Search

Canine fecal microbiota profiling provides insight into host health and disease. Standardization of methods for fecal sample storage for microbiomics is currently inconclusive, however. This study investigated the effects of homogenization, the preservative RNAlater, room temperature exposure duration, and short-term storage in the fridge prior to freezing on the canine fecal microbiota profile. Within 15 minutes after voiding, samples were left non-homogenized or homogenized and aliquoted, then kept at room temperature (20-22°C) for 0.5, 4, 8, or 24 hours. Homogenized aliquots then had RNAlater added or not. Following room temperature exposure, all aliquots were stored in the fridge (4°C) for 24 hours prior to storing in the freezer (-20°C), or stored directly in the freezer. DNA extraction, PCR amplification, then sequencing were completed on all samples. Alpha diversity (diversity, evenness, and richness), and beta diversity (community membership and structure), and relative abundances of bacterial genera were compared between treatments. Homogenization and RNAlater minimized changes in the microbial communities over time, although minor changes in relative abundances occurred. Non-homogenized samples had more inter-sample variability and greater changes in beta diversity than homogenized samples. Storage of canine fecal samples in the fridge for 24 h prior to storage in the freezer had little effect on the fecal microbiota profile. Our findings suggest that if immediate analysis of fecal samples is not possible, samples should at least be homogenized to preserve the existing microbiota profile.

Addition of sulfuric acid (H2SO4) to liquid dairy manure (slurry) reduces methane (CH4), nitrous oxide (N2O), and ammonia (NH3) emissions. There is interest in understanding how gaseous emissions respond to decreasing rates of acidification, to determine economically optimum application rates. Acidification rates were tested ranging from 0 to 2 g sulfuric acid (H2SO4) L−1 slurry in six meso-scale outdoor storage tanks, each filled with 10.6 m3 slurry and stored for 114 d. Results showed that the rate of acidification for maximum inhibition of CH4 and NH3 emissions varied markedly, whereas N2O reductions were modest. Reductions of CH4 increased with acid rate from 0 to 1.2 g L−1, with no additional response beyond >1.2 g L−1. In contrast to CH4, inhibitions of NH3 showed a linear response across all rates, although reductions were ≤ 30%. Thus, higher acidification rates would be required to achieve greater NH3 emission reductions. Our findings indicate that achieving >85% NH3 emissions reductions would require 4 × more acid than achieving >85% CH4 reductions. Decisions on optimum H2SO4 rates will depend on the need to mitigate CH4 emissions (the primary greenhouse gas emitted from stored liquid manure) or reduce NH3 emissions (which is regulated in some regions). These results will help develop guidelines related to the potential costs and benefits of reducing emissions through acidification.

Sulfometuron-methyl is a broad-spectrum herbicide, used throughout Brazil; however, its environmental impacts in biochar (BC) amended soils is not fully understood. Biochar is known to enhance soil quality but can also have undesired effects such as altering the bioavailability and behavior of herbicides. Microbial communities can degrade herbicides such as sulfometuron-methyl in soils; however, they are known to be affected by BC. Therefore, it is important to understand the tripartite interaction between these factors. This research aimed to evaluate the sorption-desorption and biodegradation of sulfometuron-methyl in Amazonian soils amended with BC, and to assess the effects of the interactions between BC and sulfometuron-methyl on soil bacterial communities. Soil samples were collected from field plots amended with BC at three doses (0, 40 and 80 t ha−1) applied ten years ago. The herbicide sorption and desorption were evaluated using a batch equilibrium method. Mineralization and biodegradation studies were conducted in microcosms incubated with 14C-sulfometuron-methyl for 80 days. Systematic soil sampling, followed by DNA extraction, quantification (qPCR) and 16S rRNA amplicon sequencing were performed. The presence of BC increased the sorption of the herbicide to the soil by 11% (BC40) and 16% (BC80) compared to unamended soil. The presence of BC also affected the degradation of 14C-sulfometuron-methyl, reducing the mineralization rate and increasing the degradation half-life times (DT50) from 36.67 days in unamended soil to 52.11 and 55.45 days in BC40 and BC80 soils, respectively. The herbicide application altered the bacterial communities, affecting abundance and richness, and changing the taxonomic diversity (i.e., some taxa were promoted and other inhibited). A tripartite interaction was found between BC, the herbicide and soil bacterial communities, suggesting that it is important to consider the environmental impact of soil applied herbicides in biochar amended soils.

