Environmental Isolate of Rahnella aquatilis Harbors Class 1 Integron

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Detection of antimicrobial-resistant Enterobacterales in insectivorous bats from Chile

Enterobacterales of clinical importance for humans and domestic animals are now commonly detected among wildlife worldwide. However, few studies have investigated their prevalence among bats, particularly in bat species living near humans. In this study, we assessed the occurrence of Extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-resistant (CR) Enterobacterales in rectal swabs of bats submitted to the Chilean national rabies surveillance program from 2021 to 2022. From the 307 swabs screened, 47 (15%) harboured cefotaxime-resistant Enterobacterales. Bats carrying these bacteria originated from 9 out of the 14 Chilean regions. Most positive samples were obtained from Tadarida brasiliensis (n = 42), but also Lasiurus varius, L. cinereus and Histiotus macrotus. No Enterobacterales were resistant to imipenem. All ESBL-Enterobacterales were confirmed as Rahnella aquatilis by MALDI-TOF. No other ESBL or CR Enterobacterales were detected. To our knowledge, this is the first screening of antibiotic-resistant bacteria in wild bats of Chile, showing the bat faecal carriage of R. aquatilis naturally resistant to cephalosporins, but also including acquired resistance to important antibiotics for public health such as amoxicillin with clavulanic acid. Our results suggest unknown selective pressures on R. aquatilis, but low or no carriage of ESBL or CR Escherichia coli and Klebsiella spp. Future studies should assess the zoonotic and environmental implications of R. aquatilis, which are likely present in the guano left by bats roosting in human infrastructures.

Isolation, Characterization, and Genomic Analysis of Multidrug-Resistant Rahnella aquatilis from Fruits in China

Many fruits are consumed raw and act as vehicles for spreading antibiotic-resistant bacteria to consumers; hence, preventing foodborne diseases and ensuring food safety of fresh fruits are challenging. In this study, we aimed to analyze contamination in fruits and characterize antibiotic resistance genes in pathogenic microorganisms isolated from fruits. Sixty fruit samples were collected and screened for pathogenic microorganisms. The strains were identified, and the minimum inhibitory concentration for various antibiotics was determined. Antibiotic-resistant strains were analyzed by whole-genome sequencing. We isolated strain L46 from lemon samples and identified it as Rahnella aquatilis using MALDI-TOF MS and 16S rRNA sequencing. The whole genome of R. aquatilis L46 was 4.94 Mb and contained 291 putative antibiotic resistance genes (6.53%), including the gene coding for β-lactamase RAHN-1 CTX-M-2 and conferring resistance to ampicillin, polymyxin B, nitrofurantoin, imipenem, aztreonam, and cefotaxime. Thus, fruits can pose a potential hazard to human health and require greater surveillance and attention, as they may contain pathogenic and multidrug-resistant bacteria.

The dynamic gut microbiota of zoophilic members of the Anopheles gambiae complex (Diptera: Culicidae)

The gut microbiota of mosquitoes plays a critical role in the life history of the animal. There is a growing body of research characterising the gut microbiota of a range of mosquito species, but there is still a paucity of information on some members of the Anopheles gambiae complex. In this study, the gut microbiota of four laboratory strains were characterised. SENN (Anopheles arabiensis-insecticide susceptible major vector), SENN DDT (Anopheles arabiensis-insecticide resistant major vector), MAFUS (Anopheles merus-minor vector) and SANGWE (Anopheles quadriannulatus-non-vector) were used in this study. The microbiota of fourth instar larvae, 3-day old, 15-day old non-blood fed and 15-day old blood fed females were characterised by MALDI-TOF mass spectroscopy and 16 s rRNA gene sequencing by next generation sequencing. The four strains differed in species richness but not diversity. The major vectors differ in β-diversity from that of the minor and non-vectors. There was no difference in α- or β-diversity in 15 non-blood fed females and 15-day old females that had 3 blood meals before day 15. These differences may be related to a mixture of the effect of insecticide resistance phenotype as well as a potential relationship to vector competence to a limited extent. Bacterial diversity is affected by species and age. There is also a potential relationship between the differences in gut microbiota and capacity to transmit parasites. This genetic background of the mosquitoes, however, play a major role, and must be considered in this relationship.

