Most previous studies on soil microbial communities have been focused on species abundance and diversity, but not the interactions among species. In present study, the Molecular Ecological Network Analysis tool was used to study the interactions and network organizations of fungal communities in yield-invigorating (healthy) and -debilitating (diseased) soils induced by prolonged potato monoculture, based on the relative abundances of internal transcribed spacer sequences derived using pyrosequencing. An emphasis was placed on the differences between the healthy and diseased networks. The constructed healthy and diseased networks both showed scale-free, small world and modular properties. The key topological properties and phylogenetic composition of the two networks were similar. However, major differences included: a) the healthy network had more number of functionally interrelated operational taxonomic units (OTUs) than the diseased one; b) healthy network contained 6 (4%) generalist OTUs whereas the diseased contained only 1 (0.6%) marginal generalist OTU; and c) majority (55%) of OTUs in healthy soils were stimulated by a certain set of soil variables but the majorities (63%) in diseased soils were inhibited. Based on these data, a conceptual picture was synthesized: a healthy community was a better organized or a better operated community than the diseased one; a healthy soil was a soil with variables that encouraged majority of fungi whereas a diseased soil discouraged. By comparing the topological roles of different sets of shared OTUs between healthy and diseased networks, it was found that role-shifts prevailed among the network members such as generalists/specialists, significant module memberships and the OTU sets irresponsive to soil variables in one network but responsive in the counterpart network. Soil organic matter was the key variable associated with healthy community, whereas ammonium nitrogen (NH4+–N) and Electrical conductivity (EC) were the key variables associated with diseased community. Major affected phylogenetic groups were Sordariales and Hypocreales

Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H_Shannon) and richness (S_Chao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.