Antarctic ice-free areas(<0.4%of the continent)represent Antarctic biodiversity oases,where microbial communities sustain terrestrial ecosystem functions.These habitats-encompassing mineral,ornithogenic soils,biolo...Antarctic ice-free areas(<0.4%of the continent)represent Antarctic biodiversity oases,where microbial communities sustain terrestrial ecosystem functions.These habitats-encompassing mineral,ornithogenic soils,biological soil crusts,and hypolithic/endolithic niches-are shaped by environmental factors such as pH,organic C/N ratios,moisture,elevation,and trace element availability.The diversity of prokaryotes,eukaryotes,and viruses is lower than in other regions,yet the communities exhibit strong endemism,with site-specific uncultivated lineages.Microorganisms persist through cold and stress adaptations,performing organic carbon decomposition,phototrophy,and oxidation of trace gases to drive carbon and nitrogen cycling in various Antarctic soil habitats.Climate change and anthropogenic disturbances are shifting communities toward copiotrophic generalists,altering elementary cycling and feeding back to climate change.Culturation and genomic-based techniques reveal novel microbial taxa with broad biotechnological potentials on bioactive compounds and cryotolerant enzymes.In summary,this review offers a foundation for exploring Antarctic microbial biodiversity,ecosystem resilience,and the development of novel biotechnologies,while also highlighting the urgent need for effective monitoring and preservation strategies to mitigate the impacts of ongoing environmental changes on Antarctic soil ecosystems.展开更多
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 depres...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.展开更多
BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of ...BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.展开更多
The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting(mesophilic,thermophilic,c...The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting(mesophilic,thermophilic,cooling and maturation phases).In addition,the physicochemical parameters of the composting system were determined in this study.The fermentation time of the thermophilic period was prolonged with the addition of urea or urea combined with a microbial agent.The ratio of C/N and germination index variation indicated that the additives were favorable for composting,because the additives directly changed the physicochemical properties of the compost and had effects on the diversity and abundance of bacteria and fungi.The abundance of operational taxonomic units(OTUs),diversity index(Shannon)and richness index(Chao1)of fungi and bacteria were found to significantly increase when urea+microbial agents were added to straw in the thermophilic phase.The relative abundance of the predominant bacteria and fungi at the phylum and genus levels differed during different composting phases.The abundance of the phyla Firmicutes and Proteobacteria declined in the order of treatments SNW>SN>S(S is straw only compost;SN is straw+5 kg t^(–1) urea compost;and SNW is straw+5 kg t^(–1) urea+1 kg t^(–1) microbial agent compost)in the thermophilic phase.The abundance of the genera Staphylococcus,Bacillus and Thermobifida followed the same order in the mesophilic phase.Ascomycota accounted for more than 92%of the total fungal sequences.With the progression of the composting process,the abundance of Ascomycota decreased gradually.The abundance of Ascomycota followed the order of S>SN>SNW during the thermophilic phase.The abundance of Aspergillus accounted for 4–59%of the total abundance of fungi and increased during the first two sampling periods.Aspergillus abundance followed the order of SNW>SN>S.Additionally,principal component analysis(PCA)revealed that the community compositions in the straw and straw+urea treatments were similar,and that the bacterial communities in treatments S,SN and SNW in the mesophilic phase(at day 1)were different from those observed in three other phases(at days 5,11,and19,respectively),while the fungal communities showed only slight variations in their structure in response to changes in the composting process.Canonical correlation analysis(CCA)and redundancy analysis(RDA)showed that total carbon(TC),NO_(3)^(–)-N(NN),electrical conductivity(EC)and p H were highly correlated with community composition.Therefore,this study highlights that the additives are beneficial to straw composting and result in good quality compost.展开更多
South China Sea （SCS） is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, ＂SONNE＂ 177 cruise found two cold seep areas ...South China Sea （SCS） is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, ＂SONNE＂ 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diver- sity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abun- dance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment （wet weight）. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diver- sity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.展开更多
In this study,the intestinal microbiota of kuruma shrimp(Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacill...In this study,the intestinal microbiota of kuruma shrimp(Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp.on intestinal microbial diversity.Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp.amended feed.PCR and denaturing gradient gel electrophoresis(DGGE) analyses were then performed on DNA extracted directly from the guts.Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons,and distinct bands in the gels were sequenced.The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp.and uncultured gamma proteobacterium.Overall,the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.展开更多
In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA direct...In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types （genera and/or species）. They included Polyangium spp., Sphingomonas spp., Variovorax spp., Hafina spp., Clostridia, Acidobacteria, the enterics and some uncultured strains. Microbes able to tolerate high concentrations of cadmium （500μmol/L and above） were also isolated from the soil. These isolates included strains of Acinetobacter （strain CD06）, Enterobacter sp. （strains CD01, CD03, CD04 and CD08） （similar strains also identified in culture-independent approach） and a strain of Stenotrophomonas sp. The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment cultures and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.展开更多
The microbial diversity in Wuli Area, Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses. A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold ...The microbial diversity in Wuli Area, Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses. A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold springs, The bacterial clones could be classified into Proteobacteria, Acid- obacteria, Deinococci, Sphingobacteria, Flavobacteria, Nitrospirae, Actinobacteria, Gemmatimona- detes, and unclassified-bacteria; and the archaeal clones could be classified into Crenarchaeota and Thaumarchaeota. Among the major groups, Proteobacteria and Crenarchaeota were dominant in the bacterial and archaeal 16S rRNA gene clone libraries, respectively. The clone sequences obtained in Wuli cold springs were closely related to those from cold habitats, such as snow/ice/soils on high mountains or at high latitude. Especially, the microbial community composition of Wuli Area was more similar to that in Tibetan glaciers than cold environments of other locations. The data presented in this study have impli- cations for a better understanding of microbial diversity in cold springs on the Qinghai-Tibetan Plateau.展开更多
