Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how woul...Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how would bacterial interaction influence the bacterial communities in permafrost of the Qinghai-Tibet Plateau(QTP)remains largely unknown.Here we collected paired soil samples from both the active and permafrost layers of two typical QTP permafrost regions in October 2020 for Tuotuohe River(TTH)and May 2022 for Aerjin(ARJ),and investigated the bacterial communities and the role of interactions in structuring the bacterial community and its assembly process through amplicon sequencing of the 16S rRNA gene.Our study revealed distinct bacterial communities,with significant differences in the relative abundances of Proteobacteria(P<0.05),Acidobacteriota(P<0.001),Bacteroidota(P<0.05),and Planctomycetota(P<0.001)between the active layer and the permafrost layer.More importantly,we found that interspecies interactions,including both positive and negative associations,were strongly correlated with bacterial alpha-diversity and played a significant role in community variation and assembly process.Our findings also showed that the community assembly in both the active and permafrost layers was primarily driven by homogeneous selection of deterministic processes,with interspecies interactions accounting for more than 58%and 63%of all assembly mechanisms,respectively.This is the first study to quantify the contribution of bacterial interactions in shaping the bacterial community and its assembly process in permafrost of QTP,highlighting the importance of considering interspecies interactions in future modeling efforts.Our work also emphasizes the necessity of including interspecies interactions in microbial process projections to reduce uncertainty.展开更多
Coral gardening has become a promising technique for restoring reefs worldwide in the Anthropocene era.The microbiome plays an important role in enhancing adaptive resilience in situ nursery propagation of corals.Howe...Coral gardening has become a promising technique for restoring reefs worldwide in the Anthropocene era.The microbiome plays an important role in enhancing adaptive resilience in situ nursery propagation of corals.However,little is known about the response patterns of bacterial community dynamics,co-occurrence networks and assembly processes of different species in coral restoration nurseries over time.Here,we collected two Acropora coral samples from transplanted fragments and source colonies at 1-month and 3-month post-transplantation(May and July 2022)in an upwelling-affected fragmented reef.Full-length 16S rRNA gene sequencing revealed that bacterial communities of coral fragments in nurseries exhibited consistent temporal shifts compared to those of the source colonies.High host specificity was observed in the bacterial community and network structure associated with source colonies.In contrast,for the two coral species within nurseries,there were no differences in bacterial diversity,composition and core microbiome.Stochastic assembly processes were identified as the primary drivers of bacterial communities in all May samples,whereas deterministic processes played a more prominent role in July.Seawater properties(e.g.,temperature and ammonium concentration)partially explained the compositional changes in the bacterial communities of these coral samples.Our findings suggested that coral nurseries contributed to the homogenization of bacterial communities in different Acropora corals,despite the apparent temporal dynamics of bacteria.These results enhance our understanding of the coral microbiome,ecological interactions and assembly principles in different host within in situ nurseries.展开更多
Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of ...Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of soil bacterial community diversity to the changes of environmental factors in different habitats,this study collected soil samples under the canopies of Tamarix ramosissima Ledeb.in oasis,transition zone,and desert habitats in the upper reaches of the Tarim River,Northwest China.High-throughput sequencing technology and PICRUSt2 software were used to explore the composition and function of soil bacterial communities in different habitats of T.ramosissima.The results showed that:(1)soil environmental factors under the canopy of T.ramosissima in the three habitats differed significantly,with soil moisture and nutrient conditions being better in the oasis;(2)Proteobacteria,Bacteroidetes,Firmicutes,Actinobacteria,and Gemmatimonadetes were the major bacterial communities in the three habitats;(3)soil bacterial community composition under the canopy of T.ramosissima varied greatly,and the richness was significantly different among the three habitats;(4)redundancy analysis indicated that soil water content and available phosphorous were the most important environmental factors influencing the composition of soil bacterial community;and(5)6 primary functions and 21 secondary functions were obtained by PICRUSt2 function prediction,with metabolism being the most dominant function.This study revealed the response of soil bacterial community composition to habitat changes and their driving factors in the upper reaches of the Tarim River,which could improve the understanding of ecological sensitivity of soil microorganisms in arid and semi-arid areas,and provide a theoretical foundation for improving soil quality and ecological protection.展开更多
Rice-fish coculture(RFC)has aroused extensive concern for its contribution to food security and resource conservation,but whether it can improve soil phosphorus(P)availability and affect microbe-mediated P turnover re...Rice-fish coculture(RFC)has aroused extensive concern for its contribution to food security and resource conservation,but whether it can improve soil phosphorus(P)availability and affect microbe-mediated P turnover remains elusive.Herein,we conducted a microcosm experiment to assess the impacts of RFC combined with(50 mg P kg^(-1)as KH2PO4)and without inorganic P addition on P fractions,P availability,and phoD-harboring bacterial community composition.The results revealed that RFC without P addition significantly improved P availability and phosphatase activity in paddy soil,while soil available P(AP),pH,and microbial biomass P(MBP)contributed to regulating P fractions.Moreover,the phoD-harboring bacterial abundance was linked to phosphatase activity,AP,total carbon(TC),and total P(TP)contents,and the ratios of TC to total nitrogen(TN)and TN to TP.We also found that the keystone taxa of phoD-harboring bacteria contributed to phosphatase production as well as organic P mineralization,thereby improving P availability.Our findings suggest that RFC without P addition is beneficial for promoting the expression of phoD-harboring bacterial functions to improve the capacity of P mineralization.Overall,our study provides insights into the responses of phoD-harboring bacterial functions for P turnover to RFC combined with and without P addition,showing the potential utilization of P resources in agricultural soil and the contribution of phosphatase activity to P acquisition in agriculture ecosystem.展开更多
