Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA

Refractory tenosynovitis caused by Mycobacterium virginiense required repeated debridement: A case report and literature review

Mycobacterium virginiense is a slow-growing mycobacterium first described in 2016 as a novel species within the Mycobacterium terrae complex. To date, 8 cases of M. virginiense tenosynovitis or osteomyelitis have been reported, though none have been relapsed cases. A previously healthy 70-year-old Japanese man presented to a local orthopedic clinic with pain, swelling, and stiffness in his right middle finger. Initially diagnosed with trigger finger, he received multiple steroid injections. He was ultimately diagnosed with M. virginiense tenosynovitis. Despite synovectomy and antimicrobial therapy with ethambutol, rifampicin, and clarithromycin, a relapse occurred, necessitating a second tenosynovectomy, which led to remission. Antimicrobial therapy continued for approximately 20 months without recurrence. This case illustrates that M. virginiense can cause refractory tenosynovitis even in immunocompetent hosts. Delayed diagnosis and repeated local steroid injections may have contributed to disease progression and treatment failure in M. virginiense tenosynovitis.

Psychrophilic insights into petroleum degradation: Gene abundance dynamics

Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.

Combining gamma-radiation and bioaugmentation enhances wastewater's quality for its reuse in agricultural purposes

The reuse of wastewater in agriculture can be environmentally beneficial due to its abundance of nutrients that promote plant growth and soil fertility. However, wastewater effluents (WWE) are often considered sources of dissemination of bacteria, antibiotics, heavy metal resistance genes, and pathogens. In this study, we employed a combination of gamma irradiation and bioaugmentation as a strategy for WWE treatment. Gamma irradiation facilitates the elimination of pathogens and the degradation of complex organic matter, while bioaugmentation utilises a consortium of microorganisms specialised in metal sorption. Bacterial strains were isolated from soils irrigated with WWE and selected based on their tolerance to Cd (0.2 g L-1), Pb (1 g L-1) and Cu (1.5 g L-1). A consortium composed of Bacillus selenatarsenatis S53, Bacillus thuringiensis S15, and Staphylococcus edaphicus S107 was selected for their metal biosorption capacity, which was evaluated after 24 h of incubation in gamma-irradiated WWE (WWEI). The treated WWE was then used for pea (Pisum sativum L.) seeds germination over a 9 days' period. The bacterial consortium successfully biosorbed 180, 8085, and 125 µg g-1 dry weight of Cd, Pb, and Cu, respectively, when incubated in WWEI. Seed imbibition with bioaugmented WWEI (WWEIB) resulted in significant increases in radicle and epicotyl elongation compared to germination in WWE (+91.6% and +123.7%, respectively). Additionally, there was an improvement in fresh biomass production for seedlings hydrated with WWEIB compared to WWE. Overall, this strategy appears highly promising for the safe reuse of WWE and enhancing crop productivity by mitigating contaminant-induced plant stress.

Sheep challenged with sheep-derived type II Mycobacterium avium subsp. paratuberculosis: the first experimental model of paratuberculosis in China

BACKGROUND

Paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is difficult to diagnose in the early stages and poses substantial challenges in prevention, control, treatment, and eradication. A well-defined animal model can help identify disease markers and serve as a platform for vaccine and drug development. This study used sheep as a ruminant model for experimental MAP infection research.

METHODS

Nine 3-month-old lambs with negative MAP antigen and antibody were divided into three groups (control group A and inoculated groups B and C). The inoculated groups were challenged with sheep-derived type II MAP. After exposure, we recorded clinical signs, assessed fecal shedding, tested blood MAP levels, and performed fecal cultures. We also measured MAP-specific antibodies and monitored IFN-γ and IL-10 responses in vivo. At 255 days after inoculation, we performed autopsy, tissue culture, pathomorphological observation, and bacterial organ burden (BOB) testing.