Through a pot experiment, effects of various microbial inoculums on soil microbial diversity and enzyme activity in a typical reclaimed mining area in Shanxi Province were discussed based on quantitative analysis of P...Through a pot experiment, effects of various microbial inoculums on soil microbial diversity and enzyme activity in a typical reclaimed mining area in Shanxi Province were discussed based on quantitative analysis of PLFA, soil urease, phosphatase and sucrase activity. The results showed that the application of microbial inoculums increased microorganism quantity in rhizosphere of rape by 2.3% -66.4%, and quantities of bac- teria, gram-positive bacteria, gram-negative bacteria, fungi and actinomycetes in the treatments with microbial inoculums were significantly higher than the contrast （P 〈0.05）, while there was no obvious change in protist quantity. In comparison with the contrast, the application of various mi- crobial inoculums also improved soil urease, sucrase and phosphatase activity by 4.2% - 61.4%, 18.0% - 32.5% and 64.2% - 199.0% respec- tively. It indicated that the application of microbial inoculums can improve soil microbial diversity and enzyme activity, so it is an effective way to sl^eed UP ecoloQical restoration of soil.展开更多
Saline lakes represent a particularly interesting aquatic environment for harboring high microbial diversity.However,the microbial diversity in different states and locations of saline lake is often overlooked.We stud...Saline lakes represent a particularly interesting aquatic environment for harboring high microbial diversity.However,the microbial diversity in different states and locations of saline lake is often overlooked.We studied for the first time the diversity and relative composition of the microbial communities in the Chagan Lake,NE China,and investigated the dif ferences in microbial species and physical and chemical factors in different geographical localities of the lake.After extracting the total DNA of the sample,we tested the library with the established library,sequenced the qualified library with Illumina HiSeq 2500,and studied the bacterial diversity by 16 S rRNA targeted metagenomics analysis.Results reveal that the highest microbial abundance in Chagan Lake at genus level was Proteobacterium followed by Actinomycetes and Bacteroides.In addition,we compared the microbial composition within the lake using alpha-and beta-diversity indices,showing that both diversity and evenness were the highest in the middle of the lake and lowest in the west of lake areas,and in the upper,middle,and lower depth of water columns,the low water column had the highest species number in the whole water environment,but the dif ference was not significant.We believe that physicochemical factors contribute to the formation of microbial community composition and diversity.In aquaculture industry,it is impossible apply horticulture for making full use of the spatial dif ferences in the microbial composition of the water.Therefore,combining cultured aquatic animal with the most suitable microbial species is a good way to boost the breeding ef fect for greater economic value.展开更多
Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier t...Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier transform infrared(FTIR),X-ray powder diffraction(XRD)and 16S rDNA high-throughput sequence analyses were used to reveal the microbial changes in planktonic and sessile phases during bioleaching.The results showed the occupation of sessile cells decreased from 66.2%to(10±3)%.After bioleaching,the planktonic and sessile cells have similar EPS,but they are different from the original cells.Pyrite dissolution mainly occurs at the early and late stages with the decreasing of particle diameter,by 50%and 40%,respectively.The 16S rDNA gene based sequence analysis results in total of 1117420 Reads across the six samples,presented among 7 phyla,9 classes,17 orders,23 families and 31 genera.Genera Leptospirillum and Sulfobacillus are the main bacteria at the early and middle stages,and Leptospirillum is the main genus at the end of bioleaching.Aquabacterium and Acidovorax are special genera in sessile cells and Weissella is special in planktonic ones.展开更多
This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems（CWs）. Our aim was to assess the impact of configuration on treatment performance...This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems（CWs）. Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100 g BOD5/（m2·day）, similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus（P）, the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10 g P/（m2·day） based on the performance results obtained within the first16 months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance.展开更多
Afforestation has an important role in biodiversity conservation and ecosystem function improvement.A meta-analysis was carried out in China,which has the largest plantation area globally,to quantify the effects of pl...Afforestation has an important role in biodiversity conservation and ecosystem function improvement.A meta-analysis was carried out in China,which has the largest plantation area globally,to quantify the effects of plantings on soil microbial diversity.The results showed that the overall effect of afforestation on soil microbial diversity was positive across the country.Random forest algorithm suggested that soil carbon was the most important factor regulating microbial diversity and the positive response was only found with new plantings on low-carbon bare lands but not on high-carbon farmlands and grasslands.In addition,afforestation with broadleaved species increased microbial diversity,whereas planting with conifers had no effect on microbial diversity.This study clarified the effects of plantings on soil microbial diversity,which has an important implication for establishing appropriate policies and practices to improve the multiple functionalities(e.g.,biodiversity conservation and climate change mitigation)during plantation establishment.展开更多
