Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms

Nadine Praeg,Paul Illmer

doi:10.1038/s41598-020-79143-y

Abstract

Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate. Here we report on the microbial diversity within the rhizosphere of Larix decidua, a dominant tree species in the Alps, as compared with the microbiome within the surrounding soil. We describe how increased light intensity influenced the rhizobiome and put emphasize on methane cycling microorganisms. Microbial taxa were classified into 26 bacterial, 4 archaeal and 6 fungal phyla revealing significant differences between bulk and rhizosphere soils. The dominant prokaryotic phyla were Proteobacteria, Acidobacteria, Actinobacteria (both, rhizosphere and bulk soil) and Bacteroidetes (rhizosphere soil only) and dominant fungal phyla in both fractions included Ascomycota and Basidiomycota. The rhizosphere community was indicated by Suillus sp., plant growth-promoting bacteria and Candidatus Saccharibacteria. Predicted genes in membrane transport and carbohydrate metabolism were significantly more abundant in rhizosphere soils while genes connected with energy metabolisms and cell motility increased in bulk soils. Dominant methanotrophic microorganisms were Upland Soil Cluster (USC) α methanotrophs, Methylogaea spp. and Methylosinus spp., while most methanogens belonged to Methanomassiliicoccales. The overall abundance of methanotrophs distinctly increased in the rhizosphere but to a very different species-specific extent. The increased light intensity only led to minor changes in the rhizobiome, nevertheless a couple of indicator species (e.g. Pseudomonas sp.) for intensified light conditions were established.

Highlights

Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate
Bacterial communities in the investigated forest bulk and rhizosphere soil samples were composed of 13,492 different operational taxonomic units (OTUs) mainly belonging to the phyla of Proteobacteria (36% on average including all samples), Acidobacteria (16%), Actinobacteria (11%), Bacteroidetes (7%), Candidatus Saccharibacteria (6%), Verrucomicrobia (5%) and Planctomycetes (4%)
The relative abundance of Acidobacteria, Planctomycetes, Verrucomicrobia and unclassified Bacteria decreased in the rhizosphere fraction while the phylum of Proteobacteria on phylum level did not significantly differ between the fractions

Summary

Introduction

Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate. 10–40% of the photosynthetically fixed C is excreted by the roots including organic acids, sugars, amino acids, lipids, coumarins, flavonoids, proteins, enzymes, aliphatics and aromatics all leading to an increased C-turnover[4,5] Such hotspots show higher microbial activities and abundances and altered community compositions compared to the surrounding bulk soil[3,4,6,7]. The aims of the study were to (1) analyze the microbiome in the rhizosphere of Larix decidua in comparison to that of the surrounding soil, (2) investigate whether Larix affects microbial communities of methanogenic and methanotrophic communities and (3) investigate whether increased light intensities can alter the plant effect on microbial communities

Objectives

Methods

Results

Conclusion