Identification of novel sRNAs involved in oxidative stress response in the fish pathogen Vibrio alginolyticus by transcriptome analysis

Investigating the metabolic and oxidative stress induced by biofouled microplastics exposure in Seriola lalandi (yellowtail kingfish)

Microorganisms quickly colonise microplastics entering the ocean, forming a biofilm that, if ingested, is consumed with the microplastics. Past research often neglects to expose fish to biofouled microplastics, opting only for clean microplastics despite the low likelihood that fish will encounter clean microplastics. Here, we investigate the physiological impacts of biofouled polyethylene microplastic (300-335 μm) exposure in juvenile fish. Intermittent flow respirometry, antioxidant enzyme activity, and lipid peroxidation were investigated after fish were exposed to clean, biofouled, or no microplastic beads. Fish exposed to biofouled microplastics had a wider aerobic scope than those exposed to clean microplastics while antioxidant enzyme and lipid peroxidation levels were higher in clean microplastics. Clean microplastic exposure indicated higher fitness costs, potentially due to a nutritional advantage of the biofilm or varying bioavailability. These findings highlight the importance of replicating natural factors in exposure experiments when predicting the impacts of increasing pollutants in marine systems.

Deletion of ArmPT, a LamB-like protein, increases cell membrane permeability and antibiotic sensitivity in Vibrio alginolyticus

Vibrio bacterial species are dominant pathogens in mariculture animals. However, the extensive use of antibiotics and other chemicals has increased drug resistance in Vibrio bacteria. Despite rigorous investigative studies, the mechanism of drug resistance in Vibrio remains a mystery. In this study, we found that a gene encoding LamB-like outer membrane protein, named ArmPT, was upregulated in Va under antibiotic stress by RT-qPCR. We speculated that ArmPT might play a role in Va's drug resistance. Subsequently, using ArmPT gene knockout and gene complementation experiments, we confirmed its role in resistance against a variety of antibiotics, particularly kanamycin (KA). Transcriptomic and proteomic analyses identified 188 and 83 differentially expressed genes in the mutant strain compared with the wild-type (WT) before and after KA stress, respectively. Bioinformatic analysis predicted that ArmPT might control cell membrane permeability by changing cadaverine biosynthesis, thereby influencing the cell entry of antibiotics in Va. The higher levels of intracellular reactive oxygen species and the infused content of KA showed that antibiotics are more likely to enter the Va mutant strain. These results uncover the drug resistance mechanism of Va that can also exist in other similar pathogenic bacteria.

The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

Comprehensive depiction of novel heavy metal tolerant and EPS producing bioluminescent Vibrio alginolyticus PBR1 and V. rotiferianus PBL1 confined from marine organisms

The current study depicts the isolation of luminescent bacteria from fish and squid samples that were collected from Veraval fish harbour. From Indian mackerel, total 14 and from squid, total 23 bioluminescent bacteria were isolated using luminescence agar medium. Two bioluminescent bacteria with highest relative luminescence intensity PBR1 and PBL1 were selected. These two isolates were subjected to detailed biochemical characterization and were tested positive for 5 out of 13 biochemical tests. Furthermore, both PBR1 and PBL1 were able to ferment cellobiose, dextrose, fructose, galactose, maltose, mannose, sucrose and trehalose with acid production. Based on 16S rRNA partial gene sequence analysis, PBR1 was identified as Vibrio alginolyticus and PBL1 as V. rotiferianus. Antibiotic susceptibility test using paper-disc method showed that PBR1 and PBL1 were sensitive to chloramphenicol, ciprofloxacin, co-trimoxazole, gatifloxacin, levofloxacin, linezolid ad roxithromycin out of 18 antibiotics tested. Moreover, both strains were evaluated for their exopolysachharide (EPS) producing ability where PBR1 and PBL1 were able to yield 1.34 g% (w/v) and 2.45 g% (w/v) EPS respectively from 5 g% (v/v) sucrose concentration. Heavy metal toxicity assessment was carried out using agar well diffusion method with eight heavy metals and both the strains were sensitive to As(III), Cd(II), Ce(II), Cr(III), Cu(II), Hg(II) and while they showed resistance to Pb(II) and Sr(II). Based on these results, a study was conducted to demonstrate bio-removal of Pb and Sr by EPS of PBR1 and PBL1. Fourier transform infrared (FTIR) spectra revealed the functional groups of EPS involved in interaction with the heavy metals. Owing to the sensitivity for the remaining heavy metals, these bioluminescent bacteria can be used further for the development of luminescence-based biosensor.

Genes and novel sRNAs involved in PAHs degradation in marine bacteria Rhodococcus sp. P14 revealed by the genome and transcriptome analysis

Rhodococcus sp. P14 is able to degrade various polycyclic aromatic hydrocarbons (PAHs). In this study, 6 ring-hydroxylating dioxygenases and 24 monooxygenases genes related to PAHs degradation were identified in its genome. Moreover, various genes, like serine hydrolase, hydratase, alcohol dehydrogenase, protocatechuate 3,4-dioxygenase, β-ketoadipate CoA transferase and β-Ketoadipyl CoA thiolase, which were supposed to be involved in PAHs degradation were also identified. Based on the genome analysis, the proposed PAHs degradation pathway was constructed in P14 strain, which showed that PAHs was degraded into the acetyl CoA and succinyl CoA, then mineralized to CO₂ via the TCA cycle. Furthermore, several genes, including cytochrome P450 (RS16725; RS16695; RS12220), catalase (RS15825), dehydrogenase (RS15755; RS18420) and hydrolase (RS16460; RS24665), showed increased expression level during PAHs degradation according to the transcriptome data. In addition, 12 novel sRNAs which were supposed to have the regulation function in PAHs degradation were identified. This study gives us the outlook of PAHs degradation pathway in Rhodococcus sp. P14. Moreover, it first demonstrates that sRNAs may harbor the regulation function in PAHs degradation.