RESULTS

All six sheep in groups B and C were infected, regardless of the challenge dose and exhibited emaciation; two had intermittent soft stools. Intermittent MAP shedding in feces was observed from 60 to 255 days after exposure. Typical MAP colonies formed after 4-6 weeks of fecal and tissue culture, and Ziehl-Neelsen staining showed positive results. In the groups challenged with MAP, some blood samples tested positive for MAP and MAP-specific antibodies were detected in some serum samples. IFN-γ response was significantly higher in groups B and C than that in group A from day 60 post-exposure, whereas the IL-10 response was higher than that in group A from day 120 post-exposure. In the infected groups, the ileal lesions were the most severe and were classified as grade 3 PTB granulomatous inflammation (multibacillary lesions). BOB levels varied across different tissues.

CONCLUSIONS

To the best of our knowledge, this is the first experimental MAP challenge study on sheep in China. Polymerase chain reaction detection was more sensitive than MAP culture, whereas enzyme-linked immunosorbent assay was less sensitive for detecting MAP-specific antibodies. IFN-γ and IL-10 responses may serve as targets for monitoring PTB progression. The severity of ileal lesions and acid-fast bacilli grading play crucial roles in the understanding of infection dynamics. Currently, early PTB diagnosis requires a combination of multiple sample types and detection methods.

Spontaneous lung colonization in the cystic fibrosis rat model is linked to gastrointestinal obstruction

Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in CFTR protein dysfunction. CFTR dysfunction has multi-organ consequences, leading to dehydrated mucus that is adherent to epithelia. In the lungs, this leads to recalcitrant infections with bacteria such as Pseudomonas aeruginosa. In the gut, mucus-laden feces can adhere to the intestines, resulting in distal intestinal obstruction syndrome (DIOS). There is limited information on how lung colonization and DIOS are correlated in people with CF (pwCF). In this novel work, we describe the development of spontaneous lung colonization of CF pathogens in young (<3 months old) CF rats, preceding the development of DIOS. Once DIOS is established, the lung microbiome becomes predominated by taxa also observed in the feces. Induced infection with P. aeruginosa in the CF rats reflects data found in pwCF, as once CF rats are infected, they retain a higher relative abundance of P. aeruginosa than their healthy agemates. Finally, we found that ivacaftor treatment favors a healthier gut microbiome in CF rats, decreasing the relative abundance of Escherichia coli. These results indicate that the CF rat model is recapitulative of human CF disease with the spontaneous lung colonization of traditional CF pathogens and maintenance of P. aeruginosa after induced infection. Furthermore, these results indicate a possible role for the gut-lung axis in lung colonization and DIOS in CF.IMPORTANCEThese data describe for the first time the development of spontaneous lung colonization in the cystic fibrosis (CF) rat model, a hallmark aspect of human CF disease. We also find that CF rats infected with Pseudomonas aeruginosa maintain higher relative abundance following chronic infection as compared to healthy rats, similar to those is seen in people with CF. Additionally, we describe the possible contribution of the gut-lung axis linking lung health with distal intestinal obstruction syndrome, a relationship largely unexplored in the context of CF.

Photofermentative production of poly-β-hydroxybutyrate (PHB) by purple non-sulfur bacteria using olive oil by-products

This study evaluated the ability of six purple non-sulfur bacteria (PNSB) to convert olive oil by-products into poly-β-hydroxybutyrate (PHB). Strains were first independently cultivated in synthetic media with different carbon sources (acetic, lactic and malic acid) to assess their physiology and PHB production. Subsequently, their growth and PHB production using ingested pâté olive cake (IPOC) as a substrate were investigated. Transmission electron microscopy (TEM) observations were conducted on strains cultivated on IPOC to investigate their cell morphologies and inclusion bodies presence and size. Rhodopseudomonas palustris strains accumulated up to 6.8% w PHB/w cells with acetate and 0.86% w PHB/w cells with a daily productivity of 0.54 mg PHB L⁻1 culture d⁻1 on IPOC. In contrast, Cereibacter johrii and Cereibacter sphaeroides reached 58.64% w PHB/w cells and 65.45% w PHB/w cells with acetate, respectively, while C. sphaeroides achieved 21.48% w PHB/w cells and a daily productivity of 10.85 mg PHB L⁻1 culture d⁻1 when cultivated on IPOC. All strains exhibited growth and PHB accumulation in both synthetic media and IPOC substrate. Specifically, R. palustris strains 42OL, AV33 and CGA009 displayed growth capability in all substrates, while C. johrii strains 9Cis and PISA 7, and C. sphaeroides F17 showed promising PHB synthesis capabilities. TEM observations revealed that R. palustris strains, with smaller cell and inclusion body sizes, exhibited lower PHB accumulations, while C. johrii and C. sphaeroides strains, characterized by larger cells and inclusion bodies, demonstrated higher PHB production, recognizing them as promising candidates for PHB production using olive oil by-products. Further investigations under laboratory-scale conditions will be necessary to optimize operating parameters and develop integrated strategies for simultaneous PHB synthesis and the co-production of value-added products, thereby enhancing the economic feasibility of the process within a biorefinery framework.

