In microbial ecology,there is limited understanding of the mechanisms governing patterns in community structure across space and time.Here,we studied the changes of bacterial co-occurrence network structure over four ...In microbial ecology,there is limited understanding of the mechanisms governing patterns in community structure across space and time.Here,we studied the changes of bacterial co-occurrence network structure over four primary successional soils after glacier retreat,including a sand dune system and three glacier foreland series,varying in timescale from centuries to millennia.We found that in all series,network structure was most complex in the earliest stages of succession,and became simpler over time.Richness and abundance of keystone species and network stability also declined over time.It appears that with less productive,nutrient poor and physiologically extreme conditions of early succession,closer interactions among bacterial species are ecologically selected for.These may take the form of consortia(with positive interactions)or stronger niche exclusion(with negative interactions).Additionally,we quantified the relative roles of different structuring processes on bacterial community using a bin-based null model analysis(iCAMP).With each successional series,community composition was initially governed by stochasticity,but as succession proceeded there was a progressive increase in deterministic selection over time,correlated with decreasing pH.Overall,our results show a consistency among the four series in long-term processes of community succession,with more integrated networks and greater stochasticity in early stages.展开更多
Although fairy rings are widely observed,little is known about the community processes associated with them.Here,we studied fairy rings in a natural grassland in northern Mongolia by sampling soils outside(future stag...Although fairy rings are widely observed,little is known about the community processes associated with them.Here,we studied fairy rings in a natural grassland in northern Mongolia by sampling soils outside(future stage),directly under(present stage),and within(past stage)the rings,to represent different time stages during the expansion of fairy rings.Soil DNA was extracted for amplicon sequencing of the fungal ITS1 region.The present stage had reduced fungal diversity and different fungal communities toward the other stages.Most strikingly,there was an increase in the pathogenic fungus Gibberella baccata in the present stage of most rings and the saprotrophic fairy ring fungus Lepista luscina in several.However,no mushrooms of Lepista had been recorded from any of these rings during several years of observation.Known fairy ring fungi were not found in the present stage of every ring,even in some known rings to have previously displayed mushrooms of such species.It is possible that these fungi occurred or were more abundant at the unsampled leading edge of the ring.The increase in G.baccata is intriguing,but its importance,if any,is unclear.It is also unclear whether consortia of fungi or other microbes might be present in these rings.The absence or low abundance of the previously reported fairy ring fungal species suggests that their presence is transient,with rapid replacement by other fungi.No differences in soil parameters were found between the fairy ring stages,except for aluminum.There is a need for broader sampling,including analysis of non-fungal biota,to understand the functional diversity of fairy ring fungi and the consequences for plant communities.展开更多
Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic p...Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.展开更多
The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production.Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycl...The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production.Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services,thus providing valuable insights to improve food production.The North China Plain(NCP)is one of the world’s key agricultural regions,supplying more than 50% of the cereal consumed in Asia.However,it is unknown whether soil microbial diversity is predictable across the NCP.Using the MiSeq Illumina platform,we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP,which cover nearly 0.3 million km^(2).Based on observed bacterial communities and their relationships with environmental factors,we generated a map of bacterial communities across the NCP.The highest bacterial diversity was found in the middle part of the NCP,with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria.These findings provide important baseline information for analyzing the relationships between microbial community,soil functionality and crop yields.展开更多
White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial comm...White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.展开更多
Mineral extraction is known to affect soil fungi in polar environments,but it is unknown how long these effects persist.Here,by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi,we compare...Mineral extraction is known to affect soil fungi in polar environments,but it is unknown how long these effects persist.Here,by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi,we compared soil fungal community in intact natural tundra with that in a nearby former coal mining area,abandoned 52 years previously,on Svalbard in the High Arctic.Compared with those in intact tundra,soils in the former mining area were more acidic and had lower plant coverage.Despite of similar diversity in the two areas,the fungal community was dominated by Basidiomycota in the intact tundra,but by Ascomycota in the former mining area.Ectomycorrhizal genera formed a major part of the tundra community,but were notably less abundant in the mining area.The principal variation among samples was soil pH.Surprisingly,network connectivity analysis indicated that the fungal community in the former mining area had greater network connectivity than that in the tundra area.Overall,the ecosystem in the former mining area has made only limited recovery towards the natural tundra state even after more than five decades.It is unclear whether the recovery of the fungal community is limited more by the low primary productivity,slow migration of fungi and plants,or slow changes in soil parameters.Our findings emphasize the susceptibility of polar ecosystems to disturbance,given their particularly slow recovery back towards the natural state.展开更多
