In search of practical and affordable tools for wastewater-based surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three independent field experiments were conducted using three passive sampler sorbents (electronegative membrane, cotton bud, and gauze) in Guelph, Ontario, Canada. Total daily cases during this study ranged from 2 to 17/100,000 people and 43/54 traditionally collected wastewater samples were positive for SARS-CoV-2 with mean detectable concentrations ranging from 8.4 to 1780 copies/ml. Viral levels on the passive samplers were assessed after 4, 8, 24, 48, 72, and 96 hrs of deployment in the wastewater and 43/54 membrane, 42/54 gauze, and 27/54 cotton bud samples were positive. A linear accumulation rate of SARS-CoV-2 on the membranes was observed up to 48 hours, suggesting the passive sampler could adequately reflect wastewater levels for up to two days of deployment. Due the variability in accumulation observed for the cotton buds and gauzes, and the pre-processing steps required for the gauzes, we recommend membrane filters as a simple cost-effective option for wastewater-based surveillance of SARS-CoV-2.

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.

This study investigated the efficacy of a single strain of Bacillus subtilis (SSB) in modulating the composition of cecal microbiota and its link to the concentration of short-chain fatty acids (SCFA) and apparent retention (AR) of components. A total of 720, 4-week-old Shaver White chicks were allotted to control (CON), 1.1Eϩ08 (low, LSSB), 2.2Eϩ08 (medium, MSSB), or 1.1Eϩ09 (high, HSSB) CFU/kg of diet groups. At grower (10-week), developer (16-week), and laying (28-week) phases, excreta and cecal digesta samples were taken for AR, microbial, and SCFA analyses. Microbial analysis involved high-throughput sequencing of the V3-V4 hypervariable regions of 16S rRNA gene. Bacterial diversity decreased (P Ͻ 0.05) at the developer phase as the SSB dose increased; however, a distinct clustering pattern (P Ͻ 0.05) of bacterial community was noted. Bacteroides and Faecalibacterium were differentially enriched in the developer for SSB-fed compared to CON-fed birds. Although no differences in microbial diversity were detected in grower and layer phases, different species of Clostridium (XVIII, XIVa, IV, and XIVb)-major butyrate producers-were identified in all phases, with stronger effect sizes for SSB-fed compared to CON-fed birds. Isobutyric acid was elevated in dose response (P ϭ 0.034) in layer phase. In addition, the relative abundances of Alistipes, Lactobacillus, and Bifidobacterium were positively correlated (P Ͻ 0.05), with AR of most components for SSB-fed birds in the pullet phase. The results suggested that supplementing chickens' diet with B. subtilis DSM 29784 may selectively enrich beneficial bacterial communities, which in turn are critical in promoting the growth and performance of hens. IMPORTANCE In egg-laying chickens, the trend in the move away from the cage to alternative housing systems and restriction in antimicrobial use requires alternative approaches to maintain health and prevent diseases. There is increased research and commercial interest toward alternative gut health solutions while improving the performance and product safety in poultry production systems. One such approach, in recognition of the importance of the gut microbial community, is the use of microbes as feed supplements (such as probiotics). Unlike meat-type chickens, studies assessing the efficacy of such microbial supplements are limited for egg-laying chickens. Thus, by conducting a comprehensive assessment of the hen microbiota in response to various levels of B. subtilis DSM 29784 during the pullet phase (grower and developer) and the layer phase, the present study demonstrates the importance of direct-fed microbes in modulating gut microbiome, which may relate to improved performance efficiency in the pullet and layer phases.Citation Neijat M, Habtewold J, Shirley RB, Welsher A, Barton J, Thiery P, Kiarie E. 2019. Bacillus subtilis strain DSM 29784 modulates the cecal microbiome, concentration of shortchain fatty acids, and apparent retention of dietary components in Shaver White chickens during grower, developer, and laying ...

