The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges

Abstract

Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na+/K+), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake microbialites. Strain RW2 could also contribute to microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C30 carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., microbialites/microbial mats), and a blueprint model for diverse metabolic processes.

Influence of the digestive/reproductive tract microbiota on chicken egg production beyond host genetics

“…Consistent with a recent study in chickens [66], this finding may be related to the alkaline pH value in the chicken reproductive tract that maintains sperm motility [70,71], in contrast to the low pH in humans that prevents pathogen infection and growth [72][73][74]. Exiguobacterium is a genus of bacilli and a member of the low-GC phylum Firmicutes; it has been found in areas covering a wide range of temperatures, pH values, salinity and other conditions [75], and it also produces organic acids and hydrolytic enzymes [76], even having some potential function in the degradation of toxic substances [77]. Given that the reproductive tract and digestive tract share a common exit in the cloaca, we propose that microbial exchange occurs at this site, resulting in similar microbiotas at the distal end of both tracts.…”

Pan‐genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11

“…In 1980, it was changed to Brevibacterium acetylicum incertae sedis . Since 1984, 19 new species have been added to the genus Exiguobacterium (Chaturvedi and Shivaji, 2006; Crapart et al ., 2007; Singh et al ., 2013; Dastager et al ., 2015; White III et al ., 2019; Meng et al ., 2020). In 2001, Boone and team assigned this genus to the family bacillaceae, however, later on shifted this genus to order Bacillales (Boone and Castenholz, 2001; Vos et al ., 2009).…”

A rationally identified marine GH1 β‐glucosidase has distinguishing functional features for simultaneous saccharification and fermentation

“…[26][27][28][29][30][31] The versatile genus Exiguobacterium comprises a diverse group of pigmented gram-positive bacteria thriving in extreme environments over a wide temperature range (12-55 °C), such as glacial ice, hot springs, plant rhizospheres, Siberian permafrost, tropical soils, and temperate soils. [32][33][34][35] The ability to grow over a broad range of temperatures makes this genus an interesting source of hydrolytic enzymes with industrial and environmental applications becoming a model for evolutionary and biotechnological studies. [32][33][34][35] Exiguobacterium sp.…”

“…[32][33][34][35] The ability to grow over a broad range of temperatures makes this genus an interesting source of hydrolytic enzymes with industrial and environmental applications becoming a model for evolutionary and biotechnological studies. [32][33][34][35] Exiguobacterium sp. VSG-1, for instance, which has been investigated for the production of bioethanol from sugarcane bagasse, harbors a rich variety of enzymes such as cellulases, pectinases, mannanases, xylanases, and tannases.…”

“…Based on phylogenetic analysis, 38 we have verified that the β-glucosidase from Exiguobacterium marinum (EmBgl) is the closest to EaBgl (83.94% sequence identity), which is found in a strain categorized as psychrophilic / mesophilic and with the capacity to grow in more acidic conditions. [33][34][35] In this work, therefore, we attempted to address the following questions: (i) whether EmBgl throughout the evolution maintained the characteristics of acting in milder temperatures and at high concentrations of glucose; (ii) whether, unlike its ortholog, it has the capacity to act at lower pH levels, and (iii) whether EmBgl has the potential to be employed in an SSF process to produce 2G ethanol. To the best of our knowledge, this is the first study exploring the bacterium E. marinum as source of enzymes for saccharification of lignocellulosic materials.…”