Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.

Biology Centre of the Czech Academy of Sciences Institute of Soil Biology and SoWa Research Infrastructure České Budějovice Czechia

Department of Geosciences and Natural Resource Management Faculty of Science University of Copenhagen Frederiksberg Denmark

Engineering Research Center of Soil Remediation of Fujian Province University College of Resources and Environment Fujian Agriculture and Forestry University Fuzhou China

Faculty of Science Institute for Environmental Studies Charles University Praha Czechia

Institute of Entomology Biology Centre of the Czech Academy of Sciences and University of South Bohemia České Budějovice Czechia

Laboratory of Environmental Microbiology Institute of Microbiology of the CAS Praha Czechia

New Guinea Binatang Research Center Madang Papua New Guinea

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Regional biogeography versus intra-annual dynamics of the root and soil microbiome