Liquid dairy manure storages are sources of methane (CH4), nitrous oxide (N2O), and ammonia (NH3) emissions. Both CH4 and N2O are greenhouse gases (GHGs), whereas NH3 is an indirect source of N2O emissions. Manure acidification is a strategy used to reduce NH3 emissions from swine manure; however, limited research has expanded this strategy to reducing CH4 and N2O emissions by acidifying dairy manure. This study compared control dairy manure (pH 7.4) with two treatments of acidified manure using 70% sulfuric acid (H2SO4). These included a medium pH treatment (pH 6.5, 1.4 mL acid L−1 manure) and a low pH treatment (pH 6, 2.4 mL acid L−1 manure). Emissions were measured using replicated mesoscale manure tanks (6.6 m2) enclosed by large steady state chambers. Both CH4 and N2O were continuously measured (June–December 2017) using tunable diode laser trace gas analyzers. Ammonia emissions were measured three times weekly for 24 h using acid traps. On a CO2 equivalent basis, the medium pH treatment reduced total GHG emissions by 85%, whereas the low pH treatment reduced emissions by 88%, relative to untreated (control) manure. Total CH4 emissions were reduced by 87 and 89% from medium and low pH tanks, respectively. Ammonia emissions were reduced by 41 and 53% from medium and low pH tanks, respectively. Additional research is necessary to make acidification an accessible option for farmers by optimizing acid dosage. More research is need to describe the manure buffering capacity and emission reductions and ultimately find the best approaches for treating farm‐scale liquid dairy manure tanks. Core Ideas Acidification reduced total CO2–eq GHGs from liquid dairy manure by 85 to 88%. Total CH4 emissions were reduced by 87 to 89% from acidified manure. NH3 emissions were reduced by 41 to 53% from acidified manure. A range of yearly H2SO4 cost was estimated to be Can$6.55 to $19.6 cow−1.

Microbial communities in residual slurry left after removal of stored liquid dairy manure have been presumed to increase methane emission during new storage, but these microbes have not been studied. While actual manure storage tanks are filled gradually, pilot- and farm-scale studies on methane emissions from such systems often use a batch approach. In this study, six pilot-scale outdoor storage tanks with (10% and 20%) and without residual slurry were filled (gradually or in batch) with fresh dairy manure, and methane and methanogenic and bacterial communities were studied during 120 days of storage. Regardless of filling type, increased residual slurry levels resulted in higher abundance of methanogens and bacteria after 65 days of storage. However, stronger correlation between methanogen abundance and methane flux was observed in gradually filled tanks. Despite some variations in the diversity of methanogens or bacteria with the presence of residual slurry, core phylotypes were not impacted. In all samples, the phylum Firmicutes predominated (∼57 to 70%) bacteria: >90% were members of Clostridia . Methanocorpusculum dominated (∼57 to 88%) archaeal phylotypes, while Methanosarcina gradually increased with storage time. During peak flux of methane, Methanosarcina was the major player in methane production. The results suggest that increased levels of residual slurry have little impact on the dominant methanogenic or bacterial phylotypes, but large population sizes of these organisms may result in increased methane flux during the initial phases of storage. IMPORTANCE Methane is the major greenhouse gas emitted from stored liquid dairy manure. Residual slurry left after removal of stored manure from tanks has been implicated in increasing methane emissions in new storages, and well-adapted microbial communities in it are the drivers of the increase. Linking methane flux to the abundance, diversity, and activity of microbial communities in stored slurries with different levels of residual slurry can help to improve the mitigation strategy. Mesoscale and lab-scale studies conducted so far on methane flux from manure storage systems used batch-filled tanks, while the actual condition in many farms involves gradual filling. Hence, this study provides important information toward determining levels of residual slurry that result in significant reduction of well-adapted microbial communities prior to storage, thereby reducing methane emissions from manure storage tanks filled under farm conditions.

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National inventories of methane (CH 4 ) emission from manure management are based on guidelines from the Intergovernmental Panel on Climate Change using countryspecific emission factors. These calculations must be simple and, consequently, the effects of management practices and environmental conditions are only crudely represented in the calculations. The intention of this review is to develop a detailed understanding necessary for developing accurate models for calculating CH 4 emission from liquid manure, with particular focus on the microbiological conversion of organic matter to CH 4 . Themes discussed are (a) the liquid manure environment; (b) methane production processes from a modeling perspective; (c) development and adaptation of methanogenic communities; (d) mass and electron conservation; (e) steps limiting CH 4 production; (f) inhibition of methanogens; (g) temperature effects on CH 4 production; and (h) limits of existing estimation approaches. We conclude that a model must include calculation of microbial response to variations in manure temperature, substrate availability and age, and management system, because these variables substantially affect CH 4 production. Methane production can be reduced by manipulating key variables through management procedures, and the effects may be taken into account by including a microbial component in the model. When developing new calculation procedures, it is important to include reasonably accurate algorithms of microbial adaptation. This review presents concepts for these calculations and ideas for how these may be carried out. A need for better quantification of hydrolysis kinetics is identified, and the importance of short-and long-term microbial adaptation is highlighted.