Characterization of Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov., isolated from a high-elevation wetland, by phenotypic and genomic analyses

Abstract

Two psychrotolerant facultative anaerobes, strains B7-2 and B5, were isolated from the Zoige Wetland on the Qinghai-Tibetan Plateau. The 16S rRNA gene sequences of strains B7-2 and B5 shared high similarity (>99 %) with those of the type strains of the genus Trichococcus, while their digital DNA-DNA hybridization values with each other (49 %) and with the reference type strains (48-23 %) were lower than 70 %, which suggest that they represent two novel species of the genus Trichococcus. Cells of strains B7-2 and B5 were immotile cocci, grew in the temperature range of 4-37 °C (optimum 25 °C) and were alkaliphilic with optimum growth at pH 9.0. The major components of the cellular fatty acids were C16 : 0, anteiso-C17 : 0 and C18 : 0 for strain B7-2, and C16 : 0, anteiso-C17 : 0, C18 : 1ω9c and C18 : 0 for strain B5. The genomic DNA G+C contents were 46.0 and 46.7 mol% for strains B7-2 and B5, respectively. Based on physiological and genomic characteristics, it is suggested that strains B7-2 and B5 represent two novel species within the genus Trichococcus, for which the names Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov. are proposed. The type strains are B7-2 (=DSM 104691=KCTC 33886) and B5 (=DSM 104692=KCTC 33885), respectively.

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

“…Specifically for the Trichococcus group, it is patent that using protein domains or 16S rRNA genes results in different clustering of the bacteria. This corroborates with the fact that information in the 16S rRNA gene of Trichococcus species is not enough to resolve taxonomy at species level [3,4,6], and does not predict the functional relatedness of the different species. 16S rRNA gene and protein domain clustering for the other analysed LAB species is much more conserved (Fig.…”

“…Type strains of existing Trichococcus species have been isolated from diverse and geographically spread ecosystems. Various species derive from waste treatment systems or contaminated sites: T. flocculiformis (activated sludge) [1], T. pasteurii (septic pit sludge) [2], T. collinsii (soil spilled with hydrocarbons) [2], T. ilyis (sulfate reducing anaerobic sludge) [3], T. shcherbakoviae (sludge from low-temperature anaerobic reactor) [4]; while others were isolated from natural environments: T. patagoniensis (guano from penguin, Patagonia) [5], T. palustris (swamp, Russia) [2], and T. paludicola and T. alkaliphilus (high elevation wetland, Tibet) [6].…”

“…Trichococcus species share a very high 16S rRNA gene sequence identity, in the range of 98-100% [2][3][4]6]. This often impairs the taxonomic classification of new strains within this genus on the basis of 16S rRNA gene sequence identity, and therefore whole genome comparison needs to be performed.…”

“…Trichococcus species are related to the lactic acid bacteria (LAB), and phylogenetically close to the genera Carnobacterium and Aerococcus [11]. Described Trichococcus species can all grow on glucose, cellobiose, D-mannose, fructose and sucrose [1][2][3][4][5][6]. However, T. pasteurii and Trichococcus strain ES5 are the only strains within the genus capable of converting glycerol to mainly 1,3-PDO [12], with comparable product yields to those of other 1,3-PDO producers, such as Clostridium butyricum and Klebsiella pneumoniae [13,14].…”

“…1,3-PDO is used as a building block in chemical industry [15], and the discovery of new efficient and resilient biocatalysts for its production are of interest for biotechnological industry. In general, Trichococcus species have a broad temperature range for growth (commonly from 4°C to 40°C) [1][2][3][4][5][6]. T. patagoniensis and T. shcherbakoviae can grow at negative temperatures and tolerate salinities up to 5% (w/v) NaCl [4,5], which is also the case for several related Carnobacterium species, such as C. funditum, C. alterfunditum and C. pleistocenium [16,17], but no other Trichococcus species.…”