Abstract
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.
Highlights
The rhizosphere soil influenced by root secretions contains up to one hundred billion microbial cells per gram root [1] and about thirty thousand prokaryotic species [2]
(≥100 nt). 9,660,445 non-redundant ORFs were generated from metagenomic libraries, of which 0.21 million (15.1%) were complete ORFs containing both starting and ending codons. 49.89% of the unigenes can be assigned to taxonomic annotations, which suggesting that there was a huge resource pool for novel functional gene in rhizosphere soil of the shelterbelt poplar
Through our analysis in this paper, the microbiome composition and functionality in rhizosphere of poplar are likely influenced by the health condition of poplar and available potassium (AK) of soil
Summary
The rhizosphere soil influenced by root secretions contains up to one hundred billion microbial cells per gram root [1] and about thirty thousand prokaryotic species [2]. As the second genome of the plant, the complex root-associated microbial community is crucial for nutrition and plant health [3]. A variety of organic compounds including carbohydrate, organic acids, phenol, and other substances secreted by plant roots in the surrounding soil, which are the sources of nutrients and vitamins for various bacteria, stimulating the development of soil microbial communities and changing their activity and ecological distribution [2,4]. The beneficial microbiome associated with roots, including the so-called plant growth promoting (PGP) bacteria, can contribute to alleviate plant stress by a variety of mechanisms [5]. Recent evidence suggests that differences among plant species when grown on the same soil or between plant genotypes have a significant impact on the rhizosphere microbiome [8,9]. We were unable to formulate how root microbiota change under different plant phenotype, especially artificial vegetation under natural conditions
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