Biology subjects

Andronov, E. E.

Publications and source records attributed to Andronov, E. E..

2 recordsLinked to original sources

bioRxiv2024

Metagenomic insights into the development of microbial communities of straw and leaf composts.

The objects of this study are microbial communities formed on two types of contrasting lignocellulosic biomass. To study them, a long-term experiment was set up and conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum. Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing was applied to study taxonomic, CAZy (Carbohydrate-Active enzymes), and PULs (Polysaccharide Utilization Loci) composition of microbial communities at different stages of decomposition between substrates. using a combination of 16S rRNA gene amplicon and long-read nanopore sequencing. In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified 9 MAGs (Metagenome-assembled genomes) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of degradation. MAGs classified as Bacteroidota (Chitinophaga, Ohtaekwangia), and Actinomycetota (Streptomyces) were found in both substrates, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequent PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be lacking PULs for complex substrates. ImportanceOur study explores the microbial communities from natural ecosystems, like soil and lignocellulosic waste, capable of decomposing lignocellulosic substrates. We used a comprehensive approach with chemical analyses of the substrates, amplicon and full-metagenome sequencing data. We have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

microbiology↗

bioRxiv2018

The Evolutionary Moulding in plant-microbial symbiosis: matching population diversity of rhizobial nodA and legume NFR5 genes

We propose the Evolutionary Moulding hypothesis that population diversities of partners in nitrogen-fixing rhizobium-legume symbiosis are matched, and tested it in nucleotide polymorphism of symbiotic genes encoding two components of the plant-bacteria signalling system. The first component is the rhizobial nodA acyltransferase involved in the fatty acid tail decoration of Nod factor (rhizobia signalling molecule). The second component is the plant NFR5 receptor, putatively required for Nod-factor binding.\n\nWe collected three wild growing legume species together with soil samples adjacent to the roots (soil pool) from one large 25-year fallow: Vicia sativa, Lathyrus pratensis and Trifolium hybridum nodulated by one of the two Rhizobium leguminosarum biovars (viciae and trifolii). For each plant species we prepared three pools for DNA extraction: the plant pool (30 plant indiv.), the nodule pool (90 nodules) and the soil pool (30 samples). NFR5 gene libraries from the plant pool and nodA gene libraries from nodule and soil pools were sequenced by Sanger technology and High-throughput pyrosequencing, respectively. Analysis of the data demonstrated concordance in population diversities of one symbiotic partner (rhizobia) the second partner (legume host), in line with the Evolutionary Moulding hypothesis. This effect was evinced by the following observations for each plant species: (1) significantly increased diversity in the nodule nodA popset (set of gene sequences derived from the nodule population) compared to the soil popset; (2) a monotonic relationship between the diversity in the plant NFR5 gene popset and the nodule rhizobial nodA gene popset; and (3) higher topological similarity of the NFR5 gene tree with the nodA gene tree of the nodule popset, than with the nodA gene tree of the soil popset. Both nonsynonymous diversity and Tajimas D were increased in the nodule popsets compared to the soil popsets, consistent with relaxation of negative selection and/or admixture of balancing selection underlying the Evolutionary Moulding effect. We propose that the observed genetic concordance arises from the selection of particular characteristics of the nodule nodA genes by the host plant.

evolutionary biology↗