Mechanistic Exploration Of Karst Desertification Progress By Comparative Study Of Soil Microbiome

Karst topography is the most exposed terrestrial ecosystem in the world.Once the karst ecosystem fails,karst rocky desertification is an often consequence.The desertification transforms vegetation of karst land into severe soil erosion,extensive exposure of bedrock,appearance of a desert-like landscape,and eventually leading to the dramatically decrease in soil productivity.Unfortunately,karst rocky desertification is usually difficult to reverse because the ecosystem is so fragile that the soil is weak in nutrient cycling.In the past few decades,China experienced severe karst rocky desertification.Especially,southwest China,where possess one of the largest karst areas in the world,is now facing widespread rocky desertification.This has become a heavy threaten to local agriculture,forestry,and livestock husbandry.Therefore,in this study,we carried out microbial metagenomics analyses on soils collected from karst areas of both protection zone and desertification area.We determined the soil microbiome by measuring 16S rRNA V4 and ITS1 regions.We also made several comparative analyses of microbiome changes like(1)between protection zone and desertification area,(2)over different desertification stages,and(3)with edaphic properties.We aim to portray the microbial community change during karst rocky desertification and try to answer how the microbial changes impact soil health and eventually the rocky desertification.Following are some major achievements in this study:1.The soil microbiome in karst protection zone is significantly different from that of in karst rocky desertification area.The karst protection zone has comparatively higher a-diversity(indexing by Chaol,ACE,Shannon and Simpson indices)and abundance of soil microbiome than that in rocky desertification area.Compared to bacterial community,fungal community is more sensitive to the environmental change,especially during the rocky desertification progress.2.Comparative analyses found bacteria phyla like Actinobacteria increased their abudance in the karst rocky desertification soil.To the contrary,Firmicutes,Bacteroidetes,Verrucomicrobia,and Chlorobi decreased their abudance.In addition,the fungal Basidiomycota decreased in the karst desertification soil.Furthermore,we built the soil microbial co-abundance networks using WGCNA algorithm.From the networks,we extracted six microbial co-abundance networks associated with rocky desertification,consisting of 353 microbial genera.In these networks,42 bacteria like Marmoricola,Steroidobacter,Cateruloplanes,Virgisporangium and Alistipes served as hub microbes in the six networks and to some extent determined the regulatory functions of co-abundance network.Our results may provide clues in monitoring and repairing the rocky desertification.3.Change of soil properties are correlated with soil microbiome.We monitored variation of 11 soil properties in different karst area.For instance,AK?ECa2+ and Na+ are mostly correlated with bacterial changes,while AK and Cl' have significant correlation with fungi change.Correlation network analysis of microbial community-edaphic property interactions revealed ECa2+,TP,AK and Na+ were correlated with 5 microbial co-abundance networks associated with rocky desertification.33 hubs microbes in networks also were correlation with soil properties,in which includes the core microbes,such as Alistipes,Marmoricola,Catenuloplanes and Catenuloplanes.4.To explore the differential function of soil microbiome under the protection zone and rocky desertification area,we carried out a pathway enrichment analysis microbial metagenomes predicted by the PICRUSt algorithm.71 function gene disappeared in karst rocky desertification and 59 emerged;at the meanwhile,2,573 function genes were differential.The differential function gene enriched on some metabolic pathway,such as methane metabolism,carbon fixed pathway,TCA cycle,nitrogen metabolism,PST system.Moreover,these pathways have correlation with utilization of calcium,phosphorus,potassium and sodium in the soil.5.Comparative analyses found that soil microbiome were changed under the vegetation succession process of rocky desertification,and which have correlated with 6 soil properties like calcium and phosphorus.The soil calcium and phosphorus were correlated with 2 microbial co-abundance networks associated with different karst desertification stages.Functional simulation of these microbial co-abundance networks inferred their negative impact on soil nutrition by interfering soil metabolism of organic phosphorus,carbon and nitrogen.Token all these results together,we proposed a hypothesis on molecular mechanism underlying karst desertification progress.The increase of soil calcium could be one of the key driving factors in karst desertification.The extensive clear-cutting and overgrazing in the karst rocky area cause original soil rapidly lose and rocks expose.Bare carbonate rocks usually dissolve into soil in a form of Ca2+and HCO3-.For some unknown reasons,the increase of soil Ca2+ alters the growth and function of soil microbial community.The microbial community variations then interfere some microbial herds associated with metabolism and usage of carbon,nitrogen and phosphorus,and eventually affect the growth of plants.In addition,we used the BestFirst and GreedyStepwise algorithms in weka software to search the soil microbiome genera data for minimal feature subset.Using the minimal feature subset,we built decision tree model for classification of karst rocky desertification.Validation of the model by leave-one-cut cross method yielded a classification accuracy of 86.36%,a precison of 0.867 and a recall of 0.864.Therefore,this microbiome-based model could serve as an effective karst rocky desertification predictor.In summary,this study investigates the soil microbiome changes and their impact on soil rocky desertification in karst area.As the results,we propose a hypothesis on molecular mechanism underlying karst desertification progress.Our study may introduce the possibility of reversing or rescuing the fragile karst landscape by alteration of microbial community.