Macroecology of methane-oxidizing bacteria: the β-diversity of pmoA genotypes in tropical and subtropical rice paddies

Studies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance-decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of -diversity with geographical distance across continents (12000km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in-depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three-dimensional space (multidimensional scaling). The ordination suggests that type II methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II methanotrophs

DataSheet_1_Cercozoan diversity of spring barley grown in the field is strongly plant compartment specific.pdf

Protists are an important part of the plant holobiome and influence plant growth and pathogenic pressure as consumers. Hordeum vulgare is one of the most economically important crops worldwide, and its yield depends on optimal environmental plant-growth conditions and pathogen defense. This study aimed to analyse the natural compositions of the cercozoan diversity, one of the most important and dominant protist phyla, of spring barley at different developmental stages, from different plant compartments over two years. Hordeum vulgare bulk soil samples were taken before seeding and after harvest on an organic farming field. Bulk soil, rhizosphere soil, roots and leaves were sampled at the flowering and ripening stages, and analysed with cercozoan-specific primers. Results showed a clear dominance of the families Sandonidae, Allapsidae, Cercomonadidae, Rhogostomidae and the order Glissomonadida in all sample types. Separated analyses of root, leaf and soil samples showed that members of the family Sandonidae were strongly enriched in leaf samples, while members of the Allapsidae family were enriched in the roots. No compositional differences were detected between the different plant developmental stages, except for the beta diversity of the leaf samples at the flowering and ripening stages. It can be concluded that the cercozoan diversity of spring barley is primarily affected by the plant compartment and not by the plant developmental stage. Further studies are needed to analyze the cercozoan community in greater taxonomic depth and to target their ecological function.</p