Gut microbial diversity analysis using Illumina sequencing for functional dyspepsia with liver depression-spleen deficiency syndrome and the interventional Xiaoyaosan in a rat model

AIM To investigate gut microbial diversity and the interventional effect of Xiaoyaosan(XYS) in a rat model of functional dyspepsia(FD) with liver depression-spleen deficiency syndrome. METHODS The FD with liver depression-spleen deficiency syndrome rat model was established through classic chronic mild unpredictable stimulation every day. XYS group rats received XYS 1 h before the stimulation. The models were assessed by parameters including state ofthe rat, weight, sucrose test result and open-field test result. After 3 wk, the stools of rats were collected and genomic DNA was extracted. PCR products of the V4 region of 16 S rD NA were sequenced using a barcoded Illumina paired-end sequencing technique. The primary composition of the microbiome in the stool samples was determined and analyzed by cluster analysis.RESULTS Rat models were successfully established, per data from rat state, weight and open-field test. The microbiomes contained 20 phyla from all samples. Firmicutes, Bacteroidetes, Proteobacteria, Cyanobacteria and Tenericutes were the most abundant taxonomic groups. The relative abundance of Firmicutes, Proteobacteria and Cyanobacteria in the model group was higher than that in the normal group. On the contrary, the relative abundance of Bacteroidetes in the model group was lower than that in the normal group. Upon XYS treatment, the relative abundance of all dysregulated phyla was restored to levels similar to those observed in the normal group. Abundance clustering heat map of phyla corroborated the taxonomic distribution. CONCLUSION The microbiome relative abundance of FD rats with liver depression-spleen deficiency syndrome was significantly different from the normal cohort. XYS intervention may effectively adjust the gut dysbacteriosis in FD.

Comparison of rhizosphere and endophytic microbial communities of Chinese leek through high-throughput 16S rRNA gene Illumina sequencing

Chinese leek（Allium tuberosum Rottler ex Sprengel） is a common vegetable in China. In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity. This study＇s aim was to investigate the potential antifungal and nematicidal activity associated with rhizosphere or endophytic microbes of Chinese leek. Thus, a total of 79 261 high-quality sequences were obtained from Chinese leek rhizosphere soil, leaf and root samples. In the rhizosphere soil, the bacterial community comprised five dominant phyla： Proteobacteria（37.85%）, Acidobacteria（10.99%）, Bacteroidetes（8.24%）, Cyanobacteria（7.79%） and Planctomycetes（7.1%）. The leaf and root bacterial communities comprised two dominant phyla： Cyanobacteria（83.42% in leaf and 75.44% in root） and Proteobacteria（14.75% in leaf and 21.04% in root）. Microbial diversity, richness and evenness in the rhizosphere soil bacterial community were higher than that in the endophytic bacterial communities. The rhizosphere bacterial community was significantly different from the endophytic bacterial communities. The endophytic bacterial communities from the leaf and the root were slightly, but not significantly different from each other. This study＇s findings would contribute to the isolation and identification of nematicidal and antifungal bacterial communities in Chinese leek.

Analysis of Microbial Community Structure and Diversity in Crop Rhizosphere Soil Based on Illumina NovaSeq Sequencing Platform

[Objectives]To make full use of crop rhizosphere microbial resources.[Methods]Illumina NovaSeq sequencing platform was used to analyze the richness and diversity of microbial community structure in rhizosphere soil of rice and maize crops in Baitu Town,Gaoyao District,Zhaoqing City.[Results]A total of 14936 OTUs of bacteria and 1905 OTUs of fungi were obtained from three samples of rice rhizosphere soil,and 13437 OTUs of bacteria and 1413 OTUs of fungi were obtained from three samples of maize rhizosphere soil.The diversity and richness of bacterial communities were higher than those of fungi.There are differences in soil bacterial and fungal communities among different crop samples.The analysis of species with bacteria difference at genus level among crop rhizosphere soil samples showed that 18 genera with significant differences were obtained from 6 samples;species analysis of fungi at the genus level showed that 3 genera with significant differences were obtained from 6 samples.[Conclusions]The research results of this paper have positive significance for the development and utilization of soil resources in Zhaoqing City and the full exploitation of rice and maize rhizosphere microbial resources.

