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The ISME Journal Jan 2024Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing... (Review)
Review
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
Topics: Methane; Oxidation-Reduction; Aerobiosis; Metabolic Networks and Pathways; Models, Biological
PubMed: 38861460
DOI: 10.1093/ismejo/wrae102 -
Heliyon Nov 2023Combined application of biochar and nitrogen (N) fertilizer could offer opportunities to increase rice yield and reduce methane emissions from paddy fields. However,... (Review)
Review
Combined application of biochar and nitrogen (N) fertilizer could offer opportunities to increase rice yield and reduce methane emissions from paddy fields. However, this strategy may increase nitrous oxide (NO) emissions, hence its interactive effects on GHG emissions, global warming potential (GWP) and GHG intensity (GHGI) remained poorly understood. We conducted a systematic review to i) evaluate the overall effects of combined application of biochar and N fertilizer rates on GHGs emissions, GWP, rice yield, and GHGI, ii) determine the quantities of biochar and N-fertilizer application that increase rice yield and reduce GHGs emissions and GHGI, and iii) examine the effects of biochar and different types of nitrogen fertilizers on rice yield, GHGs, GWP, and GHGI using data from 45 research articles and 183 paired observations. The extracted data were grouped based on biochar and N rates used by researchers as well as N fertiliser types. Accordingly, biochar rates were grouped into low (≤9 tons/ha), medium (>9 and ≤ 20 ton/ha) and high (>20 tons/ha), while N rates were grouped into three categories: low (≤140 kg N/ha), medium (>140 and ≤ 240 kg N/ha), and high (>240 kg N/ha). For fertiliser types, N rates were grouped as: low (≤150 kg N/ha), medium (>150 and ≤250 kg N/ha), and high (>250 kg N/ha) and N types into: urea, NPK, NPK plus urea (NPK_urea) and NPK plus (NH)SO (NPK_(NH)SO). Results showed that biochar and N fertiliser significantly affected GHGs emissions, GWP, GHGI and rice yield. Compared to control (i.e., sole N application), co-application of high biochar and medium N rates significantly decreased CH emission (82 %) while low biochar with low N rates enhanced CH emission (114 %). In contrast, high biochar combined with low N decreased NO emission by 91 % whereas medium biochar and high N rates resulted in 82 % increase in NO emission relative to control. The highest GWP and GHGI were observed under co-application of medium biochar and low N rates. Highest rice yield was observed under low biochar rate and high N rate. Regardless of N fertiliser type and biochar rates, increasing N rates increased rice yield and NO emissions. The highest GWP and GHGI were recorded under sole NPK application. Combination of low biochar and medium N produced low GHGs emissions, high grain yield, and the lowest GHGI, and could be recommended to smallholder farmers to increase rice yield and reduce greenhouse gas emissions from paddy rice field. Further studies should be conducted to evaluate the effects of biochar properties on soil characteristics and greenhouse gas emissions.
PubMed: 38045115
DOI: 10.1016/j.heliyon.2023.e22132 -
Journal of Dairy Science Jan 2024To investigate the effects of supplemental monensin administration on the metabolic responses of dairy cows, a systematic review and dose-response meta-analysis were... (Meta-Analysis)
Meta-Analysis
Effects of monensin supplementation on rumen fermentation, methane emissions, nitrogen balance, and metabolic responses of dairy cows: A systematic review and dose-response meta-analysis.
To investigate the effects of supplemental monensin administration on the metabolic responses of dairy cows, a systematic review and dose-response meta-analysis were conducted. Initially, 604 studies were identified through comprehensive database searches, including Google Scholar, Scopus, Science Direct, and PubMed, using key words related to dairy cows, monensin, and metabolic outcomes. After a 2-stage screening process, 51 articles with a total of 60 experiments were selected for meta-analysis based on criteria such as study implementation date between 2001 and 2022, presence of a control group that did not receive monensin supplementation, reporting of at least 1 outcome variable, and presentation of means and corresponding errors. The meta-analysis used the 1-stage random-effects method, and sensitivity analyses were performed to assess the robustness of the results. The results showed that the administration of monensin at a dosage of 19 to 26 mg/kg was inversely related to methane emissions and that the administration of monensin at a dosage of 18 to 50 mg/kg resulted in a significant decrease in dry matter intake. Administration of monensin at doses of 13 to 28 and 15 to 24 mg/kg also resulted in a significant decrease in ruminal acetate proportion and an increase in propionate proportion, respectively, with no effects on ruminal butyrate, NH, or pH levels. We found no effects on blood parameters or nitrogen retention, but a significant negative correlation was observed between monensin supplementation and fecal nitrogen excretion. Based on the analysis of all variables evaluated, the optimal dose range of monensin was estimated to be 19 to 24 mg/kg.