Bioleaching is confronted with problems,such as low efficiency,long production cycle length,and vegetation destruction.In order to solve problems above,fly ash and low-grade copper sulfide ores were used to investigat...Bioleaching is confronted with problems,such as low efficiency,long production cycle length,and vegetation destruction.In order to solve problems above,fly ash and low-grade copper sulfide ores were used to investigate bioleaching behaviors and bacterial community succession.Results showed that copper recovery,bacterial concentration,total proportion of main leaching bacteria including Acidithiobacillus ferrooxidans,Acidibacillus ferrooxidans,and Leptospirillum ferriphilum,were improved through using appropriate dosage of fly ash.The maximum copper recovery of 79.87%and bacterial concentration of 7.08×10^(7)cells·mL^(-1)were obtained after us-ing 0.8 g·L^(-1)fly ash.Exclusive precipitation including Zn(Fe_(3)(SO_(4))_(2)(OH)_(6))_(2)and Mg(Fe_(3)(SO_(4))_(2)(OH)_(6))_(2)was found in sample added 0.8 g·L^(-1)fly ash,which reduced the effect of hazardous ions on bacteria and thus contributing to bacterial proliferation.Bacterial com-munity structure was differentiated,which indicated difference between original inoculation and sample used 0.8 g·L^(-1)fly ash was less than others.Total proportion of the three microorganism above accounted for more than 95%in all tests,especially in sample with 0.8 g·L^(-1)fly ash up to 99.81%.Cl^(-)and Ag^(+)contained in fly ash can act as catalytic agent,which contributed to conversion from smooth and dense passivation layer to sparse and scattered one,and therefore improving contact between ores,lixiviant,and bacteria.Using appropri-ate dosage of fly ash showed prospects in bioleaching.展开更多
Woodchip bioreactors are an eco-friendly technology for removing nitrogen(N)pollution.However,there needs to be more clarity regarding the dissolved organicmatter(DOM)characteristics and bacterial community succession...Woodchip bioreactors are an eco-friendly technology for removing nitrogen(N)pollution.However,there needs to be more clarity regarding the dissolved organicmatter(DOM)characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors.The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments,and the results showed that the average removal rate of TN was 45.80 g N/(m^(3)·day)when the influent N level was 100 mg N/L,which was better than 10 mg N/L and 50 mg N/L.Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates.Medium to high N levels enriched a copiotroph bacterial module(Module 1)detected by network analysis,including Phenylobacterium,Xanthobacteraceae,Burkholderiaceae,Pseudomonas,and Magnetospirillaceae,carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM.Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophswith fewer N-cycle potentials(Module 2).Together,this study reveals that the compositional change ofDOMand bacterial community succession are closely related to N removal performance,providing an ecological basis for developing techniques for N-rich effluent treatment.展开更多
Plant growth-promoting rhizobacteria(PGPR)have been widely used for the promotion of plant performance.Predatory protists can influence the taxonomic and functional composition of rhizosphere bacteria.However,research...Plant growth-promoting rhizobacteria(PGPR)have been widely used for the promotion of plant performance.Predatory protists can influence the taxonomic and functional composition of rhizosphere bacteria.However,research on the impact of the interaction between protist and PGPR on plant performance remains at a very early stage.Here,we examined the impacts of individual inoculation of protist(Colpoda inflata,Dimastigella trypaniformis,or Vermamoeba vermiformis)or the PGPR strain Bacillus velezensis SQR9 as well as the co-inoculation of the protist C.inflata and B.velezensis SQR9 on the growth of tomato plants.We found that all individual protists and Bacillus could promote plant growth compared to the control with no microbe inoculation,with the co-inoculation of C.inflata and B.velezensis SQR9 achieving the greatest performance,including plant height,fresh weight,and dry weight.Different protists harbored distinct rhizosphere bacterial communities,with the co-inoculation of protist and Bacillus resulting in the lowest bacterial diversity and driving significant changes in community structure and composition,particularly by increasing the relative abundance of Proteobacteria.Random forest model highlighted Cellvibrio as the most important bacterial predictor of plant growth,which was enriched after protist inoculation,especially after the mixed inoculation of protist and Bacillus.We further found that bacterial functional genes of nitrogen metabolism were the key determinants of plant growth.These results indicate that the interaction between protists and Bacillus can support plant growth by reshaping rhizosphere bacterial community composition and function.Understanding the interaction mechanisms between protist and PGPR is crucial for their effective utilization in sustainable agriculture.展开更多
Nitrogen deposition and water tables are important factors to control soil microbial community structure.However,the specific effects and mechanisms of nitrogen deposition and water tables coupling on bacterial divers...Nitrogen deposition and water tables are important factors to control soil microbial community structure.However,the specific effects and mechanisms of nitrogen deposition and water tables coupling on bacterial diversity,abundance,and community structure in arid alpine wetlands remain unclear.The nitrogen deposition(0,10,and 20 kg N/(hm^(2)•a))experiments were conducted in the Bayinbulak alpine wetland with different water tables(perennial flooding,seasonal waterlogging,and perennial drying).The 16S rRNA(ribosomal ribonucleic acid)gene sequencing technology was employed to analyze the changes in bacterial community diversity,network structure,and function in the soil.Results indicated that bacterial diversity was the highest under seasonal waterlogging condition.However,nitrogen deposition only affected the bacterial Chao1 and beta diversity indices under seasonal waterlogging condition.The abundance of bacterial communities under different water tables showed significant differences at the phylum and genus levels.The dominant phylum,Proteobacteria,was sensitive to soil moisture and its abundance decreased with decreasing water tables.Although nitrogen deposition led to changes in bacterial abundance,such changes were small compared with the effects of water tables.Nitrogen deposition with 10 kg N/(hm^(2)•a)decreased bacterial edge number,average path length,and robustness.However,perennial flooding and drying conditions could simply resist environmental changes caused by 20 kg N/(hm^(2)•a)nitrogen deposition and their network structure remain unchanged.The sulfur cycle function was dominant under perennial flooding condition,and carbon and nitrogen cycle functions were dominant under seasonal waterlogging and perennial drying conditions.Nitrogen application increased the potential function of part of nitrogen cycle and decreased the potential function of sulfur cycle in bacterial community.In summary,composition of bacterial community in the arid alpine wetland was determined by water tables,and diversity of bacterial community was inhibited by a lower water table.Effect of nitrogen deposition on bacterial community structure and function depended on water tables.展开更多