Using probiotics as animal feed additives instead of antibiotics is gaining momentum to avert adverse negative effects on human health. Liquid brewers yeast (LBY) is an industrial by-product containing probiotic micro...Using probiotics as animal feed additives instead of antibiotics is gaining momentum to avert adverse negative effects on human health. Liquid brewers yeast (LBY) is an industrial by-product containing probiotic microorganisms and is also used as a protein supplement for dairy animals. Nevertheless, value chain actors lack of appropriate handling practices compromises the by-products quality and safety. This study aimed to determine the effect of variation in temperature on microbial diversity and probiotic effects during the storage time of LBY sampled from distributors and farmers from Githunguri sub-county of Kenya. The samples were stored at 20C, 25C and 30C, then tested on 0, 5, 10, 15 and 20 days. The studys parameters involved determining the pH levels, lactic acid bacteria (LAB), total coliform count (TCC), mould, and yeast in LBY. The rate (k) of the reaction kinetics model was used to extrapolate the expected probiotic shelf life. The LAB and yeast populations were reduced in a first-order reaction at all storage temperatures. The rate of reduction in the numbers of LAB reduced with an increase in temperature (k = 0.019 and 0.023) at 20C and 30C, respectively. Yeasts highest rate of growth reduction was 25C (k = 0.009) and least at 30C (k = 0.043). The minimum effective concentration for probiotics of 106 CFU/mL needed to observe the beneficial physiological impact on farm animals was achieved between 34.9 and 35.5 days at the tested storage temperatures. The study provides insight into the unexploited low-cost probiotic potential of LBY in dairy production. Conversely, handling practices and environmental microbial contamination along the value chain can compromise product quality and safety. There is a need to advocate its use in dairy for improved productivity and sensitize farmers to appropriate hygienic measures along the LBY value chain.展开更多
Fumigation is a widely applied approach to mitigate the soil-borne diseases.However,the potential effects of currently applied fumigants on ammonification remain unclear.An 84-day incubation experiment was conducted b...Fumigation is a widely applied approach to mitigate the soil-borne diseases.However,the potential effects of currently applied fumigants on ammonification remain unclear.An 84-day incubation experiment was conducted based on non-fumigated soil(CK)and fumigated soil using three common fumigants,i.e.,chloropicrin(CP),1,3-dichloropropene(1,3-D),and metam sodium(MS).The results showed that,the three fumigants all decreased the microbial C,and the largest reduction(84.7%)occurred with the application of CP.After fumigation,the microbial diversity in the CP treatment rapidly recovered,but that in the 1,3-D treatment decreased and did not recover by the end of the experiment.The application of MS showed no impact on the microbial diversity during the assay,indicating that significantly different microbial diversity can be achieved by choosing different fumigants.Futhermore,the three fumigants showed divergent effects on the enzymes involved in ammonification.The analysis showed that the enzyme variation with CP application was mainly associated with the changed microbial C and N(P<0.05),and not with the microbial community,which was different from the observed effects of 1,3-D or MS application.In addition,the soil quality index showed that CP was still significantly harmful at the end of incubation compared with the good resilience of MS,indicating that CP may not be a suitable fumigant.展开更多
A positive biodiversity-ecosystem functioning(BEF)relationship is frequently reported for biotic communities with low diversity levels.However,whether this is also true for highly diverse soil microbial communities re...A positive biodiversity-ecosystem functioning(BEF)relationship is frequently reported for biotic communities with low diversity levels.However,whether this is also true for highly diverse soil microbial communities remains unclear.The study explored the BEF relationships between species richness and nitrogen(N)-transforming capability of nirK-and nirS-nitrite reducers,nitrous oxide reducers,and nitrite oxidizer communities in soils from five different vegetation types.The results consistently indicated negative BEF patterns in these N-transforming microbes.The relative abundance of keystone taxa from co-occurrence networks increased substantially with species richness but was negatively correlated with functional performance.Network complexity decreased in communities with high species richness.These findings suggest that negative selection and biotic competition may simultaneously generate negative BEF patterns.A conceptual model was also proposed in which the BEF relationship followed a quadratic curve that varied with the level of diversity.Microbial diversity is crucial for maintaining the balance of ecological systems because microorganisms play key roles in nutrient cycling and other essential biogeochemical processes.Recent studies have shown that increased diversity may not always lead to improved ecosystem function.The current study indicated that function decreased with species richness in soil Ntransforming bacterial communities.Keystone taxa were positively correlated with species richness but negatively correlated with function.Community complexity decreased with increasing species richness.These findings suggest that both negative selection effects and biotic competition may simultaneously generate negative biodiversity-ecosystem functional relationships.展开更多
Many alpine ecosystems are undergoing vegetation degradation because of global changes,which are affecting ecosystem functioning and biodiversity.The ecological consequences of alpine pioneer community degradation hav...Many alpine ecosystems are undergoing vegetation degradation because of global changes,which are affecting ecosystem functioning and biodiversity.The ecological consequences of alpine pioneer community degradation have been less studied than glacial retreat or meadow degradation in alpine ecosystems.We document the comprehensive responses of microbial community characteristics to degradation processes using field-based sampling,conduct soil microcosm experiments to simulate the effects of global change on microorganisms,and explore their relationships to ecosystem functioning across stages of alpine pioneer community degradation.Our work provides the first evidence that alpine pioneer community degradation led to declines of 27%in fungal richness,8%in bacterial richness,and about 50%in endemic microorganisms.As vegetation degraded,key ecosystem functions such as nutrient availability,soil enzymatic activity,microbial biomass,and ecosystem multifunctionality progressively increased.However,soil respiration rate and carbon storage exhibited unbalanced dynamics.Respiration rate increased by 190%during the middle stage of degradation compared with the primary stage,and it decreased by 38%in the later stage.This indicates that soil carbon loss or emission increases during the mid-successional stage,whereas in later successional stages,alpine meadows become significant carbon sinks.Compared with microbial community characteristics(such as richness of total and functional taxa,and network complexity),community resistance contributes more significantly to ecosystem functions.Especially,the bacterial community resistance is crucial for ecosystem functioning,yet it is greatly impaired by nitrogen addition.Based on microbial network,community assembly,and community resistance analyses,we conclude that fungi are more vulnerable to environmental changes and show smaller contributions to ecosystem functions than bacteria in degrading alpine ecosystems.Our findings enhance the knowledge of the distinct and synergistic functional contributions of microbial communities in degrading alpine ecosystems and offer guidance for developing restoration strategies that optimize ecosystem functioning of degraded alpine plant communities.展开更多
