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Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.

Wildfire plays an important role in restructuring bacterial and protist taxonomic and functional communities in forest ecosystems. Yet, the recovery of bacterial and protist communities following wildfire has not been rigorously investigated across long-term wildfire chronosequences. We compared changes in bacterial and protist alpha diversity, community composition, co-occurrence networks and determinant edaphic factors between burnt and unburnt (reference) soils at 11 different sites representing a 76-year wildfire chronosequence in Canadian boreal forests. The fire increased bacterial and protist alpha diversity and altered community composition (beta diversity) as compared to the site-specific controls during the early recovery stage (30 years) recovery stages. Bacterial and protist communities showed similar patterns of change across the wildfire chronosequence. The post-fire recovery of bacterial communities was associated with changes in soil chemical properties (e.g., nutrient status and pH) and vegetation succession. The protist community assembly was co-influenced by changes in bacterial communities and vegetation succession/soil properties. The concurrent recovery of bacterial and protist communities, and their influencing factors of vegetation and soil properties, imply the above- and belowground living communities are strongly linked in wildfire-perturbed forest ecosystems.

Although pyrogenic organic matter (PyOM) generated during wildfires plays a critical role in post-fire ecosystem recovery, the specific mechanisms by which PyOM controls soil microbial community assembly after wildfire perturbation remain largely uncharacterized. Herein we characterized the effect of PyOM on soil bacterial communities at two independent wildfire-perturbed forest sites. We observed that α-diversity of bacterial communities was the highest in wildfire-perturbed soils and that bacterial communities gradually changed along a sequence of unburnt soil → burnt soil → PyOM. The microbial communities reconstructed from unburnt soil and PyOM resembled the real bacterial communities in wildfire-perturbed soils in their α-diversity and community structure. Bacterial specialists in PyOM and soils clustered in phylogenetic coherent lineages with intra-lineage pH-niche conservatism and inter-lineage pH-niche divergence. Our results suggest that PyOM mediates bacterial community assembly in wildfire-perturbed soils by a combination of environmental selection and dispersal of phylogenetic coherent specialists with habitat preference in the heterogeneous microhabitats of burnt soils with distinct PyOM patches.

Abstract: Background: Co-occurrence pattern provides vital insight into complex microbial interactions of microbiomes. Although network analysis offers useful tools for describing microbial co-occurrence pattern, evolution of co-occurrence networks remains largely uncharacterized. Here, we simulated the evolution of the Earth microbial co-occurrence network and estimated topological fitness of its nodes based on the degree growth exponent.Results: We showed that the Earth microbial co-occurrence network evolved following Bianconi-Barabasi model. The Earth microbial co-occurrence network had reached to a stable status with around 500 nodes. Degree growth exponent was the major determinant of accumulated degree of taxa. The positive correlation between topological fitness and gene numbers in corresponding genomes suggests the intrinsic feature of topological fitness. The gamma distribution of topological fitness suggests the extinction of taxa with low topological fitness. We then examined the impact of node extinction and decay, finding that the link acquisition of hub nodes was not affected.Conclusions: This study glimpses the evolution feature of Earth microbial co-occurrence network and provides a framework for predicting potential hubs in the evolving network in future.

Networks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assembly. However, microbial ecological networks are in their infancy of both network inference and biological interpretation. In this perspective, we articulate the theory gaps and limitations in building and interpreting microbial ecological networks, emphasize developing tools for evaluating the predicted microbial interaction relationships, and predict the potential applications of microbial ecological networks in the long run.

Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within specific functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, reflecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial community functions.

BACKGROUND: Kidney Renal Clear Cell Carcinoma (KIRC) is a malignant tumor that seriously threatens human health. Rho GTPase-activating protein 4 (ARHGAP4) plays an important role in the occurrence and development of tumors. OBJECTIVE: The purpose of this study was to explore the role of ARHGAP4 in the progression of KIRC and its diagnostic and prognostic value. METHODS: Multiple analytical methods and in vitro cell assays were used to explore the expression of ARHGAP4 and its value in the progression, diagnosis and prognosis of KIRC. The biological function of ARHGAP4 was studied by GO analysis and KEGG pathway analysis, and then the relationship between ARHGAP4 and immune infiltration was analyzed. RESULTS: The expression of ARHGAP4 was significantly up-regulated in KIRC. We found that the high expression of ARHGAP4 was related to the progression of KIRC and suggested a poor prognosis. Compared with normal tissues, ARHGAP4 had a better diagnostic value in KIRC. The biological function of ARHGAP4 was related to immunity, and its expression was also closely related to tumor immune infiltration and immune checkpoints. CONCLUSIONS: Our study demonstrated that ARHGAP4 may be a biomarker, which is related to the progression, diagnosis and prognosis of KIRC. Its biological functions are related to tumor immune infiltration. [ABSTRACT FROM AUTHOR]