Seasonal changes in gut microbiota of sea cucumber over natural aestivation cycle

Sea cucumber Apostichopus japonicus is an ideal model organism for marine invertebrate aestivation;it annually enters a“sleeping state”for nearly 3 months when ambient water temperature range is 25–30℃.The natural fasting is accompanied by remodeling the intestinal biota and function,which is a part of host biology and could affect the gut microbiota.We investigatesd the impact of annual aestivation on gut microbiota using high-throughput sequencing of 16S rRNA amplicons.Results reveal a notable alteration in the composition of gut bacteria during aestivation during which various indigenous families and genera that exhibit a preference for dietary glycans(e.g.,family Rhodobacteraceae and Flavobacteriaceae)decreased,while the taxa capable of utilizing substrates derived from the host(e.g.,genus Akkermansia and Prevotella)increased,and so did certain opportunistic pathogenic bacteria.Moreover,the investigation delved into the gut morphology and immunity response of A.japonicus and reveal that the intestine of A.japonicus undergoes substantial atrophy and degeneration during aestivation.However,there was an observed augmentation in the levels of acid and neutral mucin within mucous cells,as well as an enhanced immune defense response(as evidenced by increased gene expression of AjTLR3,LITAF,Ajp105,and LYZ).These results imply that the composition of sea cucumber gut microbiota differed between aestivation and active periods,which potentially affects the intestinal functions of the host and the symbiotic relationship between host and its microbiota over the activeaestivation cycle.

不同落叶果树根际微生物群落代谢与组成的差异性研究

【目的】从根际微生物群落代谢与组成方面探讨不同落叶果树根际差异性。【方法】利用Biolog ECO板方法与Illumina Miseq sequencing技术,以未种植果树区域土壤为对照,研究苹果、梨及葡萄等8种落叶果树根际微生物群落的代谢与组成。【结果】8种果树根际微生物的代谢活性与功能多样性指数(除Pielou均匀度指数E外)均显著高于对照。比较8种果树根际微生物群落的碳源利用特征情况发现,杏树根际微生物群落对酚酸类物质(PC,phenolic compounds)的利用比率显著下降,对碳水化合物(CH,carbohydrate)的利用比率显著上升,而对照土壤微生物群落对氨基酸类(AA,amino acids)碳源利用比率最高。细菌与真菌群落纲水平相对丰度表明,8种果树根际细菌与真菌群落相对丰度存在明显差异,其中苹果与核桃γ-变形菌纲相对丰度较其他果树显著上升;而与细菌群落相比,8种果树根际真菌群落在纲水平上差异更为明显。基于纲水平优势菌与微生物群落代谢之间的相关性分析表明,微生物群落代谢与Betaproteobacteria、Alphaproteobacteria及Sphingobacteriia呈显著正相关,而与Gemmatimonadetes、Sordariomycetes、Glomeromycetes及Chytridiomycetes均呈显著负相关。另外,RDA分析表明,微生物功能多样性(除E外)与细菌α多样性呈正相关,而与真菌α多样性呈负相关。【结论】8种果树微生物群落碳代谢存在显著差异。8种果树根际细菌与真菌群落均存在显著差异,而真菌群落较细菌差异更为显著。根际微生物群落代谢与细菌群落呈正相关,而与真菌群落呈负相关。

Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680

Platichthys stellatus is an economically important marine bony fish species that is cultured in China on a large scale.However,very little is known about its immune-related genes.In this study,the transcriptome of the immune organs ofP.stellatus that were intraperitoneally challenged with the pathogen Edwardsiella ictaluri JCM1680 is analyzed.Total RNA from four tissues(spleen,kidney,liver,and intestine) was mixed equally and then sequenced on an Illumina HiSeq 2000 platform.Overall,28 465 813 quality reads were generated and assembled into 43 061 unigenes.Similarity searches against public protein sequence databases were used to annotate 28 291 unigenes(65.7%of the total),368 of which were associated with immunoregulation,including 188 related to immunity response.Additionally,the transcript levels of immunity response unigenes annotated as related to tumor necrosis factor(TNF),TNF receptor,chemokine,major histocompatibility complex,and interleukin-6 were investigated in the different tissues of normal and infected P.stellatus by real-time quantitative PCR.The results confirmed that the unigenes identified in the transcriptome database were indeed expressed and up-regulated in infected P.stellatus.To our knowledge,this is the first report of the sequencing and analysis of the transcriptome of P.stellatus.These findings provide insights into the transcriptomics and immunogenetics of bony fish.

Marginal bone loss around non-submerged implants is associated with salivary microbiome during bone healing

Marginal bone loss during bone healing exists around non-submerged dental implants. The aim of this study was to identify the relationship between different degrees of marginal bone loss during bone healing and the salivary microbiome. One hundred patients were recruited, and marginal bone loss around their implants was measured using cone beam computed tomography during a 3-month healing period. The patients were divided into three groups according to the severity of marginal bone loss.Saliva samples were collected from all subjected and were analysed using 16 SMiSeq sequencing. Although the overall structure of the microbial community was not dramatically altered, the relative abundance of several taxonomic groups noticeably changed. The abundance of species in the phyla Spirochaeta and Synergistetes increased significantly as the bone loss became more severe. Species within the genus Treponema also exhibited increased abundance, whereas Veillonella, Haemophilus and Leptotrichia exhibited reduced abundances, in groups with more bone loss. Porphyromonasgingivalis, Treponemadenticola and Streptococcus intermedius were significantly more abundant in the moderate group and/or severe group. The severity of marginal bone loss around the non-submerged implant was associated with dissimilar taxonomic compositions. An increased severity of marginal bone loss was related to increased proportions of periodontal pathogenic species. These data suggest a potential role of microbes in the progression of marginal bone loss during bone healing.

Infl uence of the slope aspect on the ectomycorrhizal fungal community of Quercus variabilis Blume in the middle part of the Taihang Mountains,North China

The slope aspect is one of the most critical topographic factors in mountainous areas.Little is known,however,about the eff ect of the aspect on the ectomycorrhizal(ECM)fungal community.Additionally,we know very little about the composition of ECM fungal communities associated with Quercus variabilis,which is widely distributed in East Asia.In this study,we compared the richness,community composition,and exploration types of ECM fungi associated with Q.variabilis between predominantly south-and north-facing slopes in the Taihang Mountain,North China for the fi rst time.DNA was extracted from the root tips of Q.variabilis,and Illumina MiSeq sequencing was used to identify ECM fungi.In total,168 operational taxonomic units belonging to 28 genera were detected,and the ECM community was found to be dominated by Russula,Inocybe,Tomentella,Scleroderma,and Cortinarius.Compared with the north-facing slopes,the ECM communities on the south-facing slopes had higher diversity.The community composition and exploration types were directly aff ected by the slope aspect.Also,the aspect-induced edaphic variables,such as total phosphorus,total nitrogen,total potassium,pH,and soil water content,were important sources of variation in ECM fungal richness and distributions of exploration types.Diff erent genera tended to be distributed in various slope aspects.Cenococcum,Genea,and Clavulina were signifi cantly enriched in north-facing slopes,while Geopora,Helvelosebacina,Scleroderma,Gyroporus,Astraeus,Boletus,Tricholoma,Hebeloma,Cortinarius and unclassifi ed Thelephoraceae were more abundant in south-facing slopes.Hydrophobic ECM fungi were obviously enriched in the south-facing slope,but there was no statistical diff erence between hydrophilic among the south-and north-facing slopes.Our study deepened our knowledge of the aspect-driven variation in ECM fungal communities associated with Q.variabilis.