Soil fungi have many important ecological functions,however,their life strategies and interactions in manure fertilized soils are not well understood.The aim of this study was to investigate the effects of biochar ame...Soil fungi have many important ecological functions,however,their life strategies and interactions in manure fertilized soils are not well understood.The aim of this study was to investigate the effects of biochar amendment on the fungal life strategies and species interactions in ryegrass(Lolium perenne L.)rhizosphere soil by high-throughput sequencing.Three soil treatments were evaluated:soil and pig manure mixture without planting ryegrass and biochar application(bulk soil),mixture with ryegrass planting(rhizosphere soil(RS)),and addition of 2%(w/w)biochar with ryegrass(RS+biochar).Our results indicated that temporal turnover,defined as the slope of linear regression between community similarity and time,was significantly higher in the biochar amendment(slope=-0.2689,p<0.0001)relative to the rhizosphere soil.Following biochar addition,the percentage of species employing slow acclimation ecological strategies decreased(from 27% to 17%)and the percentage of sensitive species increased(from 40% to 50%)in comparison to the rhizosphere soil.Network analysis indicated that fungal communities in the biochar amendment enhanced positive correlations compared to the rhizosphere soil and bulk soil.Structural equation model indicated that soil pH was the most important factor in altering fungal life strategies and interactions in manure fertilized soils.展开更多
文摘In microbial ecology,there is limited understanding of the mechanisms governing patterns in community structure across space and time.Here,we studied the changes of bacterial co-occurrence network structure over four primary successional soils after glacier retreat,including a sand dune system and three glacier foreland series,varying in timescale from centuries to millennia.We found that in all series,network structure was most complex in the earliest stages of succession,and became simpler over time.Richness and abundance of keystone species and network stability also declined over time.It appears that with less productive,nutrient poor and physiologically extreme conditions of early succession,closer interactions among bacterial species are ecologically selected for.These may take the form of consortia(with positive interactions)or stronger niche exclusion(with negative interactions).Additionally,we quantified the relative roles of different structuring processes on bacterial community using a bin-based null model analysis(iCAMP).With each successional series,community composition was initially governed by stochasticity,but as succession proceeded there was a progressive increase in deterministic selection over time,correlated with decreasing pH.Overall,our results show a consistency among the four series in long-term processes of community succession,with more integrated networks and greater stochasticity in early stages.
基金supported by the PIRE Mongolia project funded by the U.S.National Science Foundation(OISE 0729786)supported by the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology,Mongoliasupported by a grant funded by the National Research Foundation of Korea(Nos.NRF-2018R1C1B6007755,NRF-2022R1F1A1066643)。
文摘Although fairy rings are widely observed,little is known about the community processes associated with them.Here,we studied fairy rings in a natural grassland in northern Mongolia by sampling soils outside(future stage),directly under(present stage),and within(past stage)the rings,to represent different time stages during the expansion of fairy rings.Soil DNA was extracted for amplicon sequencing of the fungal ITS1 region.The present stage had reduced fungal diversity and different fungal communities toward the other stages.Most strikingly,there was an increase in the pathogenic fungus Gibberella baccata in the present stage of most rings and the saprotrophic fairy ring fungus Lepista luscina in several.However,no mushrooms of Lepista had been recorded from any of these rings during several years of observation.Known fairy ring fungi were not found in the present stage of every ring,even in some known rings to have previously displayed mushrooms of such species.It is possible that these fungi occurred or were more abundant at the unsampled leading edge of the ring.The increase in G.baccata is intriguing,but its importance,if any,is unclear.It is also unclear whether consortia of fungi or other microbes might be present in these rings.The absence or low abundance of the previously reported fairy ring fungal species suggests that their presence is transient,with rapid replacement by other fungi.No differences in soil parameters were found between the fairy ring stages,except for aluminum.There is a need for broader sampling,including analysis of non-fungal biota,to understand the functional diversity of fairy ring fungi and the consequences for plant communities.