Background: Evidence for prevention strategies of radiotherapy (RT)‐related injury in patients with nasopharyngeal carcinoma (NPC) was lacking. Understanding the dynamic alterations in the cerebral white matter (WM) microstructure after RT may be helpful. Purpose: To investigate the dynamic alterations in the whole brain WM microstructure in patients with NPC in the 12 months after RT using multishell diffusion MRI (MS‐dMRI). Study Type: Single‐center longitudinal study. Population: A total of 28 treatment‐naïve patients with pathologically confirmed NPC (age: 39.68 ± 8.93 years, 11 female) and 20 healthy controls (age: 40.65 ± 9.76 years, 7 female). Field Strength/Sequences: A 3 T, MS‐dMRI using a single‐shot echo planar imaging sequence. Assessment: MS‐dMRI was acquired at baseline for the NPC patients and healthy controls, at 0–3 (acute, AC), 6 (early delayed, ED) and 12 months (late delayed, LD) after RT for the NPC patients. The mean and maximum radiation doses to the temporal lobe were acquired. The quality of images was reviewed. MS‐dMRI was analyzed using tract‐based spatial statistics (TBSS). The presentations of injury were defined by the findings of TBSS. Statistical Tests: Chi‐square, t tests, repeated ANOVA, and Spearman‐rank correlation analysis were used. P < 0.05 was considered to be statistically significant. Results: TBSS showed two WM injuries (injuries 1 and 2). Injury 1 emerged in the ED phase in the bilateral temporal poles and persisted throughout the ED and LD phases. Injury 2 developed from the AC to ED phase in the bilateral hemisphere and partially recovered in the LD phase. In the ED and LD phases, the multiple diffusion metrics were well correlated (r > 0.5 or <−0.5) with the RT dose, especially in the WM tracts in the temporal lobes. Data Conclusion: Disparate WM injuries were observed in NPC patients after RT. The injuries may be primarily or secondarily induced by radiation. Injury 1 may be irreversible, while injury 2 seems to partially recover. Evidence Level: 2. Technical Efficacy: Stage 4. [ABSTRACT FROM AUTHOR]

Background: The promoter variant rs17111237 in the CEP128 closely relates to radiotherapy (RT)‐related brain necrosis in nasopharyngeal carcinoma (NPC) patients. Purpose: To explore RT‐related dynamic alterations in brain morphology and their potential genetic mechanism, and to explore the modulatory effects of CEP128 genetic variants on RT‐related brain morphological alterations in NPC patients. Study Type: Prospective, longitudinal. Population: One hundred one patients with histopathologic ally‐proven NPC (age 41.64 ± 9.63, 46 male), analyzed at baseline (pre‐RT), 3‐months post‐RT and 6 months post‐RT, and 19 sex‐, age‐ and education‐matched healthy controls. Field Strength/Sequence: 3D gradient echo brain volume (3D‐BRAVO) and diffusion‐weighted single‐shot spin‐echo echo‐planar sequences at 3.0 T. Assessment: rs17111237 in CEP128 was detected by Sanger sequencing. Structural and diffusion images were processed with FreeSurfer and FSL. Morphometric similarity network (MSN) was constructed with nine cortical indices derived from structural and diffusion images. Statistical Tests: One‐way ANOVA, chi‐square test. Pearson's correlation analysis was conducted to measure the relationship between CEP128 gene‐expression level in human brain and MSN alterations. Repeated analysis of variance performed to assess group differences in MSN and the modulatory effects of the CEP128 gene within patients. Significance level: P < 0.05, false‐discovery rate correction. Results: RT‐related significant widespread MSN alterations were observed in the cortices of NPC patients. Notably, regional MSN alterations had a weak but significant negative correlation with the cortical pattern of CEP128 gene expression (r = −0.152). Furthermore, rs17111237 in the CEP128 had significant modulatory effects on the observed MSN alterations in NPC patients, with the modulatory effects being most obvious at 3 months post‐RT. Conclusions: MSN has potential to serve as a sensitive biomarker to detect RT‐related brain injury. Inter‐brain regional and inter‐patient variability of RT‐related brain injuries may be attributed to the cortical expression of the CEP128 gene and the modulatory effects of the promoter variant rs17111237 in CEP128. Evidence Level: 2 Technical Efficacy: Stage 2 [ABSTRACT FROM AUTHOR]

The nanometer sodium montmorillonite (Na-MMT), hexadecyl trimethyl ammonium bromide (CTAB), and octadecyl trimethyl sodium chloride (OTAC) were used as reaction monomers and ethanol as solvent, and two oil soluble viscosity reducers MMT-CTAB and MMT-OTAC were synthesized. Structural characterization experiment of modified montmorillonite were conducted by the infrared spectrometer, thermogravimetric analyzer, contact angle tester, scanning electron microscope, and dispersion observation. 20 wt% wax-containing model oil was chosen as the research object. The properties of two viscosity reducers on the pour point and viscosity of model oil were studied experimentally. The results showed that the two modified montmorillonite viscosity reducers were successfully prepared. And both can reduce the pour point and viscosity of model oil. The performance of MMT-OTAC was better than MMT-CTAB, which can reduce the pour point of model oil by 6 °C and the viscosity by 91.1%. [ABSTRACT FROM AUTHOR]