Epiphytic and Endophytic Fungal Communities of Tomato Plants

Plants harbor diverse fungal communities both on their surfaces(epiphytic)and inside of plant tissues(endophytic),and these fungi play important roles in plant health and vigor.However,comparisons of epiphytes and endophytes have rarely been performed.In this study,the soil,epiphytic and endophytic fungal assemblages of greenhouse-grown tomato plants were extensively examined and compared by Illumina sequencing of 18S rRNA amplicons.The fungal communities differed in both size and composition.The soil communities were the richest and most abundant,while the endophytes showed the lowest richness and diversity.The diversity of endophytes also differed in different tissues,with the highest diversity occurring in the roots.In both the epiphytic and endophytic samples,the majority of fungi corresponded to ascomycetes,amongwhich Sordariomycetes,Dothideomycetes and Eurotiomyceteswere the most frequent classes.Themajor non-ascomycete fungi were associated only with the class Exobasidiomycetes(Basidiomycota).At the order level,the epiphytes showed similar distribution patterns in the stems and leaves,but among the endophytes,distinct fungal orders were enriched in different tissues.Capnodialeswas recorded as amajor fungal group in the stems,leaves and seeds,and Saccharomycetales was specifically enriched in the pericarp and jelly around seeds.The present data suggested that different drivers shaped epiphytic and endophytic fungi communities and deepened our knowledge of the complex plant-fungus interaction in tomato.

Halophyte Vegetation Influences Soil Microbial Community of Coastal Salt Marsh

Coastal wetlands are the most productive ecosystems worldwide and can provide important ecosystem services,yet the characteristics of microbial community within these systems remain poorly understood.Microbial community of salt marsh vegetation and the associated soil physio-chemical properties were investigated in this study.Three typical Suaeda australis,Phragmites australis,Spartina alterniflora wetlands,and non-vegetated bare mudflats in the Zhoushan Islands were studied to advance the understanding of the characteristics of soil bacterial communities in coastal wetlands.Results showed that the bare mudflats exhibited high pH value and soil moisture content compared with the vegetated samples.In different vegetation types,the organic matter content,total nitrogen,and total potassium content decreased in the order:S.alterniflora wetland>P.australis wetland>S.australis wetland,and there was no obvious difference in total phosphorous content.The halophytes could decrease soil salinity compared with bare mudflats.Proteobacteria,Nitrospinae,Bacteroidetes,Acidobacteria,and Nitrospirae were the predominant level across all samples.Functional prediction showed that SPA-covered soil might play vital roles in sulphur cycling,while SUA and PHR covered soils were involved in nitrogen cycling.This study could provide the first insight into the microbial community of this study area and contribute to a better understanding of vegetation microbiota and bioremediation in coastal wetland ecosystem.

Immediate and legacy effects of snow exclusion on soil fungal diversity and community composition

Background:Soil fungi play crucial roles in ecosystem functions.However,how snow cover change associated with winter warming affects soil fungal communities remains unclear in the Tibetan forest.Methods:We conducted a snow manipulation experiment to explore immediate and legacy effects of snow exclusion on soil fungal community diversity and composition in a spruce forest on the eastern Tibetan Plateau.Soil fungal communities were performed by the high throughput sequencing of gene-fragments.Results:Ascomycota and Basidiomycota were the two dominant fungal phyla and Archaeorhizomyces,Aspergillus and Amanita were the three most common genera across seasons and snow manipulations.Snow exclusion did not affect the diversity and structure of soil fungal community in both snow-covered and snow-free seasons.However,the relative abundance of some fungal communities was different among seasons.Soil fungal groups were correlated with environmental factors(i.e.,temperature and moisture)and soil biochemical variables(i.e.,ammonium and enzyme).Conclusions:These results suggest that the season-driven variations had stronger impacts on soil fungal community than short-term snow cover change.Such findings may have important implications for soil microbial processes in Tibetan forests experiencing significant decreases in snowfall.

Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China

Diversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient(0-0.4043 g/g)in surface(5-10 cm)and subsurface(35-40 cm)petroleum-contaminated soil samples from the Dagang Oilfield,China.Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods,the bacterial diversity of the soil was studied.Subsequently,the environmental parameters were measured to analyze its relationship with the community variation.Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils,but no differences were observed in different depths of petroleum-contaminated soil.Meanwhile,many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties.Total petroleum hydrocarbon,total organic carbon,and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils.Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.

