Biological soil crusts(BSCs)have important ecological functions in arid and semiarid lands,but they remain poorly understood in terms of the changes in microbial communities during BSC succession under in situ field c...Biological soil crusts(BSCs)have important ecological functions in arid and semiarid lands,but they remain poorly understood in terms of the changes in microbial communities during BSC succession under in situ field conditions.Here,454 pyrosequencing was used to assess the microbial community composition of four BSC types in the Tengger Desert of China:alga,lichen(cyanolichen and green alga-lichen),and moss crusts,representing early,middle,and final successional stages of BSCs,respectively.The results showed the highest diversity of microbial communities inhabiting lichen crusts,whereas the lowest diversity was observed in moss crusts.Five phyla,Proteobacteria,Actinobacteria,Cyanobacteria,Bacteroidetes,and Acidobacteria,accounted for about 72% to 87%of total prokaryotic sequences in different BSCs.The most abundant eukaryotic microorganism was Ascomycota,accounting for 47%to 93%of the total eukaryotic sequences.Along the succession of BSCs,the abundance of photoautotrophic Cyanobacteria,Chlorophyta,and Bacillariophyta declined,and that of heterotrophic microorganisms such as bacteria and fungi increased.Statistical analysis showed clear divergency of microbial taxa at the class level among the different successional stages of BSCs.The clustering results at class level showed that the moss crusts were the farthest from the rest in prokaryotic composition;the alga crusts were the most different in terms of eukaryotic microorganisms and the two kinds of lichen crusts were relatively closer in both compositions.Ordination analysis showed that the main variations of community structure among BSCs could be explained best by the abundance of Cyanobacteria and Ascomycota and by physiochemical properties of BSCs,including mechanical composition,moisture,and electrical conductivity.In conclusion,our results indicate that Cyanobacteria and Ascomycota likely play an important role in the evolution of BSC structure and functions and highlight the importance of environmental factors in shaping microbial community structures of展开更多
Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relat...Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.展开更多
基金supported by the National Natural Science Foundation of China (Nos. 31170464, 41573111, and 31300322)
文摘Biological soil crusts(BSCs)have important ecological functions in arid and semiarid lands,but they remain poorly understood in terms of the changes in microbial communities during BSC succession under in situ field conditions.Here,454 pyrosequencing was used to assess the microbial community composition of four BSC types in the Tengger Desert of China:alga,lichen(cyanolichen and green alga-lichen),and moss crusts,representing early,middle,and final successional stages of BSCs,respectively.The results showed the highest diversity of microbial communities inhabiting lichen crusts,whereas the lowest diversity was observed in moss crusts.Five phyla,Proteobacteria,Actinobacteria,Cyanobacteria,Bacteroidetes,and Acidobacteria,accounted for about 72% to 87%of total prokaryotic sequences in different BSCs.The most abundant eukaryotic microorganism was Ascomycota,accounting for 47%to 93%of the total eukaryotic sequences.Along the succession of BSCs,the abundance of photoautotrophic Cyanobacteria,Chlorophyta,and Bacillariophyta declined,and that of heterotrophic microorganisms such as bacteria and fungi increased.Statistical analysis showed clear divergency of microbial taxa at the class level among the different successional stages of BSCs.The clustering results at class level showed that the moss crusts were the farthest from the rest in prokaryotic composition;the alga crusts were the most different in terms of eukaryotic microorganisms and the two kinds of lichen crusts were relatively closer in both compositions.Ordination analysis showed that the main variations of community structure among BSCs could be explained best by the abundance of Cyanobacteria and Ascomycota and by physiochemical properties of BSCs,including mechanical composition,moisture,and electrical conductivity.In conclusion,our results indicate that Cyanobacteria and Ascomycota likely play an important role in the evolution of BSC structure and functions and highlight the importance of environmental factors in shaping microbial community structures of
基金This work is financially supported by the National Natural Science Foundation of China(grant nos.31772400,31761143017)the National Natural Science Foundation for Young Scientists of China(grant no.31701997)+1 种基金the Key Research Program of the Chinese Academy of Sciences(grant nos.KFZD-SW-112-02-02 and KFZD-SW-219)the Key Research Program of Frontier Sciences,CAS(grant no.QYZDB-SSW-SMC021).
文摘Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.
