Alteration of desert soil microbial community structure in response to agricultural reclamation and abandonment

•Reclamation increased soil microbial biomasses that decreased after abandonment.•Reclamation increased fungal OTUs, Chao1 and Ace species richness.•Bacterial OTUs, Chao1 and Ace species richness increased during 5-year abandonment.•Microbial taxa responded differently to reclamation and abandonment.•Microbial community structures were closely related to soil moisture and chemical properties. Agricultural reclamation via the conversion of desert into cropland offers a strategy to utilize arid lands and combat desertification. However, limited irrigation water resources have forced the abandonment of reclaimed agricultural lands and succession towards unmanaged natural states, which may contribute greatly to erosion potential. Soil microorganisms can affect the degradation and wind erosion potential of soils in the desert region by mediating many ecological processes. However, little is known about how soil microbial community structures respond to desert agricultural reclamation with tillage-based farming and subsequential abandonment. Using quantitative PCR (qPCR) and 16S rRNA high-throughput sequencing approaches, we investigated the changes of bacterial, archaeal and fungal community biomasses, diversities and structures in a desert farmland soil (FS). We contrasted these to soils along a 10-year farming abandonment chronosequence (2-year, 5-year and 10-year) and with adjacent soil from a native desert (control) in the Badain Jaran desert, China. Soil bacterial and archaeal community biomasses significantly increased after reclamation compared with the control and generally decreased after farming abandonment. Species richness of communities decreased for archaea and increased for fungi in response to reclamation, whereas bacterial community species richness increased during the 5-year abandonment. Microbial community structures were divergent in reclaimed and abandoned soils and were closely related to soil moisture, total carbon (C), total nitrogen (N), available phosphorus (P) and the stoichiometry of C, N and P, which explained 24.4–89.0% of their variations. Our results indicate desert soil microbial biomass, diversity and compositions differently responded to agricultural reclamation and abandonment with some irreversible changes in compositions mainly driven by soil moisture and chemical properties changes. The insights are meaningful for sustainable development of agriculture and ethical land management in arid desert regions.