Naphthalene exerts non-target effects on the abundance of active fungi by stimulating basidiomycete abundance

As an arthropod biocide,naphthalene has been used in studies of the ecological functions of soil fauna for decades.However,its potential non-target effects on soil microorganisms may affect soil mineralization and litter decomposition processes.Therefore,we conducted an experiment with naphthalene adding to soil surface at a rate of 100 g·m-2 per month to examine the potential non-target effects of this treatment on soil fungal phospholipid fatty acids(PLFAs),18 S rDNA gene copy numbers and community diversity in a subalpine forest of western Sichuan,China.The results showed that naphthalene addition significantly increased fungal PLFAs but did not significantly alter fungal gene copy numbers.A total of 16 phyla,62 genera and 147 Operational taxonomic units(OTUs)were identified through Illumina Mi Seq sequencing analysis.Basidiomycota and Ascomycota were the most abundant phyla in both the control and naphthalene addition plots.Naphthalene addition did not affect the diversity or structure of the soil fungal community,but the increase in some genera of Basidiomycota might contribute to the increase in fungal PLFAs in the naphthalene addition plots.These results suggest that naphthalene exerts non-target effects on the active fungal abundance by stimulating the abundance of specific taxa in subalpine forest soils.The non-target effects of naphthalene on the fungal community should be taken into consideration when it is used to exclude soil fauna.

A comprehensive analysis of the response of the fungal community structure to long-term continuous cropping in three typical upland crops

Certain agricultural management practices are known to affect the soil microbial community structure;however,knowledge of the response of the fungal community structure to the long-term continuous cropping and rotation of soybean,maize and wheat in the same agroecosystem is limited.We assessed the fungal abundance,composition and diversity among soybean rotation,maize rotation and wheat rotation systems and among long-term continuous cropping systems of soybean,maize and wheat as the effect of crop types on fungal community structure.We compared these fungal parameters of same crop between long-term crop rotation and continuous cropping systems as the effect of cropping systems on fungal community structure.The fungal abundance and composition were measured by quantitative real-time PCR and Illumina MiSeq sequencing.The results revealed that long-term continuous soybean cropping increased the soil fungal abundance compared with soybean rotation,and the fungal abundance was decreased in long-term continuous maize cropping compared with maize rotation.The long-term continuous soybean cropping also exhibited increased soil fungal diversity.The variation in the fungal community structure among the three crops was greater than that between long-term continuous cropping and rotation cropping.Mortierella,Guehomyces and Alternaria were the most important contributors to the dissimilarity of the fungal communities between the continuous cropping and rotation cropping of soybean,maize and wheat.There were 11 potential pathogen and 11 potential biocontrol fungi identified,and the relative abundance of most of the potential pathogenic fungi increased during the long-term continuous cropping of all three crops.The relative abundance of most biocontrol fungi increased in long-term continuous soybean cropping but decreased in long-term continuous maize and wheat cropping.Our results indicate that the response of the soil fungal community structure to long-term continuous cropping varies based upon crop types.

Comparative population genetic analyses suggest hybrid origin of Rhododendron pubicostatum,an endangered plant species with extremely small populations endemic to Yunnan,China

Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species.In the present study,we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach.Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus.Interestingly,genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh.pubicostatum.This sympatry should be considered a unimodal hybrid zone,since Rh.pubicostatum is predominant here.Unimodal hybrid zones are uncommon in Rhododendron,despite the fact that hybridization frequently occurs in the genus.Issues pertaining to the conservation of Rh.pubicostatum resulting from admixture of genetic material from its parental species are discussed.

