanol-utilization is currently thought to be limited to Euryarchaeota and TACK (Verstraetaearchaeota 6 , Korarchaeota 17 ) archaea and some bacteria (Firmicutes and Deltaproteobacteria) 18 .…”

Section: Utilization Of C1 Compounds and Central Carbon Metabolismmentioning

confidence: 99%

Brockarchaeota, a novel archaeal lineage capable of methylotrophy

Anda¹,

Chen²,

Dombrowski³

et al. 2020

Preprint

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Single carbon (C1) compounds such as methanol, methylamines and formaldehyde are ubiquitous in nature and they are large components of the carbon cycle. In anoxic environments C1-utilizing microbes (methylotrophs) play an important role in controlling global carbon degradation. Currently described anaerobic methylotrophs are limited to methanogenic archaea, acetogenic bacteria, and sulfate-reducing bacteria. Here, we report the first archaeal lineage outside of methanogenic taxa that are capable of anaerobic methylotrophy. Phylogenetic analyses suggest these archaea form a new phylum within the TACK superphylum, which we propose be named Brockarchaeota. A survey revealed Brockarchaeota are globally distributed in geothermal springs. Metabolic inference from 15 metagenome-assembled genomes from hot springs and deep-sea sediments indicates that Brockarchaeota are strict anaerobes. They contain a variety C1 metabolisms including the methanol and trimethylamine methyltransferases system, the ribulose bisphosphate pathway coupled with the non-oxidative pentoses phosphate pathway, and reductive glycine pathway. Brockarchaeota have an incomplete methyl-branch of the Wood-Ljungdahl pathway probably used for formaldehyde oxidation, since they lack several core genes involved in methanogenesis including methyl-CoM reductases. Brockarchaeota also appear to play an important role in the breakdown of plant-derived polysaccharides, especially cellulose, starch and xylan. Their broad distribution and their capacity to use both C1 compounds and complex polysaccharides via anaerobic metabolism suggest that the Brockarchaeota occupy previously overlooked roles in carbon cycling.

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Methanogenesis on Early Stages of Life: Ancient but Not Primordial

Cited by 17 publications

References 70 publications

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Brockarchaeota, a novel archaeal lineage capable of methylotrophy

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