Bacterial diversity in the honey sac during bee foraging on winter-flowering flora and dominant Bacillus subtilis inhibits Hafnia alvei

Background

The bacterial diversity of two bee species in the process of honey collection during the flowering season of three different floral sources in the winter was studied. The common bacterium in all samples was Bacillus subtilis.

Methods

In the present study, we collected nectar, honey sacs, and fresh honey during the winter flowering season of Agastache rugosa, Prunus cerasoides, and Brassica rapa. The pure culture method was used to count and analyze the number of bacteria, they were identified using 16S rRNA sequencing, similarities were compared in NCBI, and the common dominant bacterial species B. subtilis in all samples using phylogenetic analysis and intersection analysis were determined to conduct further bacteriostatic experiments.

Results

The results showed that the most abundant quantity of bacteria could be found in the honey sacs, compared to in nectar or fresh honey. At the same time, the highest abundance of bacteria could be found in the honey sacs of A. cerana when collected on Brassica rapa, while the highest abundance of bacteria could be found in the honey sacs of A. mellifera when collected on Prunus cerasoides and Agastache rugosa. A total of 33 bacterial species were isolated, with variations in their distribution across different sample types and sources. The inhibitory effect of 10-1-10-5 on Hafnia alvei by B. subtilis was very significant.

Conclusions

B. subtilis was identified in all sample sources, indicating the potential importance of B. subtilis as a probiotic in the bee gut for honey production, and B. subtilis could promote the disease resistance and health of honeybees in winter.

Investigating the Potential of Native Soil Bacteria for Diesel Biodegradation

In countries with a long petroleum extraction and processing history, such as Romania, extensive soil areas are often polluted with petroleum and its derivatives, posing significant environmental and human health risks. This study explores the diesel biodegradation potential of two native bacterial consortia isolated from hydrocarbon-polluted soils, focusing on their phenotypic and molecular characteristics, growth kinetics, alkane hydroxylase activity, hydrolase production, and biosurfactant synthesis capabilities. The bacterial consortia, CoP1 and CoP2, were successfully obtained using the standard successive enrichment culture method from two soil samples collected from a region affected by petroleum pollution. The CoP1 and CoP2 consortia demonstrated efficient diesel-degrading capabilities, achieving 50.81-84.32% degradation when cultured in a minimal medium containing 1-10% (v/v) diesel as the sole carbon and energy source. This biodegradation potential was corroborated by their significant alkane hydroxylase activity and the detection of multiple catabolic genes in their genomes. The CoP1 consortium contains at least four catabolic genes (alkB, alkM, todM, ndoM) as well as rhamnosyltransferase 1 genes (rhlAB), while the CoP2 consortium contains only two catabolic genes (ndoM, C23DO). The RND transporter gene (HAE1) was present in both consortia. Secondary metabolites, such as glycolipid-type biosurfactants, as well as extracellular hydrolases (protease, amylase, cellulase, and lipase), were produced by both consortia. The CoP1 and CoP2 consortia demonstrate exceptional efficiency in diesel degradation and biosurfactant production, making them well suited for the bioremediation of soils contaminated with petroleum and its derivatives.

