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Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression. Here, we present NERD-seq, which enables detection of multiple non-coding RNAs, excluded by the standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq expands representation of frequently modified non-coding RNAs, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, and rRFs. NERD-seq represents an RNA-seq approach to simultaneously study mRNA and ncRNA epitranscriptomes in brain tissues and beyond.

National inventories of methane (CH4) emission from manure management are based on guidelines from the Intergovernmental Panel on Climate Change using country‐specific 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 CH4emission from liquid manure, with particular focus on the microbiological conversion of organic matter to CH4. 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 CH4production; (f) inhibition of methanogens; (g) temperature effects on CH4production; 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 CH4production. 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. Current CH4emission models for stored manure have limited accuracy.A microbial model component is needed to capture CH4emission dynamics.Emission responds differently to short‐ and long‐term perturbations.Temperature dynamics, organic matter flow, and biodegradability must be known.

ABSTRACTLiquid manure storages are a significant source of methane (CH4) emissions. Farmers commonly agitate (stir) liquid manure prior to field application to homogenize nutrients and solids. During agitation, manure undergoes mechanical stress and is exposed to the air, disrupting anaerobic conditions. This on-farm study aimed to better understand the effects of agitation on CH4emissions, and explore the potential for intentional agitation (three times) to disrupt the exponential increase of CH4emissions in spring and summer. Results showed that agitation substantially increased manure temperature in the study year compared to the previous year, particularly at upper- and mid-depths of the stored manure. The temporal pattern of CH4emissions was altered by reduced emissions over the subsequent week, followed by an increase during the second week. Microbial analysis indicated that the activity of archaea and methanogens increased after each agitation event, but there was little change in the populations of methanogens, archaea, and bacteria. Overall, CH4emissions were higher than any of the previous three years, likely due to warmer manure temperatures that were higher than the previous years (despite similar air temperatures). Therefore, intermittent manure agitation with the frequency, duration, and intensity used in this study is not recommended as a CH4emission mitigation practice.Implications: The potential to mitigate methane emissions from liquid manure storages by strategically timed agitation was evaluated in a detailed farm-scale study. Agitation was conducted with readily-available farm equipment, and targeted at the early summer to disrupt methanogenic communities when CH4emissions increase exponentially. Methane emissions were reduced for about one week after agitation. However, agitation led to increased manure temperature, and was associated with increased activity of methanogens. Overall, agitation was associated with similar or higher methane emissions. Therefore, agitation is not recommended as a mitigation strategy.

Stored liquid dairy manure is a hotspot for methane (CH4) emission, thus effective mitigation strategies are required. We assessed sodium persulfate (Na2S2O8), potassium permanganate (KMnO4), and sodium hypochlorite (NaOCl) for impacts on the abundance of microbial communities and CH4production in liquid dairy manure. Liquid dairy manure treated with different rates (1, 3, 6, and 9 g or mL L−1slurry) of these chemicals or their combinations were incubated under anoxic conditions at 22.5 ± 1.3°C for 120 d. Untreated and sodium 2‐bromoethanesulfonate (BES)‐treated manures were included as negative and positive controls, respectively, whereas sulfuric acid (H2SO4)‐treated manure was used as a reference. Quantitative real‐time polymerase chain reaction was used to quantify the abundances of bacteria and methanogens on Days 0, 60, and 120. Headspace CH4/CO2ratios were used as a proxy to determine CH4production. Unlike bacterial abundance, methanogen abundance and CH4/CO2ratios varied with treatments. Addition of 1 to 9 g L−1slurry of Na2S2O8and KMnO4reduced methanogen abundance (up to ∼28%) and peak CH4/CO2ratios (up to 92‐fold). Except at the lowest rate, chemical combinations also reduced the abundance of methanogens (up to ∼17%) and CH4/CO2ratios (up to ninefold), although no impacts were observed when 3% NaOCl was used alone. With slurry acidification, the ratios reduced up to twofold, whereas methanogen abundance was unaffected. Results suggest that Na2S2O8and KMnO4may offer alternative options to reduce CH4emission from stored liquid dairy manure, but this warrants further assessment at larger scales for environmental impacts and characteristics of the treated manure. Chemical oxidants were assessed for potential effects on methanogens and methane production.The abundance of methanogens and CH4production were affected by Na2S2O8and KMnO4.Na2S2O8and KMnO4had similar effects on CH4production compared with acidification.Na2S2O8and KMnO4may provide options to mitigate CH4emissions from stored liquid dairy manure.