Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis

Abstract

Background and Aims Canyon streambeds in the hyperarid Atacama Desert surprisingly harbor magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of Equisetum xylochaetum sampled from remote sites differing in degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems. Methods To ensure that analyses were conducted on microbes most closely-associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were demonstrated with SEM. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared to those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes. Key Results Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea, Rhodoferax) inferred from taxonomic and functional gene analysis of contigs–but not unassembled reads–to occur on surfaces of (or within) plants at relatively high abundance (>50X genomic coverage), indicated roles in N, S, and other mineral cycling processes. Comparison between sites indicated impacts on biogeochemical functions, e.g., reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than Mo nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads. Conclusions Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa , a Himalayan medicinal herb

“…Bradyrhizobium as an endophyte and its role in enhancing nodulation and photosynthetic ability have been investigated in rice ( 113 – 115 ), peanut ( 116 ), and soybean ( 117 ). Phaeospirillum genera as potential nitrogen fixing bacteria was reported in Atacama desert giant horsetail plant ( 118 ), and also as an endophyte in wheat ( 119 ). These distinct plant-beneficial endophytic communities associated with different parts of wild P. kurrooa may be responsible for higher content of secondary metabolites and absence of these communities in Tc plant reduced the secondary metabolites.…”