Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas.

BACKGROUND: Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS: The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS: The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.

A comprehensive approach to how hospital effluents lead to oxidative stress and shift the gene expression in target organs of Danio rerio.

Hospital effluents represent a threat to the environment owing to the content of toxic substances capable of altering the structure and function of ecosystems. Despite the available information about the impact of hospital effluents on aquatic organisms, the molecular mechanism underlying this process has received little or no attention. The present study aimed to evaluate the oxidative stress and gene expression induced by different proportions (2 %, 2.5 %, 3 % and 3.5 %) of hospital effluent treated by hospital wastewater treatment plant (HWWTP) in liver, gut, and gills of Danio rerio at different exposure times. Significant increases in the levels of protein carbonylation content (PCC), hydroperoxides content (HPC), lipoperoxidation level (LPX) and superoxide dismutase (SOD) and catalase (CAT) activity were observed in most of the organs evaluated at the four proportions tested with respect to the control group (p < 0.05). It was found that at longer exposure times there is a lower response in SOD activity, suggesting catalytic depletion due to the oxidative environment at the intracellular level. The lack of complementarity between SOD and mRNA activity patterns indicates that the activity itself is subordinated to post-transcriptional processes. Upregulation of transcripts related to antioxidant processes (sod, cat, nrf2), detoxification (cyp1a1) and apoptosis (bax, casp6, and casp9) was observed in response to oxidative imbalance. On the other hand, the metataxonomic approach allowed the characterization of pathogenic bacterial genera such as Legionella, Pseudomonas, Clostridium XI, Parachlamydia and Mycobacterium present in the hospital effluent. Our findings indicate that although hospital effluent was treated by HWWTP, it caused oxidative stress damage and disrupted gene expression by decreasing the antioxidant response in Danio rerio.

Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.

Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.