Animal manure application as organic fertilizer does not only sustain agricultural productivity and increase soil organic carbon (SOC) stocks, but also affects soil nitrogen cycling and nitrous oxide (N O) emissions. However, given that the sign and magnitude of manure effects on soil N O emissions is uncertain, the net climatic impact of manure application in arable land is unknown. Here, we performed a global meta-analysis using field experimental data published in peer-reviewed journals prior to December 2015. In this meta-analysis, we quantified the responses of N O emissions to manure application relative to synthetic N fertilizer application from individual studies and analyzed manure characteristics, experimental duration, climate, and soil properties as explanatory factors. Manure application significantly increased N O emissions by an average 32.7% (95% confidence interval: 5.1-58.2%) compared to application of synthetic N fertilizer alone. The significant stimulation of N O emissions occurred following cattle and poultry manure applications, subsurface manure application, and raw manure application. Furthermore, the significant stimulatory effects on N O emissions were also observed for warm temperate climate, acid soils (pH < 6.5), and soil texture classes of sandy loam and clay loam. Average direct N O emission factors (EFs) of 1.87% and 0.24% were estimated for upland soils and rice paddy soils receiving manure application, respectively. Although manure application increased SOC stocks, our study suggested that the benefit of increasing SOC stocks as GHG sinks could be largely offset by stimulation of soil N O emissions and aggravated by CH emissions if, particularly for rice paddy soils, the stimulation of CH emissions by manure application was taken into account.
Background: Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. Results: Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. Conclusions: The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus. The first outbreak of PDCoV was announced from the United States in 2014, followed by reports in Asia. The nonstructural protein nsp5 is a 3C-like protease of coronavirus, and our previous study showed that PDCoV nsp5 inhibits type I interferon (IFN) production. In this study, we found that PDCoV nsp5 significantly inhibited IFN-stimulated response element (ISRE) promoter activity and transcription of IFN-stimulated genes (ISGs), suggesting that PDCoV nsp5 also suppresses IFN signaling. Detailed analysis showed that nsp5 cleaved signal transducer and activator of transcription 2 (STAT2) but not Janus kinase 1 (JAK1), tyrosine kinase 2 (TYK2), STAT1, and interferon regulatory factor 9 (IRF9), key molecules of the JAK-STAT pathway. STAT2 cleavage was dependent on the protease activity of nsp5. Interestingly, nsp5 cleaved STAT2 at two sites, glutamine 685 (Q685) and Q758, and similar cleavage was observed in PDCoV-infected cells. As expected, cleaved STAT2 impaired the ability to induce ISGs, demonstrating that STAT2 cleavage is an important mechanism utilized by PDCoV nsp5 to antagonize IFN signaling. We also discussed the substrate selection and binding mode of PDCoV nsp5 by homologous modeling of PDCoV nsp5 with the two cleaved peptide substrates. The results of our study demonstrate that PDCoV nsp5 antagonizes type I IFN signaling by cleaving STAT2 and provides structural insights for comprehending the cleavage mechanism of PDCoV nsp5, revealing a potential new function for PDCoV nsp5 in type I IFN signaling.IMPORTANCE The 3C-like protease encoded by nsp5 is a major protease of coronaviruses; thus, it is an attractive target for development of anticoronavirus drugs. Previous studies have revealed that the 3C-like protease of coronaviruses, including PDCoV and porcine epidemic diarrhea virus (PEDV), antagonizes type I IFN production by targeting the NF-B essential modulator (NEMO). Here, for the first time, we demonstrate that overexpression of PDCoV nsp5 also antagonizes IFN signaling by cleaving STAT2, an essential component of transcription factor complex ISGF3, and that PDCoV infection reduces the levels of STAT2, which may affect the innate immune response.KEYWORDS immune suppression, interferon signaling, porcine deltacoronavirus, STAT2, nonstructural protein 5 (nsp5) P orcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus (CoV) that causes acute diarrhea, vomiting, and mortality in piglets (1-4). PDCoV was first found from pig feces in Hong Kong during molecular surveillance of CoVs in avian and mammalian species in 2012 (5). The first outbreak of PDCoV was announced in the United States in 2014 (6). To date, it has been detected in at least 20
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