文摘Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.
基金supported by the Strategic Priority Research Program(XDB15010101)of the Chinese Academy of Sciencesthe National Key Research and Development Program of China(2017YFD0200604,2017YFC0803803)+2 种基金the“135”Plan and Frontiers Projects of Institute of Soil Science(ISSASIP1641)The collaborative innovation project from the Forensic Appraisal Center of The ministry of Public Security of the People’s Republic of China(2016XTCX02)the China Biodiversity Observation Networks(Sino BON).
文摘The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production.Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services,thus providing valuable insights to improve food production.The North China Plain(NCP)is one of the world’s key agricultural regions,supplying more than 50% of the cereal consumed in Asia.However,it is unknown whether soil microbial diversity is predictable across the NCP.Using the MiSeq Illumina platform,we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP,which cover nearly 0.3 million km^(2).Based on observed bacterial communities and their relationships with environmental factors,we generated a map of bacterial communities across the NCP.The highest bacterial diversity was found in the middle part of the NCP,with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria.These findings provide important baseline information for analyzing the relationships between microbial community,soil functionality and crop yields.
基金supported by the National Research Foundation (NRF) of Korea (No. NRF-040920150076)
文摘White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.
文摘Mineral extraction is known to affect soil fungi in polar environments,but it is unknown how long these effects persist.Here,by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi,we compared soil fungal community in intact natural tundra with that in a nearby former coal mining area,abandoned 52 years previously,on Svalbard in the High Arctic.Compared with those in intact tundra,soils in the former mining area were more acidic and had lower plant coverage.Despite of similar diversity in the two areas,the fungal community was dominated by Basidiomycota in the intact tundra,but by Ascomycota in the former mining area.Ectomycorrhizal genera formed a major part of the tundra community,but were notably less abundant in the mining area.The principal variation among samples was soil pH.Surprisingly,network connectivity analysis indicated that the fungal community in the former mining area had greater network connectivity than that in the tundra area.Overall,the ecosystem in the former mining area has made only limited recovery towards the natural tundra state even after more than five decades.It is unclear whether the recovery of the fungal community is limited more by the low primary productivity,slow migration of fungi and plants,or slow changes in soil parameters.Our findings emphasize the susceptibility of polar ecosystems to disturbance,given their particularly slow recovery back towards the natural state.
基金supported by Strategic Priority Research Program(B)of the Chinese Academy of Sciences(XDB15010100)the National Natural Science Foundation of China(No.41622104,41877060)+1 种基金Distinguished Young Scholar Program of the Jiangsu Province(BK20160050)Youth Innovation Promotion Association of Chinese Academy of Sciences(2016284).
文摘Soil fungi have many important ecological functions,however,their life strategies and interactions in manure fertilized soils are not well understood.The aim of this study was to investigate the effects of biochar amendment on the fungal life strategies and species interactions in ryegrass(Lolium perenne L.)rhizosphere soil by high-throughput sequencing.Three soil treatments were evaluated:soil and pig manure mixture without planting ryegrass and biochar application(bulk soil),mixture with ryegrass planting(rhizosphere soil(RS)),and addition of 2%(w/w)biochar with ryegrass(RS+biochar).Our results indicated that temporal turnover,defined as the slope of linear regression between community similarity and time,was significantly higher in the biochar amendment(slope=-0.2689,p<0.0001)relative to the rhizosphere soil.Following biochar addition,the percentage of species employing slow acclimation ecological strategies decreased(from 27% to 17%)and the percentage of sensitive species increased(from 40% to 50%)in comparison to the rhizosphere soil.Network analysis indicated that fungal communities in the biochar amendment enhanced positive correlations compared to the rhizosphere soil and bulk soil.Structural equation model indicated that soil pH was the most important factor in altering fungal life strategies and interactions in manure fertilized soils.
