Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems

Abstract

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.

Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet

“…Among the taxa with an increasing trend, we identified plant pathogens, e.g., Curtobacterium , Ceramothyrium carniolicum , and Mycosphaerelloides madeirae ( 73 – 75 ), as well as taxa potentially beneficial for the plant, e.g., bacterial strain P3OB-42 ( Myxococcaceae , suppression of phytopathogens [ 76 ]), Ampelomyces quisqualis (suppression of pathogenic fungi [ 77 ]), and Deinococcus (biodegradation of organic pollutants [ 78 ]). We suggest that these taxa may have been increasingly recruited by the plants or only dominated as a result of community succession due to their high tolerance to UV and ozone stress ( 79 – 81 ). Neutral models revealed that Curtobacterium , C. cygneicollum , C. carniolicum , M. madeirae , and A. quisqualis occurred in larvae more frequently than predicted.…”

A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility

“…This result is likely due to the hatchery receiving minimal natural sunlight, whereas BCS and the outdoor raceways receive ample amounts to support Cyanobacteria and algae. Additionally, significantly higher relative abundances of Deinococci were found at BCS (W = 3.51) and the outdoor raceways (W = 16.61) compared to the hatchery, possibly owing to the survivability of this bacterial class in high UV environments (36). Alphaproteobacteria were detected at significantly higher relative abundances in the hatchery compared to BCS (W = 9.61) and the outdoor raceways (W = 5.06), possibly indicating that this group fills the niche of photosynthetic microbes in low light environments and/or that high densities of fish support and seed Alphaproteobacteria.…”

Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

“…CircRNAs identified in the conidial and mycelial stages were compared to identify DE-circRNAs. Based on the criteria of |log 2 (fold change)| ≥1 and probability ≥0.8 [ 44 , 45 ], 940 circRNAs were considered to be significantly differentially expressed, including 930 up-regulated and 10 down-regulated circRNAs in the conidial vs. mycelial stage (Fig. 3 ).…”