Soil Fungal Diversity and Community Composition in Response to Continuous Sweet Potato Cropping Practices

Soil fungi are extremely important for maintaining soil health and plant production in agricultural systems.Currently,the effect of continuous cropping of sweet potato on soil fungal communities and physiochemical parameters has not been well documented.In the present study,four sweet potato fields consecutively monocultured for 1,2,3,and 4 years were selected to investigate the effect of monoculture on soil fungal communities through Illumina MiSeq sequencing.Continuous cropping of sweet potatoes dramatically altered the fungal community composition,whereas fungal diversity was almost unchanged.Ascomycota and Basidiomycota were the most abundant phyla in all soil samples,accounting for 32.59%and 21.14%of the average relative abundance,respectively.The abundance of some potential pathogens,such as Ascobolus spp,specifically Ascobolus stercorarius,and some unknown fungi increased significantly as the sweet potato monoculture period increased,and their presence were highly positively correlated with disease incidence.In contrast,Basidiomycota,Bullera,Fusarium and Trichocladium most likely play roles as antagonists of sweet potato disease development,as their relative abundance decreased significantly over time and were negatively correlated with disease incidence.Redundancy and correlation analyses revealed that soil pH and organic carbon content were the most important factors driving these changes.Our findings provided a dynamic overview of the fungal community and presented a clear scope for screening beneficial fungi and pathogens of sweet potato.

Bacterial community shifts in different functional zones of a reservoir with ecological purification facilities

Ecological purification in a reservoir is an important strategy to control the level of nutrients in water.The bacterial community of such a reservoir is the main agent for pollutant degradation,which has not been fully documented.Taking the Jinze Reservoir,a freshwater source for Shanghai,China as the case,its spatial distributions of water and sediment bacteria were determined using 16S rRNA gene-based Illumina MiSeq sequencing,and the environmental parameters were analyzed.The reservoir takes natural river water and functions as an ecological purification system,consisting of three functional zones,i.e.,pretreatment zone,ecological purification zone,and ecological sustaining zone.Results show that the concentrations of both total nitrogen(TN)and total phosphorus(TP)decreased considerably after the ecological treatment,and the concentration of dissolved oxygen(DO)in the ecological purification zone was boosted from that before pretreatment.In addition,patterns of bacterial communities in both water and sediment were similar and consisted of mainly Proteobacteria,Actinobacteria,and Bacteroidetes.However,difference in water bacterial composition was distinct in each functional zone,whereas the bacterial communities in sediment changed only slightly among sediment samples.Network analysis revealed nonrandom co-occurrence patterns of bacterial community composition in water and sediment,and Pseudomonas,unclassified Comamonadaceae,Variovorax,and Dechloromonas were the key taxa in the co-occurrence network.The bacterial taxa from the same module of the network had strong ecological connections,participated in C-cycles,and shared common trophic properties.PICRUSt analysis showed that bacteria were involved potentially in various essential processes;and the abundance of predicted xenobiotic biodegradation genes showed a decreasing trend in water samples from the inlet to the outlet of the reservoir.These results improve our current knowledge of the spatial distribution of bacteria in water and sediment in ecological purification reservoirs.

High-throughput 16S rDNA sequencing of the pulmonary microbiome of rats with allergic asthma

A decrease in microbial infection in adolescents is implicated with an increase in the incidence of asthma and allergic diseases in adulthood,indicating that the microbiome plays a critical role in asthma.However,the microbial composition of the lower respiratory tract remains unclear,hindering the further exploration of the pathogenesis of asthma.This study aims to explore the microbial distribution and composition in the lungs of normal rats and rats with allergic asthma via 16S rDNA sequencing.The DNA of the pulmonary microbiome was extracted from the left lungs collected from normal control group(NC),saline control group(SC),and allergic asthma group(AA)under aseptic conditions.After the 16s rDNA V4eV5 region was amplified,the products were sequenced using Illumina high-throughput technology and subjected to operational taxonomic unit(OTU)cluster and taxonomy analysis.The OTU values of AA increased significantly compared with those of NC and SC.Microbiome structure analysis showed that the dominant phylum of the pulmonary microbiome changed from Proteobacteria in NC to Firmicutes in AA.Linear discriminant analysis indicated that the key microbiomes involved in the three groups varied.

