Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota

Abstract

The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.

Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

“…The horizontal gene transfer (HGT) profile, “mobileome”, of Lactobacillaceae was identified as follows: The Integrated Microbial Genomes Annotation Pipeline (IMGAP) v.5.0 ( Markowitz et al, 2010 ) under default mode was used to identify horizontally transferred genes (HTGs) in the genomic sequences of Lactobacillaceae available at Genbank/IMG database, as conducted in previous studies ( Li et al, 2023 ). It used the following criteria to determine which genes inside the trialed genomes were horizontally transferred from remote descendants: genes with the finest BLASTP matches (most significant bit scores) or over 90% of the best hits discovered beyond the phylogenetic clade of the trialed genome (i.e., from remote phylum, class, etc.)…”