Predatory potentials of novel Bdellovibrio isolates against multidrug-resistant and extremely drug-resistant bacterial pathogens of animals and plants

Bdellovibrio and like organisms (BALOs) predate on Gram-negative bacteria selectively, which holds promise as an alternate to combat against multidrug-resistant bacterial pathogens. In this study, two Bdellovibrio strains designated MPR17 and MPR18 were isolated from water samples by double-layer agar technique using P. fluorescens as prey and investigated for their predatory potentials against six pathogenic Gram-negative, MDR and XDR bacteria. Both the BALOs preyed on all the tested bacteria including P. syringae, B. glumae, V. parahaemolyticus, P. mirabilis, M. bovis, and A. schindleri with different killing rates. Against A. schindleri, Bdellovibrio sp. MPR18 produced a maximum of 2.11 × 107 PFU/ml, but MPR17 did not produce any detectable PFUs. TEM analysis of predator-prey interactions recorded different life stages including attachment, bdelloplast formation, prey lysis, and release. Morphologically, both the Bdellovibrio isolates MPR17 and MPR18 were small vibrioid in shape with a long single polar flagellum and measured of about < 500 nm diameter in size, suggesting that they are the smallest ever described Bdellovibrio. Predatory activity was further assessed in liquid co-cultures that evidenced time-dependent decrease in the prey cell density from 24 h with significant reduction at 72 h with different degrees of predation with respective prey bacteria. Bdellovibrio sp. MPR17 and MPR18 exhibited strong bacteriolytic activity in liquid cultures, which was equivalent to the bactericidal activities of standard antibiotics especially for M. bovis (99%), P. syringae (90%) and A. schindleri (90%). The findings of this study signify the potential of novel Bdellovibrio sp. MPR17 and MPR18 as a biocontrol agent with multiple host range to eradicate different MDR and XDR bacterial infections, which could contribute positively for resolving the crisis of antimicrobial resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04230-8.

Detection and selection of dye-degrading bacteria from surface waters with different degrees of contamination

Biodegradability and resistance from indigenous bacterial communities to dyes were tested using samples from both polluted and unpolluted surface waters in Buenos Aires. Five dyes were selected for the study: Acid Black 210, Direct Orange 39, Malachite Green, Gentian Violet, and Alizarin Red. Water quality was assessed by measuring chemical oxygen demand, biochemical oxygen demand, and both Escherichia coli and enterococci counts. Biodegradability was tested using a respirometric method, while resistance was assessed by determining the minimum inhibitory concentration (MIC). No bacterial strains capable of degrading the dyes as the sole carbon source were isolated from the respirometric tests. However, from the MIC tests, 28 strains capable of dye discolouration were identified, using nutrient broth as a supplement. Two of them were able to degrade Malachite Green and Acid Black 210 at a concentration of 50 mg L-1 in less than 24 h and with an efficiency greater than 87%. These strains were identified as Aeromonas sp. and Shewanella sp. through MALDI-TOF/MS and 16S rRNA gene sequencing. The determination of biodegradability and resistance can be used to enhance the characterization of watercourses. Furthermore, this methodology provides a means to isolate biodegrading bacteria that could be applied in effluent treatment processes.

An indigenous microalgal pool containing Klebsormidium sp. K39 as a stable and efficacious biotechnological strategy for Escherichia coli removal in urban wastewater treatment

BACKGROUND

In recent decades the demand for freshwater has drastically increased as a consequence of population growth, economic development, climate change and pollution. Therefore, any strategy for wastewater treatment can play a role in alleviating the pressure on freshwater sources.

RESULTS

In the present study an autochthonous microalgal pool (MP), isolated from a constructed wetland, was proposed as an alternative to the secondary treatment of an urban wastewater treatment system. The MP removal efficacy was compared to those obtained using Chlorella vulgaris and Scenedesmus quadricauda, against E. coli. Results exhibited a comparable removal efficacy and after 2 days, in samples inoculated with E. coli at lower density, S. quadricauda and C. vulgaris induced a decrease of 2.0 units Log and the autochthonous MP of 1.8 units Log, whereas in samples with E. coli at higher density the bacteria were reduced 2.8, 3.4 and 2.0 units Log by S. quadricauda, C. vulgaris and the autochthonous MP, respectively. Moreover, the identification of microalgal strains isolated from the MP revealed the presence of Klebsormidium sp. K39, C. vulgaris, Tetradesmus obliquus and S. quadricauda. Although the MP composition remained quite constant, at the end of the treatment, a different distribution among the microalgal species was observed with Klebsormidium sp. K39 found as dominant.