Objectives:This study aims to isolate biocontrol microorganisms that inhibit Penicillium crustosum and explore their effects on microbial control and microbial diversity changes in P.crustosum causing postharvest deca...Objectives:This study aims to isolate biocontrol microorganisms that inhibit Penicillium crustosum and explore their effects on microbial control and microbial diversity changes in P.crustosum causing postharvest decay in Orah.Materials and Methods:The biocontrol effect was verified by confrontation experiments.The microbial diversity was analyzed using highthroughput sequencing technology.Metabolomic analysis was performed using liquid chromatography-tandem mass spectrometry(LC-MS/MS).Results:A strain of Meyerozyma guilliermondii PJ15 that strongly inhibited P.crustosum was isolated from the grape surface,which could effectively inhibit the mycelial growth and green spore production of P.crustosum.PJ15 could reduce the sourness and nutrient loss of Orah caused by P.crustosum.Compared with the control,PJ15 treatment increased the pH by 11.32%,the soluble protein content by 163.64%,the ascorbic acid content by 160.84%,and the total soluble sugar content by 203.53%.Microbial diversity analysis showed that PJ15 has a relatively small effect on the bacterial composition and diversity on the surface of Orah but has a significant impact on the fungal composition and diversity.It can increase the fungal diversity of Orah invaded by P.crustosum,increase the density of fungal interaction networks,and form a stronger coexisting survival interaction network.The vaccination of PJ15 downregulated the differential metabolite 5,6-epoxytetraene,which showed a positive correlation with P.crustosum and a negative correlation with PJ15.Conclusions:Meyerozyma guilliermondii PJ15 has a strong inhibitory effect on the growth of P.crustosum and has a significant impact on the fungal composition and diversity on the surface of Orah.It has potential for biocontrol of P.crustosum causing postharvest decay in Orah.展开更多
This investigation aims to delineate the spatial distribution,prevalence,and diversity of antibiotic resistance genes(ARGs)within aquatic ecosystems across four coastal aquaculture zones in Hainan Province—Danzhou,Wa...This investigation aims to delineate the spatial distribution,prevalence,and diversity of antibiotic resistance genes(ARGs)within aquatic ecosystems across four coastal aquaculture zones in Hainan Province—Danzhou,Wanning,Wenchang,and Sanya.It further assesses the impact of environmental parameters on ARGs dissemination and microbial community structure.High-throughput sequencing was utilized to analyze water samples from 42 sampling sites,complemented by absolute quantitative PCR to quantify 144 ARGs variants.This approach elucidated correlations between ARGs and microbial assemblages,as well as the influence of environmental factors on these interactions.Results indicated that the number of ARGs detected per site ranged from 61 to 123,with Danzhou exhibiting 90 to 123,Wanning 74 to 123,Wenchang 68 to 122,and Sanya 61 to 109 ARGs.Notably,16 sampling points harbored over 110 ARGs.Quantitative analysis revealed ARG concentrations ranging from 16,167 to 1,784,618 copies/ng.Co-occurrence network analysis demonstrated that most ARGs were associated with MGEs,16S rRNA genes,transposons,and integrons,indicating these elements'critical role in horizontal gene transfer.Microbial community profiling identified 27,050 operational taxonomic units(OTUs)across 72 phyla,153 classes,371 orders,459 families,and 924 genera,with Proteobacteria,Bacteroidota,Actinobacteriota,Cyanobacteria,and Planctomycetota as dominant taxa.Genus-level analysis revealed significant variations in the abundance of taxa such as Cyanobium_PCC-6307,Candidatus_Actinomarina,and HIMB11 across sampling sites.Environmental parameters,including pH,dissolved oxygen(DO),specific conductance(SPC),salinity(SAL),temperature(T),and pressure(kPa),showed strong correlations with ARG distribution and microbial community composition.Region-specific colinearity networks indicated distinct relationships between microbial taxa and ARGs;notably,Danzhou and Wanning exhibited strong correlations with over 20 ARGs per genus,whereas Wenchang displayed a more complex association pattern,suggesting a multifaceted role in ARG transmission pathways.Overall,the findings suggest that environmental factors and microbial hosts significantly influence ARG prevalence in Hainan's coastal waters,with regional variations in microbial-ARG interactions,particularly in Wenchang,indicating heightened transmission risks.This study offers vital insights for sustainable aquaculture practices and informs regional regulatory strategies for aquaculture management.展开更多
Soil microbial alpha diversity is essential for driving ecosystem functions and processes.However,little is known about the beta-diversity affect community functions.Here,we combine distinct community inocula using th...Soil microbial alpha diversity is essential for driving ecosystem functions and processes.However,little is known about the beta-diversity affect community functions.Here,we combine distinct community inocula using the dilution-to-extinction approach with two wheat genotypes to study the effect of microbial diversity loss on rhizosphere community assembly processes,which are related to beta-diversity(between-habitat diversity),and the consequences for ecosystem functions within greenhouse experiment.Compared with alpha-diversity,the bacterial and fungal community beta-diversity are stronger predictors of ecosystem functions(organic matter degradation,phosphorus supply capacity and nitrogen supply capacity),plant genotypes regulated the relationship between microbial diversity and ecosystem functions,with ecosystem functions being significant link to microbial diversity under different wheat genotypes.Loss of microbial diversity decreased the abundance of Bacterial_ASV6(Burkholderia)and increased Fungal_11(Altemaria)within the restored rhizosphere soil.Null modeling analysis showed that the deterministic assembly processes are dominant in bacterial community and fungal high-diversity(alpha-diversity)community,associating with the change of specialized functions(organic matter degradation,phosphorus supply capacity and nitrogen supply capacity)that are correlated with microbial diversity and specific microbial taxa.In addition,these two species were key role for regulating to the network cohesion.Overall,our study pointed out that the regulation of community assembly by microbial diversity loss limits the development of soil ecological functions and weakens the stability of rhizosphere microbial network,highlighting the potential regulatory effect of microbial taxa distribution on microbial community stability and changes of specific ecological functions.展开更多
基金supported by the Shanghai Frontiers Science Center of Polar Science(Grant no.SOO2024-04)the National Natural Science Foundation of China(Grant no.42476264)Lanzhou University(Grant no.lzuibky-2024-oy01).
