Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Abstract

Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0°C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094 T), is able to grow on glycerol with the production of 1,3-propanediol.

Trichococcus shcherbakoviae subsp. psychrophilus subsp. nov., a psychrotolerant facultative anaerobe isolated from a cold spring

“…Genome annotation of strain SKBG T supported its abilities to utilize a broad range of sugars which is typical for all other representatives of the genus [21]. We found numerous putative genes in the KEGG pathways of nucleotide sugar metabolism, galactose metabolism, glycolysis, gluconeogenesis, pyruvate metabolism, pentose phosphate pathway.…”

“…Genome annotation of strain SKBG T supported its abilities to utilize a broad range of sugars which is typical for all other representatives of the genus [21] Enzymatic activities of T. shcherbakoviae DSM 107162 T , T. patagoniensis DSM 18806 T , T. alkaliphilus DSM 104692 T , and strain SKBG T were determined using a set of enzymatic tests API ZYM (BioMérieux, France) according to the manufacturer's protocol. All strains were characterized by high activity of esterase and naphthol-AS-BIphosphohydrolase, and a positive reaction was observed for alkaline phosphatase.…”

“…It is interesting that all Trichococcus species possess a high number of cold-shock domains (CSD), genes related with a psychrotolerant phenotype. However, only five species were reported to grow at 0 °C [21].…”

Mechanisms Driving Microbial Community Composition in Anaerobic Co-Digestion of Waste-Activated Sewage Sludge

“…This Trichococcus (OTU 27) has regularly been reported as a typical member of wastewater treatment sludge PWASS MCC [ 71 ], and is described as a Gram-positive filamentous bacterium with coccoid cells and that is able to utilize sugars, alcohols, and polysaccharides. Recent work furthermore suggests that Trichococcus may be capable of metabolizing glycerol [ 72 ], and a role in the metabolization of lecithin seems likely. In the control reactors, the full-scale WWTP or the FW experiment, the Trichococcus relative abundance rarely, and if so, barely, exceeded 0.2%; however, it was regularly observed with relative abundances in excess of 2% in the PWASS.…”

Simultaneous Production of Multiple Antimicrobial Compounds by Bacillus velezensis ML122-2 Isolated From Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.]

“…Fastq files of the paired-end reads (2×250bp) were used as input for genome assemblies through the MEGAnnotator pipeline in default mode ( Lugli et al, 2016 ). Open reading frames prediction was performed by Prodigal v2.6.3 ( Strepis et al, 2020 ). Protein-encoding genes were automatically annotated using a BlastP v2.2.26 (cut-off value of E 0.0001) sequence alignments against the non-redundant protein (nr) database curated by NCBI.…”