Liquid manure (slurry) from livestock releases methane (CH4) that contributes significantly to global warming. Existing models for slurry CH4 production-used for mitigation and inventories-include effects of organic matter loading, temperature, and retention time but cannot predict important effects of management, or adequately capture essential temperature-driven dynamics. Here we present a new model that includes multiple methanogenic groups whose relative abundance shifts in response to changes in temperature or other environmental conditions. By default, the temperature responses of five groups correspond to those of four methanogenic species and one uncultured methanogen, although any number of groups could be defined. We argue that this simple mechanistic approach is able to describe both short- and long-term responses to temperature where other existing approaches fall short. The model is available in the open-source R package ABM (https://github.com/sashahafner/ABM) as a single flexible function that can include effects of slurry management (e.g., removal frequency and treatment methods) and changes in environmental conditions over time. Model simulations suggest that the reduction of CH4 emission by frequent emptying of slurry pits is due to washout of active methanogens. Application of the model to represent a full-scale slurry storage tank showed it can reproduce important trends, including a delayed response to temperature changes. However, the magnitude of predicted emission is uncertain, primarily as a result of sensitivity to the hydrolysis rate constant, due to a wide range in reported values. Results indicated that with additional work-particularly on the magnitude of hydrolysis rate-the model could be a tool for estimation of CH4 emissions for inventories.

Liquid manure storages are an important source of greenhouse gases (GHG) on dairy farms. Methane (CH4) and nitrous oxide (N2O) are the predominant GHGs, while ammonia (NH3) is an indirect source of N2O. Addition of acid to manure has shown promising emission reductions, however, cost of acidification may be unfeasible for farmers. Fully cleaning storages has also shown to reduce CH4, due to removal of inoculating effects of residual manure (“inoculum”) on fresh manure (FM). However, complete removal of inoculum is practically impossible on large farms, thus acidifying only the inoculum may reduce GHGs without requiring acidification of all FM. This study aimed to quantify the effect of acidified inoculum on CH4, N2O, and NH3 emissions from stored manure and quantify the changes in methanogen abundance and activity. Emissions were measured from six 10.6 m3 storages filled with 20% inoculum (1-year-old manure) and 80% FM. Inoculum was treated in three ways: untreated (control); previously acidified (1-year prior); and newly acidified with 70% H2SO4 (1.1 L m−3 manure). The CH4 and N2O emissions were continuously measured from June—November using tunable diode trace gas analyzers coupled with venturi air flow systems. The NH3 emissions were measured at 24-h intervals 3 × weekly using acid traps. The activity and abundance of methanogens were quantified by targeting the Methyl Coenzyme M Reductase A (mcrA) gene and transcript which encodes a subunit of the key enzyme that catalyzes the final step of methanogenesis. Bacterial abundance was quantified by targeting the bacterial 16S rRNA gene. Quantifications were performed using quantitative real-time PCR. CH4 emissions were reduced by 77% using newly acidified inoculum and 38% using previously acidified inoculum, compared to the control with untreated inoculum (36.1 g CH4 m−2). Significant treatment reductions in mcrA gene and transcript abundance suggest that CH4 reductions were caused by disruption of methanogen activity. NH3 and N2O emissions were reduced by 33 and 73% using acidified inoculum and 23 and 50% using previously acidified inoculum, respectively, compared to the control. Results suggest that lower acid rates and acidifying less frequently may still have good treatment effects while minimizing cost.

Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH4 emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A (mcrA) genes/transcripts, respectively. When compared with untreated slurries, acidification resulted in 69–84% reductions of cumulative CH4 emissions. The abundance, activity, and proportion of bacterial communities did not vary with manure acidification. However, the abundance and activity of methanogens (as estimated from mcrA gene and transcript copies, respectively) in acidified slurries were reduced by 6 and 20%, respectively. Up to 21% reduction in mcrA transcript/gene ratios were also detected in acidified slurries. Regardless of treatment, Methanocorpusculum predominated archaeal 16S rRNA and mcrA gene and transcript libraries. The proportion of Methanosarcina, which is the most metabolically-diverse methanogen, was the significant discriminant feature between acidified and untreated slurries. In acidified slurries, the relative proportions of Methanosarcina were ≤ 10%, whereas in untreated slurries, it represented up to 24 and 53% of the mcrA gene and transcript libraries, respectively. The low proportions of Methanosarcina in acidified slurries coincided with the reductions in CH4 emissions. The results suggest that reduction of CH4 missions achieved by acidification was due to an inhibition of the growth and activity of Methanosarcina species.

Sustainably feeding the next generation is often described as one of the most pressing "grand challenges" facing the 21st century. Generally, scholars propose addressing this problem by increasing agricultural production, investing in technology to boost yields, changing diets, or reducing food waste. In this paper, we explore whether global food production is nutritionally balanced by comparing the diet that nutritionists recommend versus global agricultural production statistics. Results show that the global agricultural system currently overproduces grains, fats, and sugars while production of fruits and vegetables and protein is not sufficient to meet the nutritional needs of the current population. Correcting this imbalance could reduce the amount of arable land used by agriculture by 51 million ha globally but would increase total land used for agriculture by 407 million ha and increase greenhouse gas emissions. For a growing population, our calculations suggest that the only way to eat a nutritionally balanced diet, save land and reduce greenhouse gas emissions is to consume and produce more fruits and vegetables as well as transition to diets higher in plant-based protein. Such a move will help protect habitats and help meet the Sustainable Development Goals.