CONCLUSION

The microalgal-based wastewater treatment appears as a valuable alternative, although further investigations, based on 'omics' approaches, could be applied to better explore any fluctuation within the MP species composition in an in situ trial. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Prevalence and pathogenic potential of Shewanella species in oysters and seawater collected from the Chesapeake Bay and Maryland Coastal Bays

Shewanella is a genus of Gram-negative marine bacteria with some species associated with human and shellfish illnesses. This study evaluated the abundance of Shewanella species in oysters and seawater from the Chesapeake and Maryland Coastal Bays at four sites between 2019 and 2021. Physicochemical parameters such as temperature, salinity, dissolved oxygen, turbidity, pH, chlorophyll-a, rainfall within the last 48 h, total dissolved solids, and atmospheric pressure were also recorded to evaluate if there was a correlation between environmental parameters and the level of Shewanella. The highest total Shewanella counts were 1.8 × 107 CFU/g in oysters and 4.0 × 102 CFU/mL in seawater. 16S rRNA sequencing was performed on 1,344 representative isolates of which 890 (713 oyster, 177 seawater) were confirmed as Shewanella within 16 species. The top four species isolated from oysters and seawater were S. khirikhana a known shrimp pathogen (49%), S. marisflavi (19%), S. loihica (11%), and S. algae (8%). Testing for alpha and beta hemolysis were performed on all confirmed Shewanella isolates. Beta hemolysis was observed in 405 (46%) of the isolates of which 313 were in oysters and 92 in seawater. In oysters, beta-hemolysis was most prevalent in S. khirikhana (233 of 344 isolates, 68%), while in seawater 64 of 92 isolates (70%) were beta-hemolytic strains. Beta-hemolysis suggests that these could be potentially pathogenic strains. Correlations were performed between physicochemical attributes of the seawater and Shewanella counts. Only seawater temperature and dissolved oxygen correlated with Shewanella counts (r = 0.45 and - 0.41), respectively. No correlations were observed between the physicochemical parameters and Shewanella abundances in oysters. Results suggest that virulent strains of Shewanella may be present in oysters and seawater from the Chesapeake and Maryland Coastal Bays, perhaps as a consequence of rising seawater temperatures.

Dispatched microbial community assembly processes driving ecological succession during phytostabilization of mercury-rich tailings

Phytostabilization is an important way for the remediation of mine tailings, but the associated microbial processes and community succession remain largely unknown. In this study, we investigated the assembly mechanisms maintaining the core and satellite subcommunities diversity during phytostabilizaion of a mercury-rich mine tailings. The contents of total Hg and methylmercury decreased with a concomitant increase of total and available phosphorus content along the successive remediation stages. Microbial community composition, profiled by 16S rRNA gene sequencing, revealed amplicon sequence variants (ASVs) that were separated according to their abundance within either the core community or the satellite community. Community dynamics analysis showed that alpha diversity indices increased for the core community while decreased for the satellite community. Both satellite and core communities were mainly driven by stochastic drift process, and homogeneous selection was relatively higher in shaping the core community organization. The core community included ASVs affiliated to Proteobacteria, Crenarchaeota, Bacteroidota, Verrucomicrobiota, Acidobacteriota, and Myxococcota phyla, which were driven primarily by heterogeneous selection and drift. The satellite community included ASVs affiliated to Acidobacteriota, Ktedonobacteria, Anaerolineae and Verrucomicrobiota phyla, which were mainly influenced by heterogeneous selection. Nineteen taxa and one taxon were identified as keystone taxa for the satellite and core communities respectively. This study provides important insights on the assemble rules within the core and satellite communities, and theoretical guidance for further ecological restoration and management during microbial remediation of metal-mined derelict land.