Background Oils are important sources of energy in pig diets.The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of o...Background Oils are important sources of energy in pig diets.The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of oil supplemented.An experiment was conducted to evaluate the effects of oils with different degree of saturation on the fat digestibility and corresponding additivity and bacterial community in growing pigs.Methods Eighteen crossbred(Duroc×Landrace×Yorkshire)barrows(initial body weight:29.3±2.8 kg)were surgically fitted with a T-cannula in the distal ileum.The experimental diets included a fat-free basal diet and 5 oil-added diets.The 5 oil-added diets were formulated by adding 6%oil with different ratio of unsaturated to saturated fatty acids(U:S)to the basal diet.The 5 oils were palm oil(U:S=1.2),canola oil(U:S=12.0),and palm oil and canola oil were mixed in different proportions to prepare a combination of U:S of 2.5,3.5 and 4.5,respectively.Results The apparent and standardized ileal digestibility(AID and SID)of fat and fatty acids increased linearly(P<0.05)as the U:S of dietary oils increased except for SID of fat and C18:2.The AID and SID of fat and fatty acids differed among the dietary treatments(P<0.05)except for SID of unsaturated fatty acids(UFA)and C18:2.Fitted one-slope broken-line analyses for the SID of fat,saturated fatty acids(SFA)and UFA indicated that the breakpoint for U:S of oil was 4.14(R^(2)=0.89,P<0.01),2.91(R^(2)=0.98,P<0.01)and 3.84(R^(2)=0.85,P<0.01),respectively.The determined SID of fat,C18:1,C18:2 and UFA in the mixtures was not different from the calculated SID of fat,C18:1,C18:2 and UFA.However,the determined SID of C16:0,C18:0 and SFA in the mixtures were greater than the calculated SID values(P<0.05).The abundance of Romboutsia and Turicibacter in pigs fed diet containing palm oil was greater than that in rapeseed oil treatment group,and the two bacteria were negatively correlated with SID of C16:0,C18:0 and SFA(P<0.05).Conclusions The optimal U:S for improving the utilization efficiency of mixed oil was 4.14.The SID of fat and UFA for palm oil and canola oil were additive in growing pigs,whereas the SID of SFA in the mixture of two oils was greater than the sum of the values of pure oils.Differences in fat digestibility caused by oils differing in degree of saturation has a significant impact on bacterial community in the foregut.展开更多
The micro-sprinkler irrigation mulched(MSM)has been suggested as a novel water-saving approach in con-trolled environment agriculture.However,the effects of microbial community structure and enzyme activity in the rhi...The micro-sprinkler irrigation mulched(MSM)has been suggested as a novel water-saving approach in con-trolled environment agriculture.However,the effects of microbial community structure and enzyme activity in the rhizosphere soil on crop growth under MSM remain unclear.This study conducted a randomized experimen-tal design using greenhouse tomatoes to investigate changes in bacterial community structure and enzyme activity in rhizosphere soil under different irrigation frequencies(F)and amounts(I)of MSM.Thefindings revealed that with the increase of F or I,The total count of soil bacteria in tomatoesfirst rose and then fell in terms of Opera-tional Taxonomic Units(OTUs)classification.Compared to other F,the most abundance of nitrogen and phos-phorus metabolism genes and enzyme activities were observed with a 5-day F.Moreover,the diversity of soil bacterial community structure initially rose before eventually declining with the increase of the I.Applying 1.00 Epan(cumulative evaporation of a 20 cm standard pan)under MSM helped boost the abundance of nitrogen and phosphorus metabolism functional genes in soil bacteria,ensuring higher enzyme activities related to nitro-gen,carbon,and phosphorus metabolism in the rhizosphere soil of tomatoes.Tomatoes’yield initially rose before eventually declining with the increase in F or I,whereas I had a more significant effect on yield.A 1.00%increase in I yielded a minimum of 39.24%increase in tomato yield.The study showed a positive correlation between soil bacterial community,soil enzyme activity,and greenhouse tomato yield under MSM.Considering the results comprehensively,the combined irrigation mode of F of 5 d and I of 1.00 Epan was recommended for greenhouse tomatoes under MSM.This conclusion provides theoretical support for water-saving practices and yield improve-ment in facility agriculture,especially tomato cultivation.展开更多
This study aimed to investigate the bacterial communities in mushroom compost piles composed of rice straw, corn stover, and cow dung. Bacterial com- munities of samples at the beginning of composting, at the end of f...This study aimed to investigate the bacterial communities in mushroom compost piles composed of rice straw, corn stover, and cow dung. Bacterial com- munities of samples at the beginning of composting, at the end of fermentation phase I and II were collected and analyzed using Polymerase Chain Reaction-De- naturing Gradient Gel Electrophoresis （PCR-DGGE） based on 16S rDNA universal primers from Escherichia coli. A total of 56 different clone sequences were obtained （GenBank accession number： KF630598-KF630653）. They were classified into seven phyla and 42 genera. Dominant microflora during composting belonged to phylum Proteobacteria, Firmicutes, and Actinobacteria, with the dominant genera of Bacillus, Paenibacillus, Thermomonospora, Thermasporomyces, Pseudomonas, and Cellvibrio. Bacterial diversity （Shannon index） analysis showed that bacterial species in com- post pile composed mainly of rice straw continuously increased during composting, while those in compost pile composed mainly of corn stover firstly increased and then reduced. Principal component analysis showed that corn stover compost sam- ples at the end of fermentation phase I and phase II were clustered into one group, suggesting that corn stover composted faster than anticipated. In general, rice straw compost has higher bacterial diversity but longer composting time period, while corn stover compost has lower bacterial diversity but shorter composting time period.展开更多
Variations of precipitation have great impacts on soil carbon cycle and decomposition of soil organic matter.Soil bacteria are crucial participants in regulating these ecological processes and vulnerable to altered pr...Variations of precipitation have great impacts on soil carbon cycle and decomposition of soil organic matter.Soil bacteria are crucial participants in regulating these ecological processes and vulnerable to altered precipitation.Studying the impacts of altered precipitation on soil bacterial community structure can provide a novel insight into the potential impacts of altered precipitation on soil carbon cycle and carbon storage of grassland.Therefore,soil bacterial community structure under a precipitation manipulation experiment was researched in a semi-arid desert grassland in Chinese Loess Plateau.Five precipitation levels,i.e.,control,reduced and increased precipitation by 40%and 20%,respectively(referred here as CK,DP40,DP20,IP40,and IP20)were set.The results showed that soil bacterial alpha diversity and rare bacteria significantly changed with altered precipitation,but the dominant bacteria and soil bacterial beta diversity did not change,which may be ascribed to the ecological strategy of soil bacteria.The linear discriminate analysis(LDA)effect size(LEfSe)method found that major response patterns of soil bacteria to altered precipitation were resource-limited and drought-tolerant populations.In addition,increasing precipitation greatly promoted inter-species competition,while decreasing precipitation highly facilitated inter-species cooperation.These changes in species interaction can promote different distribution ratios of bacterial populations under different precipitation conditions.In structural equation model(SEM)analysis,with changes in precipitation,plant growth characteristics were found to be drivers of soil bacterial community composition,while soil properties were not.In conclusion,our results indicated that in desert grassland ecosystem,the sensitive of soil rare bacteria to altered precipitation was stronger than that of dominant taxa,which may be related to the ecological strategy of bacteria,species interaction,and precipitation-induced variations of plant growth characteristics.展开更多
AIM: To investigate the protective effect of glutamine (Gln) on intestinal injury and the bacterial community in rats exposed to hypobaric hypoxia environment.
The combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis （DGGE） analysis was used to reveal the compositions and dynamics of bacterial communities in a sewage treatment pla...The combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis （DGGE） analysis was used to reveal the compositions and dynamics of bacterial communities in a sewage treatment plant with two systems, i.e., an anoxic- anaerobic-aerobic system （inverted A2O） and an anaerobic-anoxic-aerobic one （conventional A2O） over a period from February to July 2009, during which both systems experienced serious sludge bulking problems. The DGGE patterns showed that there were many common bands in both systems, suggesting the high similarity of bacterial communities of the two systems. Meanwhile, the moving window correlation analysis showed that the two systems experienced different microbial community structure changes during the period, which might be related with the different situations of the occurrence and disappearance of sludge bulking, as being reflected by sludge volume index （SVI） values. Major bands of DGGE patterns of sludge samples were further sequenced. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Firmicutes, Bacteroidetes/Chlorobi group and α- and β-Proteobacteria. Two sequences showed high similarities to typical filamentous bacteria Microthrix parvicella and Nostocoida limicola I, indicating that these bacterial species have been involved in the sludge bulking problems.展开更多
Lacustrine sediment played important roles in migration and transformation of its water soluble organic matter(WSOM), and the source and composition of WSOM would affect water trophic status and the fate of pollutants...Lacustrine sediment played important roles in migration and transformation of its water soluble organic matter(WSOM), and the source and composition of WSOM would affect water trophic status and the fate of pollutants. However, we know little about the pathway of WSOM transformation and its driving bacterial communities in lacustrine sediment. In the present study, we investigated the spatial distribution patterns of sediment WSOM and its fluorescent fractions across Lake Chaohu using fluorescence spectroscopy, and explored WSOM compositional structure through our proposed calculated ratios. In addition, we also analyzed sediment bacterial community using Illumina sequencing technology, and probed the possible pathway of sediment WSOM transformation under the mediate of indigenous bacteria. Our results showed that the inflowing rivers affected the spatial distribution patterns of WSOM and its five fractions(including tyrosine-, tryptophan-, fulvic acid-, humic acid-like substances and soluble microbial productions), and sediment WSOM originated from fresh algae detritus or bacterial sources. In parallel, we also found that Proteobacteria(mainly γ-Proteobacteria and δ-Proteobacteria), Firmicutes(mainly Bacilli), Chloroflexi, Acidobacteria, Planctomycetes and Actinobacteria dominate sediment bacterial community. Furthermore, these dominant bacteria triggered sediment WSOM transformation, specifically, the humic acid-like substances could be converted into fulvic acid-like substances, and further degraded into aromatic protein-like and SMP substances. In addition, our proposed ratios(P-L:H-L, Ar-P:SMP and H-L ratio), as supplementary tool, were effective to reveal WSOM composition structure. These results figured out possible pathway of WSOM transformation, and revealed its microbial mechanism in lacustrine sediment.展开更多
Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta.Changes of the soil bacterial community were monitored using the terminal r...Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta.Changes of the soil bacterial community were monitored using the terminal restriction fragment length polymorphism （T-RFLP） and clone library analyses.The 140-day microcosm experiments showed that low C：N：P ratio,high availability of surfactant and addition of bulking agent significantly enhanced the performance,leading to the highest total petroleum hydrocarbon removal.Meanwhile,the bacterial community was remarkably changed by the multiple biostimulation treatments,with the Deltaproteobacteria,Firmicutes,Actinobacteria,Acidobacteria and Planctomycetes being inhibited and the Alphaand Beta-proteobacteria and some unknown Gammaproteobacteria bacteria being enriched.In addition,different hydrocarbon-degraders came to power in the following turn.At the first stage,the Alcanivorax-related Gammaproteobacteria bacteria dominated in the biostimulated soil and contributed mainly to the biodegradation of easily degradable portion of the heavy crude oil.Then the bacteria belonging to Alphaproteobacteria,followed by bacteria belonging to Candidate division OD1,became the dominant oil-degraders to degrade the remaining recalcitrant constituents of the heavy crude oil.展开更多
Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extract...Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study, these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r, 341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also, we found that each DNA extraction method resulted in different community profiles, reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore, the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.展开更多
Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare f...Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10, 20 30, and 40-50 cm in a black soil （Mollisol）. Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR- DGGE）. Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrueomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as 8-Proteobacteria, Aeidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.展开更多
Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonizatio...Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic （pH = 3.78）, whereas the vegetated mine tailing was near neutral （pH ： 7.28）. The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine railings （P 〈 0.01）, whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings （P 〈 0.01）. The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.展开更多
Bacterial community structure and iron corrosion were investigated for simulated drinking water distribution systems（DWDSs） composed of annular reactors incorporating three different treatments： ozone, biologically...Bacterial community structure and iron corrosion were investigated for simulated drinking water distribution systems（DWDSs） composed of annular reactors incorporating three different treatments： ozone, biologically activated carbon and chlorination（O3-BAC-Cl2）;ozone and chlorination（O3-Cl2）; or chlorination alone（Cl2）. The lowest corrosion rate and iron release, along with more Fe3O4 formation, occurred in DWDSs with O3-BAC-Cl2 compared to those without a BAC filter. It was verified that O3-BAC influenced the bacterial community greatly to promote the relative advantage of nitrate-reducing bacteria（NRB）in DWDSs. Moreover, the advantaged NRB induced active Fe（III） reduction coupled to Fe（II） oxidation, enhancing Fe3O4 formation and inhibiting corrosion. In addition, O3-BAC pretreatment could reduce high-molecular-weight fractions of dissolved organic carbon effectively to promote iron particle aggregation and inhibit further iron release. Our findings indicated that the O3-BAC treatment, besides removing organic pollutants in water, was also a good approach for controlling cast iron corrosion and iron release in DWDSs.展开更多
基金supported by grants from the National Natural Science Foundation of China for Excellent Young Scientists Fund Program(No.42222105)the National Natural Science Foundation of China General Program(No.42171144)+1 种基金the Assessment of Ecosystem Carbon Stock and Turnover Patterns in Qinghai Province(No.2021-SFA7-1-1)the Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(No.2021QZKK0100)。
文摘Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how would bacterial interaction influence the bacterial communities in permafrost of the Qinghai-Tibet Plateau(QTP)remains largely unknown.Here we collected paired soil samples from both the active and permafrost layers of two typical QTP permafrost regions in October 2020 for Tuotuohe River(TTH)and May 2022 for Aerjin(ARJ),and investigated the bacterial communities and the role of interactions in structuring the bacterial community and its assembly process through amplicon sequencing of the 16S rRNA gene.Our study revealed distinct bacterial communities,with significant differences in the relative abundances of Proteobacteria(P<0.05),Acidobacteriota(P<0.001),Bacteroidota(P<0.05),and Planctomycetota(P<0.001)between the active layer and the permafrost layer.More importantly,we found that interspecies interactions,including both positive and negative associations,were strongly correlated with bacterial alpha-diversity and played a significant role in community variation and assembly process.Our findings also showed that the community assembly in both the active and permafrost layers was primarily driven by homogeneous selection of deterministic processes,with interspecies interactions accounting for more than 58%and 63%of all assembly mechanisms,respectively.This is the first study to quantify the contribution of bacterial interactions in shaping the bacterial community and its assembly process in permafrost of QTP,highlighting the importance of considering interspecies interactions in future modeling efforts.Our work also emphasizes the necessity of including interspecies interactions in microbial process projections to reduce uncertainty.
