Comparative analysis of microbial communities of soils under contrasting microclimates

Abstract

Understanding how microbiomes influence the life cycle and fitness of crops, and how global change drivers disrupt this network, is pivotal for an understanding of the crop as a holobiont, and of how to provide solutions for Nordic agricultural crop resilience under climate change. Despite decades of use of plant growth-promoting rhizobacteria (PGPR), there is an intrinsic problem with their applications, as it has become evident that their functionality and performance rely on interactions with the environment and with other microorganisms. The synthetic crop-promoting rhizobacterial community strains are being outcompeted by native communities, or their colonisation and active principles are being reduced to ineffective levels. This is the result of the communities being selected on taxonomic criteria rather than qualitative analysis of the microbiome-associated plant phenotypes. In this context there in an urgent need for an approach studying the microbial community and plant complementarity traits from indigenous communities. Here we report the pattern of bacterial distributions at the Evolution Canyon (EC) in Israel to gain insight into microbiomes exposed to contrasting microclimates at the North Facing Slope (NFS) and South Facing Slope (SFS) sun and shade areas using high-throughput sequencing. While the NFS and SFS shaded areas bacterial distribution didnt differ, our results show significant differences between the NFS and the SFS sunny areas. The families Geodermatophilaceae, Beijerinckiaceae, and Pseudonocardiaceae are dominant in the NFS sun area, and the families Rubrobacteriaceae, unclassified Solirubrobacterales bacterium 67-14, unclassified Actinobacteriota, class Gaiellales dominate at the SFS sun area. Likewise, both Shannon and inverse Simpsons diversity indices are higher at the NFS sun area compared to the NFS shaded area. There was no substantial difference between diversity indices in SFS sun and shaded area. Our results advance our understanding of the bacterial distributions at what is in effect a natural laboratory of ecosystems that probably evolved 5-7 million years ago. The data are an important step towards using transcriptomics, metabolomic profiles and selective plating for figuring out key strains and the supporter strains that strengthen the ecological functions of the key strains. Collectively, this will enable us to assemble redundant and stable synthetic PGPR communities consisting of key and supporter strains for promoting plant health and stress tolerance under changing climates.