Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N dee...Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N deep placement,which is critical for understanding the biodiversity and function of agricultural ecosystem.In this study,lllumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.Abundant bacteria showed ubiquitous distribution;while rare taxa exhibited uneven distribution across all samples.Stochastic processes dominated community assembly of both abundant and rare bacteria,with dispersal limitation playing a more vital role in abundant bacteria,and undominated processes playing a more important role in rare bacteria.The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer(BN)and no N fertilizer(NN)treatments in abundant and rare taxa of rhizosphere soil;while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa.Nevertheless,most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.Overall,these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.展开更多
Uncovering the mechanisms underlying the diversity patterns of abundant and rare species is crucial for terrestrial biodiversity maintenance.However,the response of abundant and rare community assembly to ecological s...Uncovering the mechanisms underlying the diversity patterns of abundant and rare species is crucial for terrestrial biodiversity maintenance.However,the response of abundant and rare community assembly to ecological succession has not been explored,particularly considering soil profiles.Here 300 soil samples were collected from reforestation ecosystems from depths of up to 300 cm and horizontal distances of 30–90 cm from a tree.We revealed that soil phosphorus not only affected alpha diversity and community structure,but also mediated the balance of stochastic and deterministic processes for abundant and rare sub-communities,which exhibited contrasting assembly strategies.The abundant sub-community changed from variable selection to stochasticity with the increase of phosphorus,while the rare sub-community shifted from homogeneous selection to stochasticity.Dispersal limitation was the main assembly process in the abundant sub-community,while the rare sub-community was governed primarily by homogeneous selection.Moreover,the relative influence of deterministic processes increased with succession for both sub-communities.At the scale of a single tree,stochastic processes increased with soil depth in rare sub-community,while deterministic processes increased with the radius from a single tree in the abundant subcommunity.Overall,our results highlight the importance of the soil phosphorus-driven assembly process in understanding the re-assembly and maintenance of soil bacterial diversity.展开更多
Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant ...Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation.Our results suggested that rare bacteria were more sensitive to changes in elevation gradient.展开更多
The removal of rare earth elements （REEs） from solution in various microorganisms was examined. Seventy-six strains from 69 species （22 bacteria, 20 actinomycetes, 18 fungi, and 16 yeasts） were tested. Initially, ...The removal of rare earth elements （REEs） from solution in various microorganisms was examined. Seventy-six strains from 69 species （22 bacteria, 20 actinomycetes, 18 fungi, and 16 yeasts） were tested. Initially, Sm was used to test the removal capabilities of the various organisms. Gram-positive bacteria, such as Bacillus licheniformis, B. subtilis, Brevibacterium helovolum, and Rhodococcus elythropolis, exhibited a particularly high capacity for accumulating Sm. In particular, the B. lichemiformis cells accumulated approximately 316 μmol Sm per gram dry wt. of microbial cells. A full suite of screenings was then conducted to compare the abilities of the organisms to remove Se, Y, La, Er, and, Lu from solution. Tests were done with solutions containing one REE at a time. Accumulation was nearly identical for the various metals and organisms. However, when solutions with equimolar amounts of two REEs were used, preferential removal from solution was observed. When an Eu/Gd solution was used, gram-positive bacteria removed more Eu and Gd as compared to actinomycetes. When Eu/Sm combination was used, gram-positive bacteria removed equal mounts of both metals and some actinomycetes removed more Eu. The selective removal was quantified by calculating separation factors （S. F.）, which indicated that Streptomyces levoris cells accumulated the greatest proportion of Eu. The removal of REEs from a solution containing five metals （Y, La, Sm, Er, and Lu） was then examined. Mucorjavanicus preferentially accumulated Sm and S. flavoviridis preferentially accumulated Lu. The effects of pH and Sm concentration on the accumulation of Sm by B. licheniformis were also examined. Accumulation increased at higher pH and at greater solution concentrations.展开更多
为探索稀土开采对土壤生态系统的影响,以长汀离子型稀土矿开采废弃地为研究对象,通过采集稀土开采前、开采后的取土场和堆浸池的土壤,通过提取土壤DNA后,利用Illumina Miseq高通量测序平台进行细菌的16S r DNA测序,分析以上3个作业区土...为探索稀土开采对土壤生态系统的影响,以长汀离子型稀土矿开采废弃地为研究对象,通过采集稀土开采前、开采后的取土场和堆浸池的土壤,通过提取土壤DNA后,利用Illumina Miseq高通量测序平台进行细菌的16S r DNA测序,分析以上3个作业区土壤细菌OTU组成,并以此为基础进行物种注释、多样性和系统发育树分析.研究结果表明:稀土开采后的取土场和堆浸池比开采前土壤细菌群落多样性以及各类群组成丰度比例发生显著变化,但土壤细菌的优势种群不变,分别从门、纲、目、科、属水平鉴定的优势种为:厚壁菌(门)、芽孢杆菌(纲)、乳杆菌(目)、肠球菌(科)、肠球菌(属),系统发育树显示厚壁菌门、变形菌门、放线菌门、拟杆菌门、疣微菌门、酸杆菌门、硝化螺旋菌门、蓝藻门、Thermi在系统发育上有一定的亲缘关系.展开更多
基金the National Key Research and Development Program of China(2016YFD0200309 and 2018YFD0301104-01).
