Rare microbes are associated with crop biomass in an acid soil with different amendments

Characterizing the roles of abundant and rare soil microorganism is vital for clarifying microbial functions and help optimize agricultural management strategies, but their responses to various amendments in acid soils and correlations with crop biomass remain poorly understood.

A 5-year field experiment was conducted to evaluate the influence of amendments, including canola straw (SC), animal manure (OM), and alkaline slag (AS), on abundant and rare bacteria or fungi in acidic bulk and rhizosphere soils in aspect of microbial diversity, compositions, potential functions, and their relationship with canola biomass.

Amendments and canola planting significantly affected both bacterial and fungal community structures. Applying AS had pronounced effect on bacterial communities and sub-communities, and the addition of OM showed the strong influence on fungal communities and sub-communities. The sub-community structures of rare bacterial and rare fungal significantly correlated to canola biomass; this correlation was stronger in the rhizosphere soil than that in the bulk soil. The α-diversity of rare rhizosphere bacteria, but not rare bulk bacteria and rare fungi, was significantly positively related to canola biomass. Rare bacteria accounted for the high proportion of nodes and most keystone species in microbial networks, and the number of edges belonging to rare bacteria positively correlated to canola biomass. The predicted functions of rare bacteria also make large contributions to crop biomass.

These findings highlight the important roles that rare microbes play in ameliorating acid soils and suggest that rare bacteria should be more closely associated with crop growth than rare fungi.