Soil microbial community composition and co-occurrence network responses to mild and severe disturbances in volcanic areas.

Soil physicochemical properties and vegetation types are the main factors affecting soil microorganisms, but there are few studies on the effects of the disturbance following volcanic eruption. To make up for this lack of knowledge, we used Illumina Miseq high-throughput sequencing to study the characteristics of soil microorganisms on both shores of a volcanically disturbed lake. Soil microorganisms in the two sites were subjected to different degrees of volcanic disturbance and showed significant heterogeneity. Mild volcanic disturbance area had higher enrichment of prokaryotic community. Co-occurrence network analysis showed that a total of 12 keystone taxa (9 prokaryotes and 3 fungi) were identified, suggesting that soil prokaryote may play a more significant role than fungi in overall community structure and function. Compared with severe volcanic disturbance area, the soil microbial community in mild volcanic disturbance area had the higher modular network (0.327 vs 0.291). The competition was stronger (positive/negative link ratio, P/N: 1.422 vs 1.159). Random forest analysis showed that soil superoxide dismutase was the most significant variable associated with soil microbial community. Structural equation model (SEM) results showed that keystone had a directly positive effect on prokaryotic (λ = 0.867, P < 0.001) and fungal (λ = 0.990, P < 0.001) multifunctionality while had also a directly positive effect on fungal diversity (λ = 0.553, P < 0.001), suggesting that keystone taxa played a key role in maintaining ecosystem stability. These results were important for understanding the effects of different levels of volcanic disturbance on soil ecosystems.

Changes of root AMF community structure and colonization levels under distribution pattern of geographical substitute for four Stipa species in arid steppe.

The establishment of symbiotic relationship between arbuscular mycorrhizal fungi (AMF) and roots is a mutually beneficial process and plays an important role in plant succession in ecosystems. However, there is less understanding of information about the AMF community in roots under vegetation succession on a large regional scale, especially the spatial variation in the AMF community and its potential ecological functions. Here, we elucidated the spatial variations in root AMF community structure and root colonization along a distribution pattern of four zonal Stipa species in arid and semiarid grassland systems and explored key factors regulating AMF structure and mycorrhizal symbiotic interactions. Four Stipa species established a symbiosis with AMF, and annual mean temperature (MAT) and soil fertility were the main positive and negative driving factors of AM colonization, respectively. The Chao richness and Shannon diversity of AMF community in the root system of Stipa species tended to increase firstly from S. baicalensis to S. grandis and then decreased from S. grandis to S. breviflora. While evenness of root AMF and root colonization showed a trend of increasing from S. baicalensis to S. breviflora, and biodiversity was principally affected by soil total phosphorus (TP), organic phosphorus (Po) and MAT. It is emphasized that Stipa species have certain dependence on AMF, especially in a warming environment, and the root AMF community structure among the four Stipa taxa was different. Additionally, the composition and spatial distribution of root AMF in host plants varied with MAT, annual mean precipitation (MAP), TP and host plant species. These results will broaden our understanding of the relationship between plant and AMF communities and their ecological role, and provide basic information for the application of AMF in the conservation and rehabilitation of forage plants in degraded semiarid grasslands.

Patterns and drivers of microbiome in different rock surface soil under the volcanic extreme environment.

Soil microbial communities were investigated under the volcanic extreme environment. Soil bacterial networks exhibited higher stability than fungal networks. Holocene granite had a more complex microbial network than basalt. Soil pH and total protein were key drivers of microbial network stability.

Changes of Arbuscular Mycorrhizal Fungal Community and Glomalin in the Rhizosphere along the Distribution Gradient of Zonal Stipa Populations across the Arid and Semiarid Steppe.

Arbuscular mycorrhizal fungi (AMF) have been reported to have a wide distribution in terrestrial ecosystems and to play a vital role in ecosystem functioning and symbiosis with Stipa grasses. However, exactly how AMF communities in the rhizosphere change and are distributed along different Stipa population with substituted distribution and their relationships remain unclear. Here, the changes and distribution of the rhizosphere AMF communities and their associations between hosts and the dynamic differences in the glomalin-related soil protein (GRSP) in the rhizosphere soil of seven Stipa species with spatial substitution distribution characteristics in arid and semiarid grasslands were investigated. Along with the substituted distribution of the Stipa populations, the community structures, taxa, species numbers, and alpha diversity index values of AMF in the rhizosphere changed. Some AMF taxa appeared only in certain Stipa species, but there was no obvious AMF taxon turnover. When the Stipa baicalensis population was replaced by the Stipa gobica population, the GRSP tended to decline, whereas the carbon contribution of the GRSP tended to increase. Stipa grandis and Stipa krylovii had a great degree of network modularity of the rhizosphere AMF community and exhibited a simple and unstable network structure, while the networks of Stipa breviflora were complex, compact, and highly stable. Furthermore, with the succession of zonal populations, the plant species, vegetation coverage, and climate gradient facilitated the differentiation of AMF community structures and quantities in the rhizospheres of different Stipa species. These findings present novel insights into ecosystem functioning and dynamics correlated with changing environments. IMPORTANCE This study fills a gap in our understanding of the soil arbuscular mycorrhizal fungal community distribution, community composition changes, and diversity of Stipa species along different Stipa population substitution distributions and of their adaptive relationships; furthermore, the differences in the glomalin-related soil protein (GRSP) contents in the rhizospheres of different Stipa species and GRSP's contribution to the grassland organic carbon pool were investigated. These findings provide a theoretical basis for the protection and utilization of regional biodiversity resources and sustainable ecosystem development.