Endophytic Bacteria from the Desiccation-Tolerant Plant Selaginella lepidophylla and Their Potential as Plant Growth-Promoting Microorganisms

Bacteria associated with plants, whether rhizospheric, epiphytic, or endophytic, play a crucial role in plant productivity and health by promoting growth through complex mechanisms known as plant growth promoters. This study aimed to isolate, characterize, identify, and evaluate the potential of endophytic bacteria from the resurrection plant Selaginella lepidophylla in enhancing plant growth, using Arabidopsis thaliana ecotype Col. 0 as a model system. Plant growth-promotion parameters were assessed on the bacterial isolates; this assessment included the quantification of indole-3-acetic acid, phosphate solubilization, and biological nitrogen fixation, a trehalose quantification, and the siderophore production from 163 endophytic bacteria isolated from S. lepidophylla. The bacterial genera identified included Agrobacterium, Burkholderia, Curtobacterium, Enterobacter, Erwinia, Pantoea, Pseudomonas, and Rhizobium. The plant growth promotion in A. thaliana was evaluated both in Murashige Skoog medium, agar-water, and direct seed inoculation. The results showed that the bacterial isolates enhanced primary root elongation and lateral root and root hair development, and increased the fresh and dry biomass. Notably, three isolates promoted early flowering in A. thaliana. Based on these findings, we propose the S. lepidophylla bacterial isolates as ideal candidates for promoting growth in other agriculturally important plants.

Photorhabdus viridis sp. nov. Isolated from Heterorhabditis zealandica Entomopathogenic Nematodes

A novel bacterial species, Photorhabdus viridis sp. nov., represented by strain GreenT, isolated from Heterorhabditis zealandica MJ2C entomopathogenic nematodes, is described. Phylogenetic reconstructions using 16S rRNA gene sequences show that strain GreenT is closely related to P. thracensis DSM 15199 T. The 16rRNA gene sequences of these two strains are 98.8% identical. Phylogenetic reconstructions using whole-genome sequences show that strain GreenT is closely related to P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T. Digital DNA-DNA hybridization (dDDH) values between strain GreenT and its three more close relative species, P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T, are 49%, 59%, and 59%, respectively. In addition, average nucleotide identity (ANI) values between GreenT and P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T are 92.4%, 94.4%, and 94.6%, respectively. The novel species also differs in their biochemical capacities from the biochemical capacities of their more closely related taxa. The following biochemical tests may be particularly useful in this context: Arginine dihydrolase, gelatinase, and glucose and mannitol oxidation. Given the clear phylogenetic separation, the sequence divergence values, and the phenotypic differences, we conclude that strain GreenT represents a novel bacterial species, for which we propose the name Photorhabdus viridis sp. nov. with GreenT (= CCM 9407 T = CCOS 2117 T = MJ2CT) as the type strain. Our study contributes to a better understanding of the taxonomy and biodiversity of an important bacterial group with great biotechnological and agricultural potential.

Profiling of secondary metabolites produced by Pseudomonas sp. isolate PY-122 and PY-142 as biocontrol agent againts fusarium wilt disease on chili

Fusarium wilt is an important disease on chili plants caused by the fungus Fusarium oxysporum. This study aims to determine the effectiveness of secondary metabolites from 2 Pseudomonad isolates in controlling Fusarium wilt in chili plants and their effect on chili plant growth. This research was conducted in two stages, namely in vitro, which was carried out in the plant health laboratory and greenhouse, Faculty of Agriculture, Universitas Pembangunan Nasional Veteran Jawa Timur, and in vivo which was carried out in chili plantations known to be endemic to Fusarium wilt in Menganti, Gresik. The research design used in this study was Completely Randomized Design for in vitro testing and Randomized Group Design for in vivo testing by testing 9 treatments repeated 3 times. The treatment tested was control, secondary metabolite application of Pseudomonas isolates PY-122 and PY-142 with concentrations of 20% 30%, 40% and 50%. The variables observed were inhibition of secondary metabolites on the growth of Fusarium fungus, disease incubation period, disease severity index, and plant growth. Sequencing results with 16rRNA gene markers for both Pseudomonas isolates showed similarities to Pseudomonas sp. The results showed that the treatment of secondary metabolite PY-142 with a concentration of 50% showed the highest consistent inhibition. In the greenhouse and field tests, the two isolates slowed down the disease incubation period and development compared to controls. In agronomical observations, the average plant height, number of leaves, root length, and appearance of the first flower on the treated plants were higher and more numerous than the control plants.