文摘Antarctic ice-free areas(<0.4%of the continent)represent Antarctic biodiversity oases,where microbial communities sustain terrestrial ecosystem functions.These habitats-encompassing mineral,ornithogenic soils,biological soil crusts,and hypolithic/endolithic niches-are shaped by environmental factors such as pH,organic C/N ratios,moisture,elevation,and trace element availability.The diversity of prokaryotes,eukaryotes,and viruses is lower than in other regions,yet the communities exhibit strong endemism,with site-specific uncultivated lineages.Microorganisms persist through cold and stress adaptations,performing organic carbon decomposition,phototrophy,and oxidation of trace gases to drive carbon and nitrogen cycling in various Antarctic soil habitats.Climate change and anthropogenic disturbances are shifting communities toward copiotrophic generalists,altering elementary cycling and feeding back to climate change.Culturation and genomic-based techniques reveal novel microbial taxa with broad biotechnological potentials on bioactive compounds and cryotolerant enzymes.In summary,this review offers a foundation for exploring Antarctic microbial biodiversity,ecosystem resilience,and the development of novel biotechnologies,while also highlighting the urgent need for effective monitoring and preservation strategies to mitigate the impacts of ongoing environmental changes on Antarctic soil ecosystems.
基金Supported by National Natural Science Foundation of China,No.81273919 and No.81673727National Basic Research Program of China(973 Program)No.2013CB531703
文摘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.
基金supported by grants from Scienceand Technology Committee of Shanghai (18411951400)KeyClinical Medical Specialties Project in Shanghai Pudong NewArea (PWZzk2017-22)+1 种基金Science and Technology Action Plan(19495810200)Leading Talent Project in Shanghai Pudong NewArea Health System (PWRl2018-08).
文摘BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.
基金the National Key R&D Program of China(2017YFD0801304)the National Natural Science Foundation of China(31972943)。
文摘The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting(mesophilic,thermophilic,cooling and maturation phases).In addition,the physicochemical parameters of the composting system were determined in this study.The fermentation time of the thermophilic period was prolonged with the addition of urea or urea combined with a microbial agent.The ratio of C/N and germination index variation indicated that the additives were favorable for composting,because the additives directly changed the physicochemical properties of the compost and had effects on the diversity and abundance of bacteria and fungi.The abundance of operational taxonomic units(OTUs),diversity index(Shannon)and richness index(Chao1)of fungi and bacteria were found to significantly increase when urea+microbial agents were added to straw in the thermophilic phase.The relative abundance of the predominant bacteria and fungi at the phylum and genus levels differed during different composting phases.The abundance of the phyla Firmicutes and Proteobacteria declined in the order of treatments SNW>SN>S(S is straw only compost;SN is straw+5 kg t^(–1) urea compost;and SNW is straw+5 kg t^(–1) urea+1 kg t^(–1) microbial agent compost)in the thermophilic phase.The abundance of the genera Staphylococcus,Bacillus and Thermobifida followed the same order in the mesophilic phase.Ascomycota accounted for more than 92%of the total fungal sequences.With the progression of the composting process,the abundance of Ascomycota decreased gradually.The abundance of Ascomycota followed the order of S>SN>SNW during the thermophilic phase.The abundance of Aspergillus accounted for 4–59%of the total abundance of fungi and increased during the first two sampling periods.Aspergillus abundance followed the order of SNW>SN>S.Additionally,principal component analysis(PCA)revealed that the community compositions in the straw and straw+urea treatments were similar,and that the bacterial communities in treatments S,SN and SNW in the mesophilic phase(at day 1)were different from those observed in three other phases(at days 5,11,and19,respectively),while the fungal communities showed only slight variations in their structure in response to changes in the composting process.Canonical correlation analysis(CCA)and redundancy analysis(RDA)showed that total carbon(TC),NO_(3)^(–)-N(NN),electrical conductivity(EC)and p H were highly correlated with community composition.Therefore,this study highlights that the additives are beneficial to straw composting and result in good quality compost.
基金supported by the National Program on Key Basic Research Project(973 Program)(Grant No.2009CB219502)National Special Foundation(Grant No.GZH200200203-02-01)Non-profit Industry Financial Program of Ministry of Land and Resources of the PRC(Grant No.200811014-02)
文摘South China Sea （SCS） is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, ＂SONNE＂ 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diver- sity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abun- dance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment （wet weight）. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diver- sity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(Nos.2006AA100311,2008AA100805)
文摘In this study,the intestinal microbiota of kuruma shrimp(Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp.on intestinal microbial diversity.Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp.amended feed.PCR and denaturing gradient gel electrophoresis(DGGE) analyses were then performed on DNA extracted directly from the guts.Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons,and distinct bands in the gels were sequenced.The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp.and uncultured gamma proteobacterium.Overall,the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.
文摘In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types （genera and/or species）. They included Polyangium spp., Sphingomonas spp., Variovorax spp., Hafina spp., Clostridia, Acidobacteria, the enterics and some uncultured strains. Microbes able to tolerate high concentrations of cadmium （500μmol/L and above） were also isolated from the soil. These isolates included strains of Acinetobacter （strain CD06）, Enterobacter sp. （strains CD01, CD03, CD04 and CD08） （similar strains also identified in culture-independent approach） and a strain of Stenotrophomonas sp. The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment cultures and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.
基金supported by grants from National Science Foundation of China(Grant Nos.41030211 and 41002123)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Edncation Ministry,Research Fund for the Doctoral Program of Higher Education of China(Grant No. 20100022120009)+1 种基金the Fundamental Research Funds for the Central Universities(Grant Nos.2010ZY16 and 2011YXL03)the Teaching Laboratory Funds from China University of Geosciences,Beijing
文摘The microbial diversity in Wuli Area, Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses. A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold springs, The bacterial clones could be classified into Proteobacteria, Acid- obacteria, Deinococci, Sphingobacteria, Flavobacteria, Nitrospirae, Actinobacteria, Gemmatimona- detes, and unclassified-bacteria; and the archaeal clones could be classified into Crenarchaeota and Thaumarchaeota. Among the major groups, Proteobacteria and Crenarchaeota were dominant in the bacterial and archaeal 16S rRNA gene clone libraries, respectively. The clone sequences obtained in Wuli cold springs were closely related to those from cold habitats, such as snow/ice/soils on high mountains or at high latitude. Especially, the microbial community composition of Wuli Area was more similar to that in Tibetan glaciers than cold environments of other locations. The data presented in this study have impli- cations for a better understanding of microbial diversity in cold springs on the Qinghai-Tibetan Plateau.