文摘Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N deep placement,which is critical for understanding the biodiversity and function of agricultural ecosystem.In this study,lllumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.Abundant bacteria showed ubiquitous distribution;while rare taxa exhibited uneven distribution across all samples.Stochastic processes dominated community assembly of both abundant and rare bacteria,with dispersal limitation playing a more vital role in abundant bacteria,and undominated processes playing a more important role in rare bacteria.The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer(BN)and no N fertilizer(NN)treatments in abundant and rare taxa of rhizosphere soil;while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa.Nevertheless,most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.Overall,these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.
基金the National Science Foundation of China(Grant Nos.:42077222,41807030 and 41830755)。
文摘Uncovering the mechanisms underlying the diversity patterns of abundant and rare species is crucial for terrestrial biodiversity maintenance.However,the response of abundant and rare community assembly to ecological succession has not been explored,particularly considering soil profiles.Here 300 soil samples were collected from reforestation ecosystems from depths of up to 300 cm and horizontal distances of 30–90 cm from a tree.We revealed that soil phosphorus not only affected alpha diversity and community structure,but also mediated the balance of stochastic and deterministic processes for abundant and rare sub-communities,which exhibited contrasting assembly strategies.The abundant sub-community changed from variable selection to stochasticity with the increase of phosphorus,while the rare sub-community shifted from homogeneous selection to stochasticity.Dispersal limitation was the main assembly process in the abundant sub-community,while the rare sub-community was governed primarily by homogeneous selection.Moreover,the relative influence of deterministic processes increased with succession for both sub-communities.At the scale of a single tree,stochastic processes increased with soil depth in rare sub-community,while deterministic processes increased with the radius from a single tree in the abundant subcommunity.Overall,our results highlight the importance of the soil phosphorus-driven assembly process in understanding the re-assembly and maintenance of soil bacterial diversity.
基金financially supported by the International Partnership Program of Chinese Academy of Sciences(Grant No.131C11KYSB20160061)the National Natural Science Foundation of China(Grant No.41425004)
文摘Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation.Our results suggested that rare bacteria were more sensitive to changes in elevation gradient.
基金This work was supported by the Japan Oil, Gas and Metals National Corporation (JOGMEC)
文摘The removal of rare earth elements （REEs） from solution in various microorganisms was examined. Seventy-six strains from 69 species （22 bacteria, 20 actinomycetes, 18 fungi, and 16 yeasts） were tested. Initially, Sm was used to test the removal capabilities of the various organisms. Gram-positive bacteria, such as Bacillus licheniformis, B. subtilis, Brevibacterium helovolum, and Rhodococcus elythropolis, exhibited a particularly high capacity for accumulating Sm. In particular, the B. lichemiformis cells accumulated approximately 316 μmol Sm per gram dry wt. of microbial cells. A full suite of screenings was then conducted to compare the abilities of the organisms to remove Se, Y, La, Er, and, Lu from solution. Tests were done with solutions containing one REE at a time. Accumulation was nearly identical for the various metals and organisms. However, when solutions with equimolar amounts of two REEs were used, preferential removal from solution was observed. When an Eu/Gd solution was used, gram-positive bacteria removed more Eu and Gd as compared to actinomycetes. When Eu/Sm combination was used, gram-positive bacteria removed equal mounts of both metals and some actinomycetes removed more Eu. The selective removal was quantified by calculating separation factors （S. F.）, which indicated that Streptomyces levoris cells accumulated the greatest proportion of Eu. The removal of REEs from a solution containing five metals （Y, La, Sm, Er, and Lu） was then examined. Mucorjavanicus preferentially accumulated Sm and S. flavoviridis preferentially accumulated Lu. The effects of pH and Sm concentration on the accumulation of Sm by B. licheniformis were also examined. Accumulation increased at higher pH and at greater solution concentrations.
文摘为探索稀土开采对土壤生态系统的影响,以长汀离子型稀土矿开采废弃地为研究对象,通过采集稀土开采前、开采后的取土场和堆浸池的土壤,通过提取土壤DNA后,利用Illumina Miseq高通量测序平台进行细菌的16S r DNA测序,分析以上3个作业区土壤细菌OTU组成,并以此为基础进行物种注释、多样性和系统发育树分析.研究结果表明:稀土开采后的取土场和堆浸池比开采前土壤细菌群落多样性以及各类群组成丰度比例发生显著变化,但土壤细菌的优势种群不变,分别从门、纲、目、科、属水平鉴定的优势种为:厚壁菌(门)、芽孢杆菌(纲)、乳杆菌(目)、肠球菌(科)、肠球菌(属),系统发育树显示厚壁菌门、变形菌门、放线菌门、拟杆菌门、疣微菌门、酸杆菌门、硝化螺旋菌门、蓝藻门、Thermi在系统发育上有一定的亲缘关系.
