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Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

The Arctic is currently warming at unprecedented rates because of global climate change, resulting in thawing of large tracts of permafrost soil. A great challenge is understanding the implications of permafrost thaw on human health and the environment. Permafrost is a reservoir of mostly uncharacterized microorganisms and viruses, many of which could be viable. Given our limited knowledge of permafrost-resident microbes, we also lack the basis to judge whether they pose risks to humans, animals, and plants. Here we delve into features of permafrost as a microbial habitat and discuss what is known about the potential for microbial pathogens to emerge in a warming climate as permafrost thaws. This review has broader implications for human health and ecosystem sustainability in the new Arctic environment that will emerge from a thawed permafrost landscape.

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

Detecting volatile organic compounds (VOCs) in exhaled breath is a promising research area for disease diagnosis. Mass transfer behavior plays a crucial role in determining the detection performance of VOCs. However, the high mobility of exhaled breath poses a substantial challenge for the mass transfer process. Here, the distinct mass transfer behavior of mobile gaseous molecules is discovered by employing the schlieren imaging technique to visualize gas flow. The results demonstrate that hollow porous structures exhibit a higher gas flow flux than solid film and microporous structures, thereby generating a sufficient probability of contact reactions for mobile gaseous molecules. The proposed colorimetric array sensors offer enhanced sensitivity and stability for detecting mobile gaseous molecules. The discovery will serve as a foundational milestone is anticipated in elucidating the behavior of gas mass transfer and promoting its potential application in disease detection through the analysis of human exhaled breath. [ABSTRACT FROM AUTHOR]

In recent years, an increasing number of observational studies have revealed an association between gut microbiota composition and psoriasis patients. However, whether this association reflects a causal relationship remains unclear. This study aimed to identify the causal relationship between gut microbiota and psoriasis through relevant research. In order to determine whether gut microbiota and psoriasis are causally related, we conducted a Mendelian randomization analysis using summary statistics from genome‐wide association studies (GWAS). As the exposure factor, we used summary statistics data from a GWAS study conducted by the MiBioGen Consortium, including 18,340 individuals with whole‐genome gut microbiota composition, and data from the FinnGen GWAS study on psoriasis, including 9267 patients and 364,071 controls as the disease outcome. Two‐sample Mendelian randomization analysis was subsequently performed with inverse variance weighted, MR‐Egger and weighted median, while sensitivity analyses were conducted to address heterogeneity and horizontal pleiotropy. The IVW results confirmed the causal relationship between certain gut microbiota groups and psoriasis. Specifically, family Veillonellaceae (OR = 1.162, 95% CI: 1.038–1.301, p = 0.009), genus Candidatus Soleaferrea (OR = 1.123, 95% CI: 1.011–1.247, p = 0.030) and genus Eubacterium fissicatena group (OR = 0.831, 95% CI: 0.755–0.915, p = 0.00016) showed significant associations. Sensitivity analysis did not reveal any abnormalities in SNPs. Currently, we have found some causal relationship between the gut microbiota and psoriasis. However, the study needs further RCTs for further validation. [ABSTRACT FROM AUTHOR]

Background: Post-stroke depression (PSD) is one of the most common complications of stroke. Electroacupuncture (EA) is an effective traditional Chinese medicine treatment for PSD, which is widely used in clinical settings. EA has a significant therapeutic effect against PSD, but the mechanism is still unclear. This study aimed to determine whether EA ameliorates depression-like behaviors in PSD rats by regulating the adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK)-mediated mitochondrial function.Methods: Middle cerebral artery occlusion (MCAO) and chronic unpredictable mild stress (CUMS) were used to develop a PSD rat model. To elucidate the role of AMPK in EA treatment, compound C, a selective inhibitor of AMPK, was injected into the lateral ventricle of rats before EA treatment. EA treatment was performed for 14 consecutive days for 30 min per day after PSD modeling. A modified Zea-Longa five-point scale scoring system was used to determine neurologic function in MCAO rats. Behavioral tests were conducted to evaluate depression-like phenotypes in rats. Depression-like behaviors were tested by sucrose preference test (SPT), novelty suppressed feeding test (NSFT), and open-field test (OFT). The structure and morphology of the prefrontal cortex were observed by histopathological hematoxylin-eosin (HE) and Nissl staining. The mitochondrial morphology and function were analyzed by colorimetry, chemiluminescence, Western blotting, and quantitative real-time polymerase chain reaction (qRT-PCR).Results: EA treatment successfully ameliorated depression-like behaviors, upregulated AMPK expression, and improved mitochondrial function. However, AMPK inhibition by Compound C exacerbated depression-like behaviors and aggravated neuronal and mitochondrial injury in PSD rats.Conclusion: EA treatment improved depression-like behaviors in PSD rats and promoted mitochondrial function by activating AMPK. [ABSTRACT FROM AUTHOR]

The coronavirus disease (COVID-19) pandemic has led to a surge in rural tourism, catering to consumers during the pandemic. However, rural tourism faces severe issues of homogeneity and environmental degradation owing to excessive development. Sustainable development of rural tourism is an urgent problem. This study, based on the average variable cost (AVC) theory, aims to explore the sustainable development of rural tourism landscapes with a focus on the Shijing area. A landscape evaluation system was established through factor analysis and weight calculations, with ten principal components contributing to a cumulative contribution rate of 77.196%. The weighted values for attractiveness, vitality, and resilience were 0.539, 0.297, and 0.164, respectively. The findings indicate that Caijiapo Village had the highest comprehensive score of 88.79 (good level of performance), whereas Laoyukou Village had the lowest comprehensive score of 80.25 (average level of performance). Caijiapo and Liyukou exhibited the strongest overall strength, whereas Liyuanpo and Xiazhuang had moderate overall strength, and Laoyukou had the weakest overall strength. The results reveal that all five villages possess rich natural landscapes and favorable geographical conditions, demonstrating the potential and attractiveness of rural tourism development. However, the overall carrying capacity was moderate and vitality was relatively weak. This supports the AVC theory application in rural tourism research and emphasizes the importance of rural landscape quality and economic vitality. The main contributions of this study are as follows: (1) the establishment of a rural tourism landscape evaluation system based on the AVC theory, providing a scientific assessment method for sustainable development; (2) the case evaluation in the Shiying area provides decision-makers with reference for development strategies; (3) emphasis on the importance of ecological conservation in rural tourism and providing recommendations to address issues of homogenization and environmental degradation. [ABSTRACT FROM AUTHOR]