基金Supported by the International Science and Technology Cooperation Program of China(2011DFR31230)Major Science and Technology Project of Shanxi Province,China(20121101009)Key Project of Shanxi Academy of Agricultural Sciences,China(2013zd12)
文摘Through a pot experiment, effects of various microbial inoculums on soil microbial diversity and enzyme activity in a typical reclaimed mining area in Shanxi Province were discussed based on quantitative analysis of PLFA, soil urease, phosphatase and sucrase activity. The results showed that the application of microbial inoculums increased microorganism quantity in rhizosphere of rape by 2.3% -66.4%, and quantities of bac- teria, gram-positive bacteria, gram-negative bacteria, fungi and actinomycetes in the treatments with microbial inoculums were significantly higher than the contrast （P 〈0.05）, while there was no obvious change in protist quantity. In comparison with the contrast, the application of various mi- crobial inoculums also improved soil urease, sucrase and phosphatase activity by 4.2% - 61.4%, 18.0% - 32.5% and 64.2% - 199.0% respec- tively. It indicated that the application of microbial inoculums can improve soil microbial diversity and enzyme activity, so it is an effective way to sl^eed UP ecoloQical restoration of soil.
基金Supported by the National Natural Sciences Foundational of China(No.30972191)the 948 Program from the Ministry of Agriculture of China(No.2014Z34)
文摘Saline lakes represent a particularly interesting aquatic environment for harboring high microbial diversity.However,the microbial diversity in different states and locations of saline lake is often overlooked.We studied for the first time the diversity and relative composition of the microbial communities in the Chagan Lake,NE China,and investigated the dif ferences in microbial species and physical and chemical factors in different geographical localities of the lake.After extracting the total DNA of the sample,we tested the library with the established library,sequenced the qualified library with Illumina HiSeq 2500,and studied the bacterial diversity by 16 S rRNA targeted metagenomics analysis.Results reveal that the highest microbial abundance in Chagan Lake at genus level was Proteobacterium followed by Actinomycetes and Bacteroides.In addition,we compared the microbial composition within the lake using alpha-and beta-diversity indices,showing that both diversity and evenness were the highest in the middle of the lake and lowest in the west of lake areas,and in the upper,middle,and lower depth of water columns,the low water column had the highest species number in the whole water environment,but the dif ference was not significant.We believe that physicochemical factors contribute to the formation of microbial community composition and diversity.In aquaculture industry,it is impossible apply horticulture for making full use of the spatial dif ferences in the microbial composition of the water.Therefore,combining cultured aquatic animal with the most suitable microbial species is a good way to boost the breeding ef fect for greater economic value.
基金Project(U1608254)supported by the Special Fund for the National Natural Science Foundation of ChinaProjects(ZJKY2017(B)KFJJ01,ZJKY2017(B)KFJJ02)supported by the Zijin Mining Group Co.,Ltd.,China。
文摘Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier transform infrared(FTIR),X-ray powder diffraction(XRD)and 16S rDNA high-throughput sequence analyses were used to reveal the microbial changes in planktonic and sessile phases during bioleaching.The results showed the occupation of sessile cells decreased from 66.2%to(10±3)%.After bioleaching,the planktonic and sessile cells have similar EPS,but they are different from the original cells.Pyrite dissolution mainly occurs at the early and late stages with the decreasing of particle diameter,by 50%and 40%,respectively.The 16S rDNA gene based sequence analysis results in total of 1117420 Reads across the six samples,presented among 7 phyla,9 classes,17 orders,23 families and 31 genera.Genera Leptospirillum and Sulfobacillus are the main bacteria at the early and middle stages,and Leptospirillum is the main genus at the end of bioleaching.Aquabacterium and Acidovorax are special genera in sessile cells and Weissella is special in planktonic ones.
文摘This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems（CWs）. Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100 g BOD5/（m2·day）, similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus（P）, the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10 g P/（m2·day） based on the performance results obtained within the first16 months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance.
基金supported by the National Key Research and Development Program of China(2021YFD2200401)the National Natural Science Foundation of China(31901293)。
文摘Afforestation has an important role in biodiversity conservation and ecosystem function improvement.A meta-analysis was carried out in China,which has the largest plantation area globally,to quantify the effects of plantings on soil microbial diversity.The results showed that the overall effect of afforestation on soil microbial diversity was positive across the country.Random forest algorithm suggested that soil carbon was the most important factor regulating microbial diversity and the positive response was only found with new plantings on low-carbon bare lands but not on high-carbon farmlands and grasslands.In addition,afforestation with broadleaved species increased microbial diversity,whereas planting with conifers had no effect on microbial diversity.This study clarified the effects of plantings on soil microbial diversity,which has an important implication for establishing appropriate policies and practices to improve the multiple functionalities(e.g.,biodiversity conservation and climate change mitigation)during plantation establishment.