Earthworms and warming alter methane uptake and methane-cycling microbial community in meadow soil

Earthworms significantly reduced soil CH_(4) uptake at both temperatures,and warming significantly promoted soil CH_(4) uptake.Earthworms significantly altered methanotroph community,and warming significantly altered methanogen community,and their interaction had a significant influence on both methanogen and methanotroph communities.Soil properties exhibited a negative impact on CH_(4) uptake,while theα-diversity of methanotrophs was associated with enhanced CH_(4) uptake.Dissolved organic carbon(DOC)was identified as the most essential factor in forecasting soil CH_(4) uptake.The function and service of biologically driven ecosystems are undergoing significant changes due to climate warming.Earthworms play a crucial role as soil engineer by modulating the effects of climate change on soil nutrient cycle through alterations to biotic and abiotic soil conditions.However,there is currently a scarcity of information regarding the impacts of earthworms and warming on soil CH_(4) uptake and their associated microbial mechanisms.This study conducted a 61-day microcosm experiment to investigate the impact of warming(temperature rise from 14.2℃ to 17.2℃)and the presence of earthworms(Eisenia fetida and Moniligaster japonicus)on soil CH_(4) uptake.We employed gas chromatography and high-throughput sequencing to investigate the fluctuations in soil CH_(4) uptake and the microbial communities involved in methane cycling.Compared to low temperature conditions(14.2℃),we observed that warming significantly increased soil CH_(4) uptake in all treatments(nonearthworm:51.85%;Eisenia fetida:50.88%;Moniligaster japonicus:71.78%).Both Eisenia fetida and Moniligaster japonicus significantly reduced soil CH_(4) uptake at two temperatures compared to the non-earthworm treatment.Nevertheless,no significant impacts were found on soil CH_(4) uptake due to the interactions between earthworms and warming.The methanotroph communities exhibited notable variations among earthworm treatments,whereas the methanogenic communities displayed significant differences among temperature treatments.The interaction between earthworm and warming also resulted in noticeable variations in both methanogenic and methanotrophic communities.The FAPROTAX analysis revealed that earthworms and warming altered relative abundance of methanogens and methanotroph associated with CH_(4) cycle functions.Soil properties exhibited a negative impact on CH_(4) uptake,with DOC identified as the most crucial variable in predicting soil CH_(4) uptake,while theα-diversity of methanotrophs was associated with enhanced CH_(4) uptake.This study emphasized the crucial role of soil fauna in adjusting soil greenhouse gas emissions under the context of global warming.

Characterization of microbial structure and function in the rhizosphere of Boehmeria nivea L.:A comparative study of volcanic cone and crater

Rhizosphere microbial network in crater had higher complexity than in volcanic cone.Bacteria were more prone to enrichment than fungi in volcanic soils.The bacteria exhibited greater resistance and resilience than fungi.Volcanic eruptions are significant natural disturbances that provide valuable opportunities to study their impacts on soil microorganisms.However,no previous studies have compared the rhizosphere microbial communities of Boehmeria nivea L.in volcanic craters and cones.To address this gap,we conducted a comprehensive investigation using Illumina MiSeq high-throughput sequencing to compare the rhizosphere microbial communities in volcanic craters and cones.Principal Coordinate Analysis revealed significant differences in the rhizosphere microbial communities between the crater and cone.The bacterial communities in the rhizosphere of the crater exhibited higher diversity and evenness compared to the cones.Moreover,the cones displayed more intricate bacterial networks than the crater(nodes 556 vs.440).Conversely,fungal networks were more complex in the crater than the cone(nodes 943 vs.967).Additionally,bacterial communities demonstrated greater stability than fungal ones within these volcanic soils(avgK 241.1 vs.499.7)and(avgCC 1.047 vs.1.092).Furthermore,the Structural Equation Model demonstrated a direct positive impact of alpha diversity on soil microbial community multifunctionality in the crater(λ=0.920,P<0.001).Our findings have presented the opportunity to investigate the characteristics of the rhizosphere microbial communities of Boehmeria nivea L.in the crater and cone.