基金The Innovative Talent Foundation of Hainan Province under contract No.KJRC2023C39the National Natural Science Foundation of China under contract Nos 42161144006 and 42076108.
文摘Coral gardening has become a promising technique for restoring reefs worldwide in the Anthropocene era.The microbiome plays an important role in enhancing adaptive resilience in situ nursery propagation of corals.However,little is known about the response patterns of bacterial community dynamics,co-occurrence networks and assembly processes of different species in coral restoration nurseries over time.Here,we collected two Acropora coral samples from transplanted fragments and source colonies at 1-month and 3-month post-transplantation(May and July 2022)in an upwelling-affected fragmented reef.Full-length 16S rRNA gene sequencing revealed that bacterial communities of coral fragments in nurseries exhibited consistent temporal shifts compared to those of the source colonies.High host specificity was observed in the bacterial community and network structure associated with source colonies.In contrast,for the two coral species within nurseries,there were no differences in bacterial diversity,composition and core microbiome.Stochastic assembly processes were identified as the primary drivers of bacterial communities in all May samples,whereas deterministic processes played a more prominent role in July.Seawater properties(e.g.,temperature and ammonium concentration)partially explained the compositional changes in the bacterial communities of these coral samples.Our findings suggested that coral nurseries contributed to the homogenization of bacterial communities in different Acropora corals,despite the apparent temporal dynamics of bacteria.These results enhance our understanding of the coral microbiome,ecological interactions and assembly principles in different host within in situ nurseries.
基金supported by the Sciences Foundation of Xinjiang Uygur Autonomous Region(2024D01C32)the Xinjiang Uygur Autonomous Region Education Department Basic Scientific Project(XJEDU2023P005)+1 种基金the National Natural Science Foundation of China(32001145)the 2024 Xinjiang Uygur Autonomous Region Postdoctoral Funding Project.
文摘Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of soil bacterial community diversity to the changes of environmental factors in different habitats,this study collected soil samples under the canopies of Tamarix ramosissima Ledeb.in oasis,transition zone,and desert habitats in the upper reaches of the Tarim River,Northwest China.High-throughput sequencing technology and PICRUSt2 software were used to explore the composition and function of soil bacterial communities in different habitats of T.ramosissima.The results showed that:(1)soil environmental factors under the canopy of T.ramosissima in the three habitats differed significantly,with soil moisture and nutrient conditions being better in the oasis;(2)Proteobacteria,Bacteroidetes,Firmicutes,Actinobacteria,and Gemmatimonadetes were the major bacterial communities in the three habitats;(3)soil bacterial community composition under the canopy of T.ramosissima varied greatly,and the richness was significantly different among the three habitats;(4)redundancy analysis indicated that soil water content and available phosphorous were the most important environmental factors influencing the composition of soil bacterial community;and(5)6 primary functions and 21 secondary functions were obtained by PICRUSt2 function prediction,with metabolism being the most dominant function.This study revealed the response of soil bacterial community composition to habitat changes and their driving factors in the upper reaches of the Tarim River,which could improve the understanding of ecological sensitivity of soil microorganisms in arid and semi-arid areas,and provide a theoretical foundation for improving soil quality and ecological protection.
基金supported by the Key-Area Research and Development Program of Guangdong Province,China(No.2021B0202030002)the Science and Technology Planning Project of Guangdong Province,China(No.2019B030301007)+2 种基金the Guangdong Provincial Special Project of Rural Revitalization Strategy,China(No.(2021)12)the Joint Team Project of Guangdong Laboratory for Lingnan Modern Agriculture,China(No.NT2021010)the Innovation Team Construction Project of Modern Agricultural Industry Technology Systems of Guangdong Province,China(No.2022KJ105).
文摘Rice-fish coculture(RFC)has aroused extensive concern for its contribution to food security and resource conservation,but whether it can improve soil phosphorus(P)availability and affect microbe-mediated P turnover remains elusive.Herein,we conducted a microcosm experiment to assess the impacts of RFC combined with(50 mg P kg^(-1)as KH2PO4)and without inorganic P addition on P fractions,P availability,and phoD-harboring bacterial community composition.The results revealed that RFC without P addition significantly improved P availability and phosphatase activity in paddy soil,while soil available P(AP),pH,and microbial biomass P(MBP)contributed to regulating P fractions.Moreover,the phoD-harboring bacterial abundance was linked to phosphatase activity,AP,total carbon(TC),and total P(TP)contents,and the ratios of TC to total nitrogen(TN)and TN to TP.We also found that the keystone taxa of phoD-harboring bacteria contributed to phosphatase production as well as organic P mineralization,thereby improving P availability.Our findings suggest that RFC without P addition is beneficial for promoting the expression of phoD-harboring bacterial functions to improve the capacity of P mineralization.Overall,our study provides insights into the responses of phoD-harboring bacterial functions for P turnover to RFC combined with and without P addition,showing the potential utilization of P resources in agricultural soil and the contribution of phosphatase activity to P acquisition in agriculture ecosystem.
基金supported by China National Postdoctoral Program for Innovative Talents(No.BX20230041)China Postdoctoral Science Foundation(No.2024M750186)+1 种基金the Key Program of National Natural Science Foundation of China(No.52034001)Open Foundation of State Environmental Protection Key Laboratory of Mineral Metallurgical Resources Utilization and Pollution Control(No.HB202303).
文摘Bioleaching is confronted with problems,such as low efficiency,long production cycle length,and vegetation destruction.In order to solve problems above,fly ash and low-grade copper sulfide ores were used to investigate bioleaching behaviors and bacterial community succession.Results showed that copper recovery,bacterial concentration,total proportion of main leaching bacteria including Acidithiobacillus ferrooxidans,Acidibacillus ferrooxidans,and Leptospirillum ferriphilum,were improved through using appropriate dosage of fly ash.The maximum copper recovery of 79.87%and bacterial concentration of 7.08×10^(7)cells·mL^(-1)were obtained after us-ing 0.8 g·L^(-1)fly ash.Exclusive precipitation including Zn(Fe_(3)(SO_(4))_(2)(OH)_(6))_(2)and Mg(Fe_(3)(SO_(4))_(2)(OH)_(6))_(2)was found in sample added 0.8 g·L^(-1)fly ash,which reduced the effect of hazardous ions on bacteria and thus contributing to bacterial proliferation.Bacterial com-munity structure was differentiated,which indicated difference between original inoculation and sample used 0.8 g·L^(-1)fly ash was less than others.Total proportion of the three microorganism above accounted for more than 95%in all tests,especially in sample with 0.8 g·L^(-1)fly ash up to 99.81%.Cl^(-)and Ag^(+)contained in fly ash can act as catalytic agent,which contributed to conversion from smooth and dense passivation layer to sparse and scattered one,and therefore improving contact between ores,lixiviant,and bacteria.Using appropri-ate dosage of fly ash showed prospects in bioleaching.