Topics: Female; Cattle; Animals; Monensin; Milk; Fermentation; Methane; Rumen; Nitrogen; Dietary Supplements; Diet; Lactation
PubMed: 37709041
DOI: 10.3168/jds.2023-23441 -
Journal of Dairy Science Jun 2024This research introduces a systematic framework for calculating sample size in studies focusing on enteric methane (CH, g/kg of DMI) yield reduction in dairy cows....
This research introduces a systematic framework for calculating sample size in studies focusing on enteric methane (CH, g/kg of DMI) yield reduction in dairy cows. Adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search across the Web of Science, Scopus, and PubMed Central databases for studies published from 2012 to 2023. The inclusion criteria were: studies reporting CH yield and its variability in dairy cows, employing specific experimental designs (Latin Square Design (LSD), Crossover Design, Randomized Complete Block Design (RCBD), and Repeated Measures Design) and measurement methods (Open-circuit respirometry chambers (RC), the GreenFeed system, and the sulfur hexafluoride tracer technique), conducted in Canada, the United States and Europe. A total of 150 studies, which included 177 reports, met our criteria and were included in the database. Our methodology for using the database for sample size calculations began by defining 6 CH yield reduction levels (5, 10, 15, 20, 30, and 50%). Utilizing an adjusted Cohen's f formula and a power analysis we calculated the sample sizes required for these reductions in balanced LSD and RCBD reports from studies involving 3 or 4 treatments. The results indicate that within-subject studies (i.e., LSD) require smaller sample sizes to detect CH yield reductions compared with between-subject studies (i.e., RCBD). Although experiments using RC typically require fewer individuals due to their higher accuracy, our results demonstrate that this expected advantage is not evident in reports from RCBD studies with 4 treatments. A key innovation of this research is the development of a web-based tool that simplifies the process of sample size calculation (samplesizecalculator.ucdavis.edu). Developed using Python, this tool leverages the extensive database to provide tailored sample size recommendations for specific experimental scenarios. It ensures that experiments are adequately powered to detect meaningful differences in CH emissions, thereby contributing to the scientific rigor of studies in this critical area of environmental and agricultural research. With its user-friendly interface and robust backend calculations, this tool represents a significant advancement in the methodology for planning and executing CH emission studies in dairy cows, aligning with global efforts toward sustainable agricultural practices and environmental conservation.
PubMed: 38876218
DOI: 10.3168/jds.2023-24529 -
Journal of Environmental Management Dec 2023Anaerobic digestion (AD) as a waste management strategy for the organic fraction of municipal waste (OFMSW) has received attention in developed countries for several...
Anaerobic digestion (AD) as a waste management strategy for the organic fraction of municipal waste (OFMSW) has received attention in developed countries for several decades, leading to the development of large-scale plants. In contrast, AD of OFMSW has only recently drawn attention in developing countries. This systematic review was carried out to investigate the implementation of AD to treat the OFMSW in developing countries, focusing on assessing pilot and full-scale AD plants reported in the last ten years. Studies that met the selection criteria were analyzed and data regarding operating parameters, feedstock characteristics, and biogas, digestate, and energy production were extracted. As outlined in this systematic review, AD plants located in developing countries are mostly one-stage mesophilic systems that treat OFMSW via mono-digestion, almost exclusively with the aim of producing electrical energy. Based on the analysis done throughout this systematic review, it was noted that there is a large difference in the maturity level of AD systems between developing and developed countries, mainly due to the economic capacity of developed countries to invest in sustainable waste management systems. However, the number of AD plants reported in scientific papers is significantly lower than the number of installed AD systems. Research articles regarding large-scale implementation of AD to treat OFMSW in developed countries were analyzed and compared with developing countries. This comparison identified practices used in plants in developed countries that could be utilized in the large-scale implementation and success of AD in developing countries. These practices include exploiting potential products with high market-values, forming partnerships with local industries to use industrial wastes as co-substrates, and exploring different biological and physical pretreatment technologies. Additionally, the analysis of capital and operational costs of AD plants showed that costs tend to be higher for developing countries due to their need to import of materials and equipment from developed countries. Technical, economical, and political challenges for the implementation of AD at a large-scale in developing countries are highlighted.
