Nitrogen-fixing bacterial community in sago palm roots in different soil environments of East Malaysia and South Thailand

Abstract

The diversity and taxonomic composition of endophytic bacteria and nitrogen-fixing bacteria (NFB) in sago palm roots were examined from two sites in East Malaysia (clay loam of mineral soil, and shallow peat soil) and five sites in South Thailand (clay loam, sandy clay loam, sandy clay, and clay soils) by the amplicon sequencing of 16S rRNA and nifH gene. As a result, Shannon diversity and Simpson’s evenness of bacteria and NFB were not different among sampling sites (although the root sample in shallow peat soil had a low value). The soil bulk density, clay content, volumetric water content, pH, EC, exchangeable cation contents, and total N affected both communities of endophytic bacteria and NFB. As a result of phylogenetic analysis of NifH (translated from nifH gene amplicon), NifH adjacent to Bradyrhizobium, Burkholderia, Cupriavidus, Frankia, Geobacter, Anaeromyxobacter, Desulfovibrio, Clostridium, and Spirochaeta were highly detected. Surprisingly, NifH close to Burkholderia xenovorans was dominant (> 30% relative abundance) in the strong acidity (pH 4.1) of shallow peat soil in Malaysia. The relative abundance of aerobic or facultative anaerobic NFB (Bradyrhizobium, Burkholderia, Frankia, and Cupriavidus genera) was negatively correlated with the relative abundance of anaerobic NFB (Clostridium, Geobacter, Anaeromyxobacter, Desulfovibrio, and Spirochaeta). It is suggested that the key players of root endophytic NFB in sago palm roots shifted by the oxygen level in the root interior affected by waterlogging in the soil.