Diversity and Activity of Bacteria Cultured from a Cup-The Sponge Calyx nicaeensis

Marine sponges are well-known for hosting rich microbial communities. Sponges are the most prolific source of marine bioactive compounds, which are frequently synthesized by their associated microbiota. Calyx nicaeensis is an endemic Mediterranean sponge with scarce information regarding its (bioactive) secondary metabolites. East Mediterranean specimens of mesophotic C. nicaeensis have never been studied. Moreover, no research has inspected its associated bacteria. Thus, we studied the sponge's bacterial diversity and examined bacterial interspecific interactions in search of a promising antibacterial candidate. Such novel antimicrobial agents are needed since extensive antibiotic use leads to bacterial drug resistance. Bacteria cultivation yielded 90 operational taxonomic units (OTUs). A competition assay enabled the testing of interspecific interactions between the cultured OTUs. The highest-ranked antagonistic bacterium, identified as Paenisporosarcina indica (previously never found in marine or cold habitats), was mass cultured, extracted, and separated using size exclusion and reversed-phase chromatographic methods, guided by antibacterial activity. A pure compound was isolated and identified as 3-oxy-anteiso-C15-fatty acid-lichenysin. Five additional active compounds await final cleaning; however, they are lichenysins and surfactins. These are the first antibacterial compounds identified from either the C. nicaeensis sponge or P. indica bacterium. It also revealed that the genus Bacillus is not an exclusive producer of lichenysin and surfactin.

Laundry Isolate Delftia sp. UBM14 Capable of Biodegrading Industrially Relevant Aminophosphonates

Phosphonates such as ethylenediaminetetra (methylenephosphonic acid) (EDTMP) and aminotris (methylenephosphonic acid) (ATMP) are used every day in water treatment processes or in household products. Their consumption is still increasing, regardless of the debates on their environmental impact. Here, the microbial characterisation and determination of the biodegradation potential of selected industrially relevant phosphonates for the isolate Delftia sp. UMB14 is reported. The opportunistic strain was isolated from a biofilm that was derived from a conventional washing machine using conventional detergents containing phosphonates. In antimicrobial susceptibility testing, the strain was only susceptible to sulfonamide, tetracycline, and chloramphenicol. Physiological and biochemical characteristics were determined using the BIOLOG EcoPlate assay. Most importantly, the strain was shown to convert D-malic acid and D-mannitol, as confirmed for strains of Delftia lacustris, and thus the new isolate could be closely related. Biodegradation tests with different phosphonates showed that the strain preferentially degrades ATMP and EDTMP but does not degrade glyphosate (GS) and amino (methylphosphonic acid) (AMPA). A specific gene amplification confirmed the presence of phnX (phosphonoacetaldehyde hydrolase) and the absence of PhnJ (the gene for the core component of C-P lyase). The presence of PhnCDE is strongly suggested for the strain, as it is common in Delftia lacustris species.

Phenotypic and genotypic antimicrobial resistance patterns in honey bee (Apis mellifera L.) bacterial symbionts

Antimicrobial resistance (AMR) is a major global public health problem. Nevertheless, the knowledge of the factors driving the spread of resistance among environmental microorganisms is limited, and few studies have been performed worldwide. Honey bees (Apis mellifera L.) have long been considered bioindicators of environmental pollution and more recently also of AMR. In this study, 53 bacterial strains isolated from the body surface of honey bees at three ontogenetic stages, collected from ten different geographic locations, were tested for their phenotypic and genotypic resistance to eight classes of the most widely used antimicrobials in human and veterinary medicine. Results showed that 83% of the strains were resistant to at least one antimicrobial and 62% were multidrug-resistant bacteria, with a prevalence of resistance to nalidixic acid, cefotaxime, and aztreonam. A high percentage of isolates harbouring at least one antimicrobial gene was also observed (85%). The gene encoding resistance to colistin mcr-1 was the most abundant, followed by those for tetracycline tetM and tetC. Geographical features influenced the distribution of these traits more than bacterial species or bee stage, supporting the use of honey bee colonies and their associated bacteria as indicators to monitor environmental resistance. This approach can improve the scientific understanding of this global threat by increasing data collection capacity.

