Contribution of Transcriptomics to Systems-Level Understanding of Methanogenic<i>Archaea</i>

Browne, Patrick; Cadillo‐Quiroz, Hinsby

doi:10.1155/2013/586369

Cited by 16 publications

(8 citation statements)

References 67 publications

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“…The lower ruminal H 2 concentration means that methanogens have to increase expression of methanogenesis genes to maintain the H 2 turnover rate. This is because enzyme concentrations as well as substrate concentrations can limit the flux through a pathway, and increasing enzyme expression partially overcomes the limitation of lower substrate concentrations Enoki et al 2011;Walker et al 2012;Browne and Cadillo-Quiroz 2013) Conversely, a high particle passage rate and high H 2 conditions would require a lower level of expression of methanogenesis pathway genes to permit the same flux.…”

Section: Discussionmentioning

confidence: 99%

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

et al. 2014

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Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH 4 mitigation at the levels of microbiota composition and transcriptional regulation.

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Section: Discussionmentioning

confidence: 99%

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

et al. 2014

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“…It is tempting to speculate that a positive relationship between CH 4 production and the abundance of genes encoding for methanogenesis enzymes or their transcripts might indicate that the rate of CH 4 formation is kinetically controlled by the activity of one or more methanogenic enzymes. Yet, cause-effect relationships were not demonstrated in the studies discussed, thus the inverse might occur and methanogens may grow and regulate the expression of genes encoding for methanogenesis enzymes depending on other limitations to producing CH 4 (Browne and Cadillo-Quiroz, 2013). Methanogenesis might be enzyme limited after feeding, when the elevation of dH 2 concentration precedes the increase in CH 4 and methanogen 16S rRNA gene copies or methanogenesis mRNA transcripts (van Lingen et al, 2017).…”

Section: The Rumen Microbiome Associated With Methane Emissionsmentioning

confidence: 94%

Review: Fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation

Beauchemin

Ungerfeld

Eckard

et al. 2020

Animal

334

241

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Meat and milk from ruminants provide an important source of protein and other nutrients for human consumption. Although ruminants have a unique advantage of being able to consume forages and graze lands not suitable for arable cropping, 2% to 12% of the gross energy consumed is converted to enteric CH4 during ruminal digestion, which contributes approximately 6% of global anthropogenic greenhouse gas emissions. Thus, ruminant producers need to find cost-effective ways to reduce emissions while meeting consumer demand for food. This paper provides a critical review of the substantial amount of ruminant CH4-related research published in past decades, highlighting hydrogen flow in the rumen, the microbiome associated with methanogenesis, current and future prospects for CH4 mitigation and insights into future challenges for science, governments, farmers and associated industries. Methane emission intensity, measured as emissions per unit of meat and milk, has continuously declined over the past decades due to improvements in production efficiency and animal performance, and this trend is expected to continue. However, continued decline in emission intensity will likely be insufficient to offset the rising emissions from increasing demand for animal protein. Thus, decreases in both emission intensity (g CH4/animal product) and absolute emissions (g CH4/day) are needed if the ruminant industries continue to grow. Providing producers with cost-effective options for decreasing CH4 emissions is therefore imperative, yet few cost-effective approaches are currently available. Future abatement may be achieved through animal genetics, vaccine development, early life programming, diet formulation, use of alternative hydrogen sinks, chemical inhibitors and fermentation modifiers. Individually, these strategies are expected to have moderate effects (<20% decrease), with the exception of the experimental inhibitor 3-nitrooxypropanol for which decreases in CH4 have consistently been greater (20% to 40% decrease). Therefore, it will be necessary to combine strategies to attain the sizable reduction in CH4 needed, but further research is required to determine whether combining anti-methanogenic strategies will have consistent additive effects. It is also not clear whether a decrease in CH4 production leads to consistent improved animal performance, information that will be necessary for adoption by producers. Major constraints for decreasing global enteric CH4 emissions from ruminants are continued expansion of the industry, the cost of mitigation, the difficulty of applying mitigation strategies to grazing ruminants, the inconsistent effects on animal performance and the paucity of information on animal health, reproduction, product quality, cost-benefit, safety and consumer acceptance.

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“…Such approaches contribute to obtaining more detailed molecular profiles as well as to achieve greater insights into interspecies interactions. Data obtained from syntrophic co-culture systems showed drastic changes in the gene expression profiles in both syntrophic bacterial [29, 30] and methanogenic archaeal populations [31], and the key genes for a syntrophic cooperative lifestyle were clarified. Transcriptome analysis was utilized in other model dual-culture systems [6, 32].…”

Section: Two-species Co-culture - the Simplest Communitiesmentioning

confidence: 99%

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

Haruta

Yamamoto

2018

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A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

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Contribution of Transcriptomics to Systems-Level Understanding of MethanogenicArchaea

Cited by 16 publications

References 67 publications

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Review: Fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

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