基金supported by the National Key Research and Development Program of China (Nos.2018YFE0105600 and 2020YFC1806803)the New Zealand MBIE Catalyst Fund (No.92846082).
文摘Woodchip bioreactors are an eco-friendly technology for removing nitrogen(N)pollution.However,there needs to be more clarity regarding the dissolved organicmatter(DOM)characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors.The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments,and the results showed that the average removal rate of TN was 45.80 g N/(m^(3)·day)when the influent N level was 100 mg N/L,which was better than 10 mg N/L and 50 mg N/L.Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates.Medium to high N levels enriched a copiotroph bacterial module(Module 1)detected by network analysis,including Phenylobacterium,Xanthobacteraceae,Burkholderiaceae,Pseudomonas,and Magnetospirillaceae,carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM.Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophswith fewer N-cycle potentials(Module 2).Together,this study reveals that the compositional change ofDOMand bacterial community succession are closely related to N removal performance,providing an ecological basis for developing techniques for N-rich effluent treatment.
基金supported by the National Natural Science Foundation of China(Nos.42377296 and 42107141)the National Key Research and Development Program of China(Nos.2023YFD1901402 and 2023YFD1901105)the Fundamental Research Funds for the Central Universities,China(No.YDZX2025046).
文摘Plant growth-promoting rhizobacteria(PGPR)have been widely used for the promotion of plant performance.Predatory protists can influence the taxonomic and functional composition of rhizosphere bacteria.However,research on the impact of the interaction between protist and PGPR on plant performance remains at a very early stage.Here,we examined the impacts of individual inoculation of protist(Colpoda inflata,Dimastigella trypaniformis,or Vermamoeba vermiformis)or the PGPR strain Bacillus velezensis SQR9 as well as the co-inoculation of the protist C.inflata and B.velezensis SQR9 on the growth of tomato plants.We found that all individual protists and Bacillus could promote plant growth compared to the control with no microbe inoculation,with the co-inoculation of C.inflata and B.velezensis SQR9 achieving the greatest performance,including plant height,fresh weight,and dry weight.Different protists harbored distinct rhizosphere bacterial communities,with the co-inoculation of protist and Bacillus resulting in the lowest bacterial diversity and driving significant changes in community structure and composition,particularly by increasing the relative abundance of Proteobacteria.Random forest model highlighted Cellvibrio as the most important bacterial predictor of plant growth,which was enriched after protist inoculation,especially after the mixed inoculation of protist and Bacillus.We further found that bacterial functional genes of nitrogen metabolism were the key determinants of plant growth.These results indicate that the interaction between protists and Bacillus can support plant growth by reshaping rhizosphere bacterial community composition and function.Understanding the interaction mechanisms between protist and PGPR is crucial for their effective utilization in sustainable agriculture.
基金supported by the National Natural Science Foundation of China(31960258)the Graduate Research Innovation Project of Xinjiang Uygur Autonomous Region(XJ2023G119).
文摘Nitrogen deposition and water tables are important factors to control soil microbial community structure.However,the specific effects and mechanisms of nitrogen deposition and water tables coupling on bacterial diversity,abundance,and community structure in arid alpine wetlands remain unclear.The nitrogen deposition(0,10,and 20 kg N/(hm^(2)•a))experiments were conducted in the Bayinbulak alpine wetland with different water tables(perennial flooding,seasonal waterlogging,and perennial drying).The 16S rRNA(ribosomal ribonucleic acid)gene sequencing technology was employed to analyze the changes in bacterial community diversity,network structure,and function in the soil.Results indicated that bacterial diversity was the highest under seasonal waterlogging condition.However,nitrogen deposition only affected the bacterial Chao1 and beta diversity indices under seasonal waterlogging condition.The abundance of bacterial communities under different water tables showed significant differences at the phylum and genus levels.The dominant phylum,Proteobacteria,was sensitive to soil moisture and its abundance decreased with decreasing water tables.Although nitrogen deposition led to changes in bacterial abundance,such changes were small compared with the effects of water tables.Nitrogen deposition with 10 kg N/(hm^(2)•a)decreased bacterial edge number,average path length,and robustness.However,perennial flooding and drying conditions could simply resist environmental changes caused by 20 kg N/(hm^(2)•a)nitrogen deposition and their network structure remain unchanged.The sulfur cycle function was dominant under perennial flooding condition,and carbon and nitrogen cycle functions were dominant under seasonal waterlogging and perennial drying conditions.Nitrogen application increased the potential function of part of nitrogen cycle and decreased the potential function of sulfur cycle in bacterial community.In summary,composition of bacterial community in the arid alpine wetland was determined by water tables,and diversity of bacterial community was inhibited by a lower water table.Effect of nitrogen deposition on bacterial community structure and function depended on water tables.
基金supported by National Natural Science Foundation of China(31972597 and 32302793)。
文摘Background Oils are important sources of energy in pig diets.The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of oil supplemented.An experiment was conducted to evaluate the effects of oils with different degree of saturation on the fat digestibility and corresponding additivity and bacterial community in growing pigs.Methods Eighteen crossbred(Duroc×Landrace×Yorkshire)barrows(initial body weight:29.3±2.8 kg)were surgically fitted with a T-cannula in the distal ileum.The experimental diets included a fat-free basal diet and 5 oil-added diets.The 5 oil-added diets were formulated by adding 6%oil with different ratio of unsaturated to saturated fatty acids(U:S)to the basal diet.The 5 oils were palm oil(U:S=1.2),canola oil(U:S=12.0),and palm oil and canola oil were mixed in different proportions to prepare a combination of U:S of 2.5,3.5 and 4.5,respectively.Results The apparent and standardized ileal digestibility(AID and SID)of fat and fatty acids increased linearly(P<0.05)as the U:S of dietary oils increased except for SID of fat and C18:2.The AID and SID of fat and fatty acids differed among the dietary treatments(P<0.05)except for SID of unsaturated fatty acids(UFA)and C18:2.Fitted one-slope broken-line analyses for the SID of fat,saturated fatty acids(SFA)and UFA indicated that the breakpoint for U:S of oil was 4.14(R^(2)=0.89,P<0.01),2.91(R^(2)=0.98,P<0.01)and 3.84(R^(2)=0.85,P<0.01),respectively.The determined SID of fat,C18:1,C18:2 and UFA in the mixtures was not different from the calculated SID of fat,C18:1,C18:2 and UFA.However,the determined SID of C16:0,C18:0 and SFA in the mixtures were greater than the calculated SID values(P<0.05).The abundance of Romboutsia and Turicibacter in pigs fed diet containing palm oil was greater than that in rapeseed oil treatment group,and the two bacteria were negatively correlated with SID of C16:0,C18:0 and SFA(P<0.05).Conclusions The optimal U:S for improving the utilization efficiency of mixed oil was 4.14.The SID of fat and UFA for palm oil and canola oil were additive in growing pigs,whereas the SID of SFA in the mixture of two oils was greater than the sum of the values of pure oils.Differences in fat digestibility caused by oils differing in degree of saturation has a significant impact on bacterial community in the foregut.
