Biology subjects

Lapidus, A.

Publications and source records attributed to Lapidus, A..

5 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↗

bioRxiv2023

Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil

Chernevaya taiga in Western Siberia, Russia, is a special environment with fertile soil, extraordinarily high herbaceous plant sizes, and incredibly quick rates of plant residues breakdown. We postulated that a unique rhizospheric fungal community would be created when growing crops on chernevaya soil, which has never been used for agriculture. These may be the source for the novel effective biostimulator and biocontrol fungal agents for modern agriculture. In this study, we analyzed the fungal communities in the rhizosphere of spring wheat and radish cultivated in greenhouse experiments on chernevaya and control soils using high-throughput ITS sequencing. Additionally reprehensive fungal strains were isolated and examined for the stimulation of wheat seedlings growth. The research shows that Ascomycota and Mortierellomycota were the most abundant phyla in the rhizospheric fungal community, mainly composed of Mortierella species. The control soils were abundant in Mucoromycota, represented mostly by Mucor and Umbelopsis. Potentially plant-pathogenic fungi Fusarium and Oidiodendron were found only in the rhizosphere of crops grown in the control soil. Whereas plants grown on chernevaya soil have a wide variety of possible biocontrol fungi. Novel fungal isolates demonstrated stimulating effect on the growth and biomass accumulation of wheat seedlings. The findings of the study imply that the creation of biorational products for crop growth and protection may depend on the taxonomic composition analysis of the rhizospheric mycobiota of the crops growing on the soil with the unique characteristics.

microbiology↗

bioRxiv2020

Extending rnaSPAdes functionality for hybridtranscriptome assembly

BackgroundDe novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. ResultsIn this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. ConclusionTo evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used. Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available for Linux and MacOS under GPLv2 license at cab.spbu.ru/software/rnaspades/ and github.com/ablab/spades.

bioinformatics↗

bioRxiv2018

Genome-wide analysis of drug resistant Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in Russia

Mycobacterium tuberculosis is a highly studied pathogen due to public health importance. Despite progress in M.tuberculosis genome diversity analysis there remain insufficient data on genome analysis of M.tuberculosis strains associated with pulmonary vs. extrapulmonary TB (PTB or XPTB respectively) tissue localization. Here we conduct comparative analysis of whole-genome sequence (WGS) for clinical M.tuberculosis strains collected from patients with PTB (n=72) and XPTB (n=73) localization. We further analyze the incidence of point mutations widely used for drug resistance detection in laboratory practice.\n\nM.tuberculosis isolates were collected from patients with varying clinical status from 2007 to 2014 in Russia. Bacterial DNA was extracted and sequenced using MiSeq platform (Illumina).\n\nWGS data allowed identifying M.tuberculosis substrains associated with distinctions in the occurrence in PTB v s. XPTB cases. There occurred little statistically significant specific DNA variants or genotypes diagnostic of tissue distribution, however phylogenetic analyses did reveal M.tuberculosis genetic substrains associated with TB localization. XPTB was associated with Beijing CAO, A and 4.8 groups, while PTB localization was associated with group LAM (4.3). Further, XPTB strain in some cases showed elevated drug resistance patterns relative to PTB isolates. HIV is significantly associated with the development of XPTB in the Beijing B0/W148 group and among unclustered Beijing isolates.\n\nThis research analysis pinpointed genomic markers identified in XPTB and PTB with detailed characterization of drug-resistance markers of Russian M.tuberculosis isolates. We suggest that further comprehensive analysis of bacterial and human biological signatures might allow for better understanding consistent pattern of XPTB development.\n\nSummaryThis paper gives genome-wide characteristics of Mycobacterium tuberculosis strains collected from pulmonary and extrapulmonary tuberculosis patients:\n\n- M.tuberculosis genetic strains associated with TB tissue localization,\n\n- influence of HIV co-infection on TB dissemination;\n\n- mutations associated with M.tuberculosis drug resistance.

genomics↗

bioRxiv2018

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

SummaryPossibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.\n\nAvailability and implementationrnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.

bioinformatics↗