A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli

Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges

Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.

Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.

Exploring Endophytic Bacteria from Artemisia spp. and Beneficial Traits on Pea Plants

Endophytic microorganisms represent promising solutions to environmental challenges inherent in conventional agricultural practices. This study concentrates on the identification of endophytic bacteria isolated from the root, stem, and leaf tissues of four Artemisia plant species. Sixty-one strains were isolated and sequenced by 16S rDNA. Sequencing revealed diverse genera among the isolated bacteria from different Artemisia species, including Bacillus, Pseudomonas, Enterobacter, and Lysinibacillus. AR11 and VR24 obtained from the roots of A. absinthium and A. vulgaris demonstrated significant inhibition on Fusarium c.f. oxysporum mycelial growth. In addition, AR11, AR32, and CR25 exhibited significant activity in phosphatase solubilization, nitrogen fixation, and indole production, highlighting their potential to facilitate plant growth. A comparative analysis of Artemisia species showed that root isolates from A. absinthium, A. campestris, and A. vulgaris have beneficial properties for inhibiting pathogen growth and enhancing plant growth. AR11 with 100% similarity to Bacillus thuringiensis, could be considered a promising candidate for further investigation as microbial biofertilizers. This finding highlights their potential as environmentally friendly alternatives to chemical pesticides, thereby contributing to sustainable crop protection practices.

Ice nucleation active bacteria metabolites as antibiofilm agent to control Aeromonas hydrophila and Streptococcus agalactiae infections in Aquaculture

OBJECTIVES

The aim of this study was to quantify and identify metabolites of Ice Nucleation Active (INA) bacteria as an anti-biofilm agent against biofilms of fish pathogens such as Aeromonas hydrophila and Streptococcus agalactiae.

RESULTS

Ice nucleation active bacteria, which have the ability to catalyze ice nucleation, isolated from rainwater in previous studies, were used. All INA isolates were tested in several assays, including the antimicrobial test, which uses streptomycin as the positive control and none of the isolates were found positive in the antimicrobial test. As for the quorum quenching assay, it was found that four out of ten isolates were able to disturb the communication system in Chromobacterium violaceum wild type, which was used as the indicator bacteria. On the next assay, all ten isolates were tested for Biofilm Inhibition and Destruction and showed anti-biofilm activity with the highest percentage inhibition of 33.49% by isolate A40 against A. hydrophila and 77.26% by isolate A19 against S. agalactiae. C1 performed the highest destruction against A. hydrophila and S. agalactiae, with percentages of 32.11% and 51.88%, respectively. As for the GC-MS analysis, supernatants of INA bacteria contain bioactive compounds such as sarcosine and fatty acids, which are known to have antibiofilm activity against several biofilm-forming bacteria. Through 16s rRNA sequencing, identified bacteria are from the Pantoea, Enterobacter, and Acinetobacter genera. As for the conclusion, ice nucleation active bacteria metabolites tested showed positive results against pathogenic bacteria Aeromonas hydrophila and Streptococcus agalactiae in destructing and inhibiting biofilm growth.

Antibiotic Resistance in Enterococci and Enterobacteriaceae from Laboratory-Reared Fresh Mealworm Larvae (Tenebrio molitor L.) and Their Frass

The occurrence of antibiotic-resistant bacteria in foodstuff involves a human health risk. Edible insects are a precious resource; however, their consumption raises food safety issues. In this study, the occurrence of antibiotic resistant bacteria in laboratory-reared fresh mealworm larvae (Tenebrio molitor L.) and frass was assessed. Antibiotics were not used during the rearing. Enterobacteriaceae and enterococci were isolated from 17 larvae and eight frass samples. In total, 62 and 69 isolates presumed to belong to Enterobacteriaceae and Enterococcus spp., respectively, were obtained and tested for antibiotic susceptibility via disk diffusion. Based on the results, isolates were grouped, and representative resistant isolates were identified at species level through 16S rRNA gene sequencing. For enterococci resistance, percentages higher than 15% were observed for vancomycin and quinupