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Genetic resources for methane production from biomass described with the Gene Ontology.

ABSTRACT: Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing "gold standards" for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).

SUBMITTER: Purwantini E

PROVIDER: S-EPMC4253957 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Genetic resources for methane production from biomass described with the Gene Ontology.

Purwantini Endang E Torto-Alalibo Trudy T Lomax Jane J Setubal João C JC Tyler Brett M BM Mukhopadhyay Biswarup B

Frontiers in microbiology 20141203

Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis ...[more]

PMID: 25520705

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Project description:The extent of diversity in the indigenous chicken breeds of Uganda was assessed for their potential utilisation in breeding programmes. A total of 293 indigenous-chicken-keeping households in villages across 35 districts forming 12 sub-regions of the four regions were randomly sampled for 586 mature chickens of both sexes. While only 20.8% of households were headed by women, 40.6% of indigenous chicken keepers were women. The production objectives mainly focused on chickens as sources of income from sales and household food. The chickens were predominantly managed in a scavenging (94.2%) feeding system in a mainly (96.9%) mixed crop-livestock system. The average flock size was 19.80 ± 1.21 chickens with 3.83 ± 0.29 laying hens, each producing an average of 13.41 ± 0.20 eggs/clutch and 40.3 ± 0.6 eggs/annum of 5.20 ± 0.03-month egg production age. Normal-feather strains predominated (>90%), with scattered incidences of naked neck, frizzles, polydactyl, and ptilopody traits in both sexes. Dark (49.0% hen; 43.8% cock) and white (38.3% hen; 42.4% cock) skin colours were most common among the chickens compared to yellow skin. However, yellow-coloured shanks were proportionally the most observed (41% cock; 29% hen). Orange and brown iris (eye) colours were the most common in both sexes. The hens commonly had small round earlobes with varying colours, while cocks had large oval-shaped, mainly red (70%) earlobes. The single-comb type was dominant in both sexes, with wattles almost universally present. Frizzle and polydactyl allele frequencies were significantly lower (p < 0.05) than the expected Mendelian proportions, indicating a possible state of endangerment. Meanwhile, the estimated allele frequencies of ptilopody, tufted-crest, and rose comb alleles in the population were similar (p > 0.05) to the expected Mendelian frequencies. However, these strains did not show any significant (p > 0.05) influence on the body weight or the linear morphometric estimates except for being marginally higher than the normal strains. The phenotypic correlations of body weight and morphometric traits ranged from 0.457 to 0.668 and 0.292 to 0.454 in cocks and hens, respectively. These findings provide hints about the prospects for improved performance with modifications in the production environment. The wide phenotypic diversity would support management efforts for their sustainable utilisation and preservation.

Dataset Information

Genetic resources for methane production from biomass described with the Gene Ontology.

Publications

Genetic resources for methane production from biomass described with the Gene Ontology.

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