基金funded by the Natural Science Foundation of China(No.41807041)the Science and Technology Research Project of Henan Province(242102111101)the Mechanical Design,Manufacturing,and Automation Key Discipline of Henan Province(JG[2018]No.119).
文摘The micro-sprinkler irrigation mulched(MSM)has been suggested as a novel water-saving approach in con-trolled environment agriculture.However,the effects of microbial community structure and enzyme activity in the rhizosphere soil on crop growth under MSM remain unclear.This study conducted a randomized experimen-tal design using greenhouse tomatoes to investigate changes in bacterial community structure and enzyme activity in rhizosphere soil under different irrigation frequencies(F)and amounts(I)of MSM.Thefindings revealed that with the increase of F or I,The total count of soil bacteria in tomatoesfirst rose and then fell in terms of Opera-tional Taxonomic Units(OTUs)classification.Compared to other F,the most abundance of nitrogen and phos-phorus metabolism genes and enzyme activities were observed with a 5-day F.Moreover,the diversity of soil bacterial community structure initially rose before eventually declining with the increase of the I.Applying 1.00 Epan(cumulative evaporation of a 20 cm standard pan)under MSM helped boost the abundance of nitrogen and phosphorus metabolism functional genes in soil bacteria,ensuring higher enzyme activities related to nitro-gen,carbon,and phosphorus metabolism in the rhizosphere soil of tomatoes.Tomatoes’yield initially rose before eventually declining with the increase in F or I,whereas I had a more significant effect on yield.A 1.00%increase in I yielded a minimum of 39.24%increase in tomato yield.The study showed a positive correlation between soil bacterial community,soil enzyme activity,and greenhouse tomato yield under MSM.Considering the results comprehensively,the combined irrigation mode of F of 5 d and I of 1.00 Epan was recommended for greenhouse tomatoes under MSM.This conclusion provides theoretical support for water-saving practices and yield improve-ment in facility agriculture,especially tomato cultivation.
基金Supported by the National Key Technology Research and Development Program during the 12th Five-Year Plan Period of China(2012BAD14B09)Earmarked Fund for China Agriculture Research System(PXM2013-014207-000096)Beijing Higher Education Young Elite Teacher Project(YETP1714)~~
文摘This study aimed to investigate the bacterial communities in mushroom compost piles composed of rice straw, corn stover, and cow dung. Bacterial com- munities of samples at the beginning of composting, at the end of fermentation phase I and II were collected and analyzed using Polymerase Chain Reaction-De- naturing Gradient Gel Electrophoresis （PCR-DGGE） based on 16S rDNA universal primers from Escherichia coli. A total of 56 different clone sequences were obtained （GenBank accession number： KF630598-KF630653）. They were classified into seven phyla and 42 genera. Dominant microflora during composting belonged to phylum Proteobacteria, Firmicutes, and Actinobacteria, with the dominant genera of Bacillus, Paenibacillus, Thermomonospora, Thermasporomyces, Pseudomonas, and Cellvibrio. Bacterial diversity （Shannon index） analysis showed that bacterial species in com- post pile composed mainly of rice straw continuously increased during composting, while those in compost pile composed mainly of corn stover firstly increased and then reduced. Principal component analysis showed that corn stover compost sam- ples at the end of fermentation phase I and phase II were clustered into one group, suggesting that corn stover composted faster than anticipated. In general, rice straw compost has higher bacterial diversity but longer composting time period, while corn stover compost has lower bacterial diversity but shorter composting time period.
基金supported by the National Natural Science Foundation of China (41761043, 41201196)the Youth Teacher Scientific Capability Promoting Project of Northwest Normal University, China (NWNU-LKQN2020-06, NWNU-LKQN-17-7)the Key Research and Development Program of Gansu Province, China (20YF3FA042)
文摘Variations of precipitation have great impacts on soil carbon cycle and decomposition of soil organic matter.Soil bacteria are crucial participants in regulating these ecological processes and vulnerable to altered precipitation.Studying the impacts of altered precipitation on soil bacterial community structure can provide a novel insight into the potential impacts of altered precipitation on soil carbon cycle and carbon storage of grassland.Therefore,soil bacterial community structure under a precipitation manipulation experiment was researched in a semi-arid desert grassland in Chinese Loess Plateau.Five precipitation levels,i.e.,control,reduced and increased precipitation by 40%and 20%,respectively(referred here as CK,DP40,DP20,IP40,and IP20)were set.The results showed that soil bacterial alpha diversity and rare bacteria significantly changed with altered precipitation,but the dominant bacteria and soil bacterial beta diversity did not change,which may be ascribed to the ecological strategy of soil bacteria.The linear discriminate analysis(LDA)effect size(LEfSe)method found that major response patterns of soil bacteria to altered precipitation were resource-limited and drought-tolerant populations.In addition,increasing precipitation greatly promoted inter-species competition,while decreasing precipitation highly facilitated inter-species cooperation.These changes in species interaction can promote different distribution ratios of bacterial populations under different precipitation conditions.In structural equation model(SEM)analysis,with changes in precipitation,plant growth characteristics were found to be drivers of soil bacterial community composition,while soil properties were not.In conclusion,our results indicated that in desert grassland ecosystem,the sensitive of soil rare bacteria to altered precipitation was stronger than that of dominant taxa,which may be related to the ecological strategy of bacteria,species interaction,and precipitation-induced variations of plant growth characteristics.
基金Supported by National Natural Science Foundation of China,No.31001012 and No.31101304Programs for Agricultural Science and Technology Development of Shaanxi Province,China,No.2013K02-16Northwestern Polytechnical University Foundation Science Research Fund,No.JC201278
文摘AIM: To investigate the protective effect of glutamine (Gln) on intestinal injury and the bacterial community in rats exposed to hypobaric hypoxia environment.