Topics: Solid Waste; Refuse Disposal; Anaerobiosis; Developing Countries; Bioreactors; Biofuels; Methane
PubMed: 37751665
DOI: 10.1016/j.jenvman.2023.118993 -
Journal of Dairy Science Jan 2024A systematic literature review of in vitro studies was performed to identify methane (CH) mitigation interventions with a potential to reduce CH emission in vivo. Data... (Meta-Analysis)
Meta-Analysis
A systematic literature review of in vitro studies was performed to identify methane (CH) mitigation interventions with a potential to reduce CH emission in vivo. Data from 277 peer-reviewed studies published between 1979 and 2018 were reviewed. Individual CH mitigation interventions were classified into 14 categories of feed additives based on their type, chemical composition, and mode of action. Response variables evaluated were absolute CH emission (number of treatment means comparisons = 1,325); total volatile fatty acids (n = 1,007), acetate (n = 783), propionate (n = 792), and butyrate (n = 776) concentrations; acetate to propionate ratio (n = 675); digestibility of dry matter (n = 489), organic matter (n = 277), and neutral detergent fiber (n = 177). Total gas production was used as an explanatory variable in the model for CH production. Relative mean difference between treatment and control means reported in the studies was calculated and used for statistical analysis. The robust variance estimation method was used to analyze the effects of CH mitigation interventions. In vitro CH production was decreased by antibodies (-38.9%), chemical inhibitors (-29.2%), electron sinks (-18.9%), essential oils (-18.2%), plant extracts (-14.5%), plant inclusion (-11.7%), saponins (-14.8%), and tannins (-14.5%). Overall effects of direct-fed microbials, enzymes, macroalgae, and organic acids supplementation did not affect CH production in the current meta-analysis. When considering the effects of individual mitigation interventions containing a minimum number of 4 degrees of freedom within feed additives categories, Enterococcus spp. (i.e., direct-fed microbial), nitrophenol (i.e., electron sink), and Leucaena spp. (i.e., tannins) decreased CH production by 20.3%, 27.1%, and 23.5%, respectively, without extensively, or only slightly, affecting ruminal fermentation and digestibility of nutrients. It should be noted, however, that although the total number of publications (n = 277) and treatment means comparisons (n = 1,325 for CH production) in the current analysis were high, data for most mitigation interventions were obtained from less than 5 observations (e.g., maximum number of observations was 4, 7, and 22 for nitrophenol, Enterococcus spp., and Leucaena spp., respectively), because of limited data available in the literature. These should be further evaluated in vitro and in vivo to determine their true potential to decrease enteric CH production, yield, and intensity. Some mitigation interventions (e.g., magnesium, Heracleum spp., nitroglycerin, β-cyclodextrin, Leptospermum pattersoni, Fructulus Ligustri, Salix caprea, and Sesbania grandiflora) decreased in vitro CH production by over 50% but did not have enough observations in the database. These should be more extensively investigated in vitro, and the dose effect must be considered before adoption of mitigation interventions in vivo.
Topics: Female; Animals; Diet; Milk; Lactation; Propionates; Methane; Tannins; Rumen; Acetates; Nitrophenols; Fermentation; Digestion; Animal Feed
PubMed: 38353472
DOI: 10.1016/S0022-0302(23)00819-6 -
Frontiers in Microbiology 2024Grasslands are among the most widespread environments on Earth, yet we still have poor knowledge of their microbial-mediated carbon cycling in the context of human...
Grasslands are among the most widespread environments on Earth, yet we still have poor knowledge of their microbial-mediated carbon cycling in the context of human activity and climate change. We conducted a systematic bibliometric analysis of 1,660 literature focusing on microbial-mediated grassland carbon cycling in the Scopus database from 1990 to 2022. We observed a steep increase in the number of multidisciplinary and interdisciplinary studies since the 2000s, with focus areas on the top 10 subject categories, especially in Agricultural and Biological Sciences. Additionally, the USA, Australia, Germany, the United Kingdom, China, and Austria exhibited high levels of productivity. We revealed that the eight papers have been pivotal in shaping future research in this field, and the main research topics concentrate on microbial respiration, interaction relationships, microbial biomass carbon, methane oxidation, and high-throughput sequencing. We further highlight that the new research hotspots in microbial-mediated grassland carbon cycling are mainly focused on the keywords "carbon use efficiency," "enzyme activity," "microbial community," and "high throughput sequencing." Our bibliometric analysis in the past three decades has provided insights into a multidisciplinary and evolving field of microbial-mediated grassland carbon cycling, not merely summarizing the literature but also critically identifying research hotspots and trends, the intellectual base, and interconnections within the existing body of collective knowledge and signposting the path for future research directions.
PubMed: 38741733
DOI: 10.3389/fmicb.2024.1377338