Prevalence of Antimicrobial Resistance and Hemolytic Phenotypes in Culturable Arctic Bacteria

Many Arctic biomes, which are populated with abundant and diverse microbial life, are under threat: climate change and warming temperatures have raised concerns about diversity loss and possible emergence of pathogenic microorganisms. At present, there is little information on the occurrence of Arctic virulence-associated phenotypes. In this study we worked with 118 strains of bacteria (from 10 sampling sites in the Arctic region, located in Greenland and the Svalbard Archipelago) isolated using R2A medium. These strains belong to 4 phyla and represent 36 different bacterial genera. Phenotypic resistance to 8 clinically important antimicrobials (ampicillin, chloramphenicol, ciprofloxacin, cefotaxime, erythromycin, imipenem, kanamycin, and tetracycline) and thermotolerance range were determined. In addition, a screening of all isolates on blood agar media and erythrocytes suspension of bovine and sheep erythrocytes for virulence-linked hemolytic activity was performed. Although antimicrobial resistance profiles varied among the isolates, they were consistent within bacterial families and genera. Interestingly, a high number of isolates (83/104) were resistant to the tested concentration of imipenem (4 mg/L). In addition, one third of the isolates showed hemolytic activity on blood agar, however, in only 5% of the isolates hemolytic activity was also observed in the cell extracts when added to erythrocyte suspensions for 60 min. The observed microbial phenotypes contribute to our understanding of the presence of virulence-associated factors in the Arctic environments, while highlighting the potential risks associated with changes in the polar areas in the light of climate change.

Game animals as a reservoir of rarely recorded opportunistic bacteria

In Poland, the population of game animals, including wild boars, roe and deer, is constantly increasing. The tonsils of wild game animals are a place of large variety of microorganisms. The pathogenic bacteria present in them, such as E. coli, Y. enterocolitica and Salmonella sp. are the most common source of meat infection. The opportunistic bacteria R. aquatilis, P. fluorescens, S. liquefaciens, S. fonticola and S. plymuthica also play an important role in public health. S. liquefaciens may be an opportunistic pathogen and in people causes sepsis and inflammation of the cornea. The protease, nuclease, phospholipase A, flagella, elastase and toxins haemolysin and proteolysin are responsible for its ability to cause disease symptoms. S. plymuthica, a rod commonly found in the environment, produces a red dye. It is most often isolated from soil, water and food. In humans, it causes infections of burn wounds, soft leg tissue as well as post-operative wounds and bacteraemia. Typically, the environmental rod S. fonticola differs from other Serratia sp. by the lack of extracellular enzymes. It causes wound infections and bacteraemia resulting from urinary tract infections. Bacteria from the genus Serratia sp. show a natural resistance to glycopeptides, rifampicin and erythromycin. The aquatic rod R. aquatilis in humans causes opportunistic infections of the urinary tract, wounds, bacteraemia and endocarditis. It exhibits natural resistance to antibiotics from the group of cephalosporins, penicillins and macrolides and quinolones. It is conditioned by the presence of class 1 integrons and class A β-lactamases. The virulence factors of R. aquatilis are also LPS and adhesin. P. fluorescens in humans is responsible for bacteraemia. It also exhibits resistance to human serum thanks to outer membrane proteins and has T3SS, which effectively infects the host.

The complete genome sequence of Rahnella aquatilis ZF7 reveals potential beneficial properties and stress tolerance capabilities

Rahnella aquatilis ZF7 is a plant beneficial strain isolated from Sakura tree soil with potential for biocontrol. Here, we present the complete genome sequence of R. aquatilis ZF7, which consists of one 4.49 Mb circular chromosome and a 54-kb plasmid named pRAZF7. Phylogenetic analyses revealed that R. aquatilis ZF7 is much similar to the strains Rahnella sp. Y9602 and R. aquatilis HX2 than others evaluated. In this study, multiple genes encoding functions that likely contribute to plant growth promotion, biocontrol and stress tolerance were identified by comparative genome analyses, including IAA production, phosphate solubilization, antibiotic resistance and formation of Se nanoparticles (SeNPs). In addition, these functions were also confirmed by in vitro experiments. Considering its ability to form SeNPs, strain R. aquatilis ZF7 will contribute to nano-agriculture. Overall, the features of R. aquatilis ZF7 make it a high potential and competitive strain in biocontrol, and the genome data will help further studies on the mechanisms of plant growth promotion and biocontrol.