基金supported by the National Research Foundation, China (No. 20921140094)the Chinese Academy of Sciences, Knowledge innovation Project(No. KSCX2-YW-G-054, KZCX2-YW-JC407)CASTWAS Postdoctoral Fellowships 2009
文摘The combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis （DGGE） analysis was used to reveal the compositions and dynamics of bacterial communities in a sewage treatment plant with two systems, i.e., an anoxic- anaerobic-aerobic system （inverted A2O） and an anaerobic-anoxic-aerobic one （conventional A2O） over a period from February to July 2009, during which both systems experienced serious sludge bulking problems. The DGGE patterns showed that there were many common bands in both systems, suggesting the high similarity of bacterial communities of the two systems. Meanwhile, the moving window correlation analysis showed that the two systems experienced different microbial community structure changes during the period, which might be related with the different situations of the occurrence and disappearance of sludge bulking, as being reflected by sludge volume index （SVI） values. Major bands of DGGE patterns of sludge samples were further sequenced. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Firmicutes, Bacteroidetes/Chlorobi group and α- and β-Proteobacteria. Two sequences showed high similarities to typical filamentous bacteria Microthrix parvicella and Nostocoida limicola I, indicating that these bacterial species have been involved in the sludge bulking problems.
基金supported by the National Nature Science Foundation of China (No. 51608002)the China National Critical Project for Science and Technology on Water Pollution Prevention and Control (No. 2017ZX07603-003)the Nture Science Foundation of Anhui Province of China (No. 1908085QD167)。
文摘Lacustrine sediment played important roles in migration and transformation of its water soluble organic matter(WSOM), and the source and composition of WSOM would affect water trophic status and the fate of pollutants. However, we know little about the pathway of WSOM transformation and its driving bacterial communities in lacustrine sediment. In the present study, we investigated the spatial distribution patterns of sediment WSOM and its fluorescent fractions across Lake Chaohu using fluorescence spectroscopy, and explored WSOM compositional structure through our proposed calculated ratios. In addition, we also analyzed sediment bacterial community using Illumina sequencing technology, and probed the possible pathway of sediment WSOM transformation under the mediate of indigenous bacteria. Our results showed that the inflowing rivers affected the spatial distribution patterns of WSOM and its five fractions(including tyrosine-, tryptophan-, fulvic acid-, humic acid-like substances and soluble microbial productions), and sediment WSOM originated from fresh algae detritus or bacterial sources. In parallel, we also found that Proteobacteria(mainly γ-Proteobacteria and δ-Proteobacteria), Firmicutes(mainly Bacilli), Chloroflexi, Acidobacteria, Planctomycetes and Actinobacteria dominate sediment bacterial community. Furthermore, these dominant bacteria triggered sediment WSOM transformation, specifically, the humic acid-like substances could be converted into fulvic acid-like substances, and further degraded into aromatic protein-like and SMP substances. In addition, our proposed ratios(P-L:H-L, Ar-P:SMP and H-L ratio), as supplementary tool, were effective to reveal WSOM composition structure. These results figured out possible pathway of WSOM transformation, and revealed its microbial mechanism in lacustrine sediment.
基金supported by the International Cooperation Project of National Natural Science Foundation of China (No.40821140541)the National High Technology Research and Development Program (863) of China (No.2009AA063501)
文摘Multiple biostimulation treatments were applied to enhance the removal of heavy crude oil pollutants in the saline soil of Yellow River Delta.Changes of the soil bacterial community were monitored using the terminal restriction fragment length polymorphism （T-RFLP） and clone library analyses.The 140-day microcosm experiments showed that low C：N：P ratio,high availability of surfactant and addition of bulking agent significantly enhanced the performance,leading to the highest total petroleum hydrocarbon removal.Meanwhile,the bacterial community was remarkably changed by the multiple biostimulation treatments,with the Deltaproteobacteria,Firmicutes,Actinobacteria,Acidobacteria and Planctomycetes being inhibited and the Alphaand Beta-proteobacteria and some unknown Gammaproteobacteria bacteria being enriched.In addition,different hydrocarbon-degraders came to power in the following turn.At the first stage,the Alcanivorax-related Gammaproteobacteria bacteria dominated in the biostimulated soil and contributed mainly to the biodegradation of easily degradable portion of the heavy crude oil.Then the bacteria belonging to Alphaproteobacteria,followed by bacteria belonging to Candidate division OD1,became the dominant oil-degraders to degrade the remaining recalcitrant constituents of the heavy crude oil.
基金This work was funded by the Special Scientific Foundation of Guangdong Province (No. A305030301)was partly supported by a grant from KLFEE, Ministry of Agriculture (2003-04).
文摘Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE), limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study, these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r, 341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also, we found that each DNA extraction method resulted in different community profiles, reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore, the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.
基金Project supported by the National Natural Science Foundation of China (No.40671099)
文摘Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10, 20 30, and 40-50 cm in a black soil （Mollisol）. Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR- DGGE）. Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrueomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as 8-Proteobacteria, Aeidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.
基金the National Natural Science Foundation of China (Nos.39830310 and 30070134)the NationalKey Basic Research Support Foundation (NKBRSF) of China (No.2002CB111504).
文摘Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic （pH = 3.78）, whereas the vegetated mine tailing was near neutral （pH ： 7.28）. The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine railings （P 〈 0.01）, whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings （P 〈 0.01）. The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.
基金supported by the National Natural Science Foundation of China(Nos.51308529,51290281)
文摘Bacterial community structure and iron corrosion were investigated for simulated drinking water distribution systems（DWDSs） composed of annular reactors incorporating three different treatments： ozone, biologically activated carbon and chlorination（O3-BAC-Cl2）;ozone and chlorination（O3-Cl2）; or chlorination alone（Cl2）. The lowest corrosion rate and iron release, along with more Fe3O4 formation, occurred in DWDSs with O3-BAC-Cl2 compared to those without a BAC filter. It was verified that O3-BAC influenced the bacterial community greatly to promote the relative advantage of nitrate-reducing bacteria（NRB）in DWDSs. Moreover, the advantaged NRB induced active Fe（III） reduction coupled to Fe（II） oxidation, enhancing Fe3O4 formation and inhibiting corrosion. In addition, O3-BAC pretreatment could reduce high-molecular-weight fractions of dissolved organic carbon effectively to promote iron particle aggregation and inhibit further iron release. Our findings indicated that the O3-BAC treatment, besides removing organic pollutants in water, was also a good approach for controlling cast iron corrosion and iron release in DWDSs.
