The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress

Abstract

Members of the bacterial genus Agrococcus are globally distributed and found across environments so highly diverse that they include forests, deserts, and coal mines, as well as in potatoes and cheese. Despite how widely Agrococcus occurs, the extent of its physiology, genomes, and potential roles in the environment are poorly understood. Here we use whole-genome analysis, chemotaxonomic markers, morphology, and 16S rRNA gene phylogeny to describe a new isolate of the genus Agrococcus from freshwater microbialites in Pavilion Lake, British Columbia, Canada. We characterize this isolate as a new species Agrococcus pavilionensis strain RW1 and provide the first complete genome from a member of the genus Agrococcus. The A. pavilionensis genome consists of one chromosome (2,627,177 bp) as well as two plasmids (HC-CG1 1,427 bp, and LC-RRW783 31,795 bp). The genome reveals considerable genetic promiscuity via mobile elements, including a prophage and plasmids involved in integration, transposition, and heavy-metal stress. A. pavilionensis strain RW1 differs from other members of the Agrococcus genus by having a novel phospholipid fatty acid iso-C15:1Δ4, β-galactosidase activity and amygdalin utilization. Carotenoid biosynthesis is predicted by genomic metabolic reconstruction, which explains the characteristic yellow pigmentation of A. pavilionensis. Metabolic reconstructions of strain RW1 genome predicts a pathway for releasing ammonia via ammonification amino acids, which could increase the saturation index leading to carbonate precipitation. Our genomic analyses suggest signatures of environmental adaption to the relatively cold and oligotrophic conditions of Pavilion Lake microbialites. A. pavilionensis strain RW1 in modern microbialites has an ecological significance in Pavilion Lake microbialites, which include potential roles in heavy-metal cycling and carbonate precipitation (e.g., ammonification of amino acids and filamentation which many trap carbonate minerals).

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere

“…On other hand, comparing only the genera also revealed 22 genera exclusively present in CD samples. Most of these genera are commonly found in soil, forest and water sources including marine ( Aamot, Hofgaard & Lysoe, 2017 ; Bennur et al, 2015 ; Chase et al, 2016 ; Hayashi et al, 2018 ; Kumari, Singh & Lal, 2016 ; Li et al, 2020 ; Orsini et al, 2014 ; White et al, 2018 ; Zheng et al, 2017 ). However, few of the genera like Kocuria , Cronobacter , Aeromonas are also linked to human infection as per some recent studies ( Kandi et al, 2016 ; Parra-Flores et al, 2018 ).…”

First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna

“…A hypothesis is that antibiotic pressure helps maintaining the presence of metal resistance as they are both physically linked on plasmids (Foster, 1983). Moreover, White et al (2018) have proposed the alternative hypothesis that initially these genes may have conferred heavy-metal resistance, but now they are operating under other stressors.…”

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

“…Bacteria at this depth should be adapted to cold temperature, low phosphorus, and alkaline conditions. Recently, we have described another heterotrophic pigmented isolate Agrococcus pavilionensis strain RW1 (White et al, 2013b, 2018a), that was co-isolated with strain RW2 from the same microbialite and enrichment.…”

“…All microscopy (i.e., SEM/light) and culture plate photo (C–E) were completed at strain RW2 standard growth parameters on solidified M-agar at 30°C, pH 7 and concentration 1% (w/v) NaCl. Panels (A,B) adapted from White et al (2018a).…”