文摘Using probiotics as animal feed additives instead of antibiotics is gaining momentum to avert adverse negative effects on human health. Liquid brewers yeast (LBY) is an industrial by-product containing probiotic microorganisms and is also used as a protein supplement for dairy animals. Nevertheless, value chain actors lack of appropriate handling practices compromises the by-products quality and safety. This study aimed to determine the effect of variation in temperature on microbial diversity and probiotic effects during the storage time of LBY sampled from distributors and farmers from Githunguri sub-county of Kenya. The samples were stored at 20C, 25C and 30C, then tested on 0, 5, 10, 15 and 20 days. The studys parameters involved determining the pH levels, lactic acid bacteria (LAB), total coliform count (TCC), mould, and yeast in LBY. The rate (k) of the reaction kinetics model was used to extrapolate the expected probiotic shelf life. The LAB and yeast populations were reduced in a first-order reaction at all storage temperatures. The rate of reduction in the numbers of LAB reduced with an increase in temperature (k = 0.019 and 0.023) at 20C and 30C, respectively. Yeasts highest rate of growth reduction was 25C (k = 0.009) and least at 30C (k = 0.043). The minimum effective concentration for probiotics of 106 CFU/mL needed to observe the beneficial physiological impact on farm animals was achieved between 34.9 and 35.5 days at the tested storage temperatures. The study provides insight into the unexploited low-cost probiotic potential of LBY in dairy production. Conversely, handling practices and environmental microbial contamination along the value chain can compromise product quality and safety. There is a need to advocate its use in dairy for improved productivity and sensitize farmers to appropriate hygienic measures along the LBY value chain.
基金Supported by the National Key Research and Development Program of China(2018YFD0300505)the National Key Technologies Project of China in Urban Agriculture during the 12th Five-Year Plan(2014BAD14B03).
文摘Fumigation is a widely applied approach to mitigate the soil-borne diseases.However,the potential effects of currently applied fumigants on ammonification remain unclear.An 84-day incubation experiment was conducted based on non-fumigated soil(CK)and fumigated soil using three common fumigants,i.e.,chloropicrin(CP),1,3-dichloropropene(1,3-D),and metam sodium(MS).The results showed that,the three fumigants all decreased the microbial C,and the largest reduction(84.7%)occurred with the application of CP.After fumigation,the microbial diversity in the CP treatment rapidly recovered,but that in the 1,3-D treatment decreased and did not recover by the end of the experiment.The application of MS showed no impact on the microbial diversity during the assay,indicating that significantly different microbial diversity can be achieved by choosing different fumigants.Futhermore,the three fumigants showed divergent effects on the enzymes involved in ammonification.The analysis showed that the enzyme variation with CP application was mainly associated with the changed microbial C and N(P<0.05),and not with the microbial community,which was different from the observed effects of 1,3-D or MS application.In addition,the soil quality index showed that CP was still significantly harmful at the end of incubation compared with the good resilience of MS,indicating that CP may not be a suitable fumigant.
基金supported by the Central Public-Interest Scientific Institution Basal Research Fund(Grant No.CAFYBB2019QB001)the National Key R&D Fund(Grant No.2023YFF130440302)the Natural Science Foundation of China(Grant No.31870099).
文摘A positive biodiversity-ecosystem functioning(BEF)relationship is frequently reported for biotic communities with low diversity levels.However,whether this is also true for highly diverse soil microbial communities remains unclear.The study explored the BEF relationships between species richness and nitrogen(N)-transforming capability of nirK-and nirS-nitrite reducers,nitrous oxide reducers,and nitrite oxidizer communities in soils from five different vegetation types.The results consistently indicated negative BEF patterns in these N-transforming microbes.The relative abundance of keystone taxa from co-occurrence networks increased substantially with species richness but was negatively correlated with functional performance.Network complexity decreased in communities with high species richness.These findings suggest that negative selection and biotic competition may simultaneously generate negative BEF patterns.A conceptual model was also proposed in which the BEF relationship followed a quadratic curve that varied with the level of diversity.Microbial diversity is crucial for maintaining the balance of ecological systems because microorganisms play key roles in nutrient cycling and other essential biogeochemical processes.Recent studies have shown that increased diversity may not always lead to improved ecosystem function.The current study indicated that function decreased with species richness in soil Ntransforming bacterial communities.Keystone taxa were positively correlated with species richness but negatively correlated with function.Community complexity decreased with increasing species richness.These findings suggest that both negative selection effects and biotic competition may simultaneously generate negative biodiversity-ecosystem functional relationships.
基金supported by the Yunnan Applied Basic Research Project(202401CF070057)the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)+4 种基金the National Natural Science Foundation of China(32171552)the Preparatory Talents for Yunnan Middle-Age and Young Academic&Technology Champions Project(202205AC160053)Yunnan Revitalization Talent Support Program“Young Talent”ProjectIntroducing talents start-up fund of Kunming Institute of Botany,Chinese Academy of SciencesYunnan Caiyun Postdoctor Program。
文摘Many alpine ecosystems are undergoing vegetation degradation because of global changes,which are affecting ecosystem functioning and biodiversity.The ecological consequences of alpine pioneer community degradation have been less studied than glacial retreat or meadow degradation in alpine ecosystems.We document the comprehensive responses of microbial community characteristics to degradation processes using field-based sampling,conduct soil microcosm experiments to simulate the effects of global change on microorganisms,and explore their relationships to ecosystem functioning across stages of alpine pioneer community degradation.Our work provides the first evidence that alpine pioneer community degradation led to declines of 27%in fungal richness,8%in bacterial richness,and about 50%in endemic microorganisms.As vegetation degraded,key ecosystem functions such as nutrient availability,soil enzymatic activity,microbial biomass,and ecosystem multifunctionality progressively increased.However,soil respiration rate and carbon storage exhibited unbalanced dynamics.Respiration rate increased by 190%during the middle stage of degradation compared with the primary stage,and it decreased by 38%in the later stage.This indicates that soil carbon loss or emission increases during the mid-successional stage,whereas in later successional stages,alpine meadows become significant carbon sinks.Compared with microbial community characteristics(such as richness of total and functional taxa,and network complexity),community resistance contributes more significantly to ecosystem functions.Especially,the bacterial community resistance is crucial for ecosystem functioning,yet it is greatly impaired by nitrogen addition.Based on microbial network,community assembly,and community resistance analyses,we conclude that fungi are more vulnerable to environmental changes and show smaller contributions to ecosystem functions than bacteria in degrading alpine ecosystems.Our findings enhance the knowledge of the distinct and synergistic functional contributions of microbial communities in degrading alpine ecosystems and offer guidance for developing restoration strategies that optimize ecosystem functioning of degraded alpine plant communities.
基金funded by the Guangxi Key Research and Development Program(No.2021AB26001)The Central Government Guides Local Science and Technology Development Funds(No.2020ZYZX3027).
文摘Objectives:This study aims to isolate biocontrol microorganisms that inhibit Penicillium crustosum and explore their effects on microbial control and microbial diversity changes in P.crustosum causing postharvest decay in Orah.Materials and Methods:The biocontrol effect was verified by confrontation experiments.The microbial diversity was analyzed using highthroughput sequencing technology.Metabolomic analysis was performed using liquid chromatography-tandem mass spectrometry(LC-MS/MS).Results:A strain of Meyerozyma guilliermondii PJ15 that strongly inhibited P.crustosum was isolated from the grape surface,which could effectively inhibit the mycelial growth and green spore production of P.crustosum.PJ15 could reduce the sourness and nutrient loss of Orah caused by P.crustosum.Compared with the control,PJ15 treatment increased the pH by 11.32%,the soluble protein content by 163.64%,the ascorbic acid content by 160.84%,and the total soluble sugar content by 203.53%.Microbial diversity analysis showed that PJ15 has a relatively small effect on the bacterial composition and diversity on the surface of Orah but has a significant impact on the fungal composition and diversity.It can increase the fungal diversity of Orah invaded by P.crustosum,increase the density of fungal interaction networks,and form a stronger coexisting survival interaction network.The vaccination of PJ15 downregulated the differential metabolite 5,6-epoxytetraene,which showed a positive correlation with P.crustosum and a negative correlation with PJ15.Conclusions:Meyerozyma guilliermondii PJ15 has a strong inhibitory effect on the growth of P.crustosum and has a significant impact on the fungal composition and diversity on the surface of Orah.It has potential for biocontrol of P.crustosum causing postharvest decay in Orah.
文摘This investigation aims to delineate the spatial distribution,prevalence,and diversity of antibiotic resistance genes(ARGs)within aquatic ecosystems across four coastal aquaculture zones in Hainan Province—Danzhou,Wanning,Wenchang,and Sanya.It further assesses the impact of environmental parameters on ARGs dissemination and microbial community structure.High-throughput sequencing was utilized to analyze water samples from 42 sampling sites,complemented by absolute quantitative PCR to quantify 144 ARGs variants.This approach elucidated correlations between ARGs and microbial assemblages,as well as the influence of environmental factors on these interactions.Results indicated that the number of ARGs detected per site ranged from 61 to 123,with Danzhou exhibiting 90 to 123,Wanning 74 to 123,Wenchang 68 to 122,and Sanya 61 to 109 ARGs.Notably,16 sampling points harbored over 110 ARGs.Quantitative analysis revealed ARG concentrations ranging from 16,167 to 1,784,618 copies/ng.Co-occurrence network analysis demonstrated that most ARGs were associated with MGEs,16S rRNA genes,transposons,and integrons,indicating these elements'critical role in horizontal gene transfer.Microbial community profiling identified 27,050 operational taxonomic units(OTUs)across 72 phyla,153 classes,371 orders,459 families,and 924 genera,with Proteobacteria,Bacteroidota,Actinobacteriota,Cyanobacteria,and Planctomycetota as dominant taxa.Genus-level analysis revealed significant variations in the abundance of taxa such as Cyanobium_PCC-6307,Candidatus_Actinomarina,and HIMB11 across sampling sites.Environmental parameters,including pH,dissolved oxygen(DO),specific conductance(SPC),salinity(SAL),temperature(T),and pressure(kPa),showed strong correlations with ARG distribution and microbial community composition.Region-specific colinearity networks indicated distinct relationships between microbial taxa and ARGs;notably,Danzhou and Wanning exhibited strong correlations with over 20 ARGs per genus,whereas Wenchang displayed a more complex association pattern,suggesting a multifaceted role in ARG transmission pathways.Overall,the findings suggest that environmental factors and microbial hosts significantly influence ARG prevalence in Hainan's coastal waters,with regional variations in microbial-ARG interactions,particularly in Wenchang,indicating heightened transmission risks.This study offers vital insights for sustainable aquaculture practices and informs regional regulatory strategies for aquaculture management.
文摘Soil microbial alpha diversity is essential for driving ecosystem functions and processes.However,little is known about the beta-diversity affect community functions.Here,we combine distinct community inocula using the dilution-to-extinction approach with two wheat genotypes to study the effect of microbial diversity loss on rhizosphere community assembly processes,which are related to beta-diversity(between-habitat diversity),and the consequences for ecosystem functions within greenhouse experiment.Compared with alpha-diversity,the bacterial and fungal community beta-diversity are stronger predictors of ecosystem functions(organic matter degradation,phosphorus supply capacity and nitrogen supply capacity),plant genotypes regulated the relationship between microbial diversity and ecosystem functions,with ecosystem functions being significant link to microbial diversity under different wheat genotypes.Loss of microbial diversity decreased the abundance of Bacterial_ASV6(Burkholderia)and increased Fungal_11(Altemaria)within the restored rhizosphere soil.Null modeling analysis showed that the deterministic assembly processes are dominant in bacterial community and fungal high-diversity(alpha-diversity)community,associating with the change of specialized functions(organic matter degradation,phosphorus supply capacity and nitrogen supply capacity)that are correlated with microbial diversity and specific microbial taxa.In addition,these two species were key role for regulating to the network cohesion.Overall,our study pointed out that the regulation of community assembly by microbial diversity loss limits the development of soil ecological functions and weakens the stability of rhizosphere microbial network,highlighting the potential regulatory effect of microbial taxa distribution on microbial community stability and changes of specific ecological functions.