The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe.

The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east-west humidity and north-south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis.

Root-associated microbiomes play significant roles in plant productivity, health and ecological services. However, our current understanding of the microbial assemblages in the rhizosphere and endosphere of herbage is still limited. To gain insights into these microbial assemblages, Illumina MiSeq high-throughput sequencing was performed to investigate the characteristics of microbial communities of an herbage, Leymus chinensis. Hierarchical clustering analysis and principal coordinate analysis (PCoA) results showed that microbial communities of the rhizosphere and endosphere samples were clearly distinguished. Rhizosphere soil communities showed a greater sensitivity than root endosphere communities using linear discriminant analysis (LDA) effect size (LEfSe). Rhizosphere and endosphere communities performed their respective functions in the soil as a cohesive collective, and Rhizobiales were observed to function as generalists. Redundancy analysis (RDA) and variance partitioning analysis (VPA) results revealed that the contribution of the interaction between soil physicochemical parameters and soil enzymes was greater than their individual contributions. In summary, this study is the first to elucidate the microbial diversity and community structure of L. chinensis and compare the diversity and composition between rhizospheric and endosphere microbiomes.

Prognostic nomogram for the combination therapy of percutaneous catheter drainage and antibiotics in pyogenic liver abscess patients.

PURPOSE: To identify the predictors for recovery of pyogenic liver abscess (PLA) patients treated with percutaneous catheter drainage (PCD) and antibiotics, and then develop an effective nomogram to predict the recovery time. MATERIALS AND METHODS: The retrospective study included consecutive PLA patients treated with PCD and antibiotics. We defined the overall recovery time (ORT) as the time from the PCD procedure to the time of clinical success or failure. Based on the ORT, its predictors were identified with univariate and multivariate analyses. Then, a nomogram was developed to predict the ORT, and was internally validated by using Harrell's c statistic. RESULTS: A total of 116 patients and 142 PCD procedures with a median ORT of 15.0±10.6 days were included. Gas-formation (GF; HR: 0.486 [95% CI 0.312-0.757]; P = 0.001), diabetes mellitus (DM; HR: 0.455 [95% CI 0.303-0.682]; P<0.001), and preinterventional septic shock (PSS; HR: 0.276 [95% CI 0.158-0.483]; P < 0.001) were identified as predictors for the ORT of combination therapy after univariate and multivariate analyses, which indicated a significantly longer ORT than those patients without. The prognostic analyses demonstrated that the more predictors (GF, DM, and PSS) a patient exhibited, the longer ORT for the combination therapy. A nomogram was developed to predict the ORT and revealed high accuracy, with Harrell's c statistic of 0.73. CONCLUSION: GF, DM, and PSS were predictors for the recovery of PLA patients treated with PCD and antibiotics. The nomogram was effective in predicting the ORT of combination therapy.

Comprehensive analysis of key genes, microRNAs and long non-coding RNAs in hepatocellular carcinoma.

Human hepatocellular carcinoma (HCC) is a common aggressive cancer whose molecular mechanism remains elusive. We aimed to identify the key genes, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) involved with HCC. We obtained mRNA, miRNA and lncRNA profiles for HCC from The Cancer Genome Atlas and then identified differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs). We performed functional annotation of DEmRNAs and then constructed HCC-specific DEmiRNA-DEmRNA, DEmiRNA-DElncRNA and DElncRNA-DEmiRNA-DEmRNA interaction networks. We searched for nearby target cis-DEmRNAs of DElncRNAs and performed receiver operating characteristic and survival analyses. A total of 1239 DEmRNAs, 33 DEmiRNAs and 167 DElncRNAs in HCC were obtained. Retinol metabolism [false discovery rate (FDR) = 7.02 × 10-14] and metabolism of xenobiotics by cytochrome P450 (FDR = 7.30 × 10-11) were two significantly enriched pathways in HCC. We obtained 545 DEmiRNA-DEmRNA pairs that consisted of 258 DEmRNAs and 28 DEmiRNAs in HCC. mir-424, miR-93 and miR-3607 are three hub DEmiRNAs of the HCC-specific DEmiRNA-DEmRNA interaction network. HAND2-AS1/ENSG00000232855-miR-93-LRAT/RND3, ENSG00000232855-miR-877-RCAN1 and ENSG00000232855-miR-224-RND3 interactions were found in the HCC-specific DElncRNA-DEmiRNA-DEmRNA interaction network. A total of three DElncRNA-nearby target DEmRNA pairs (HCG25-KIFC1, LOC105378687-CDC20 and LOC101927043-EPCAM) in HCC were obtained. Diagnostic and prognostic values of several selected DElncRNAs, DEmRNAs and DEmiRNAs for HCC were assessed. Our study identified several DEmRNAs, DEmiRNAs and DElncRNAs with great diagnostic or prognostic value for HCC, which may facilitate studies into the molecular mechanisms, and development of potential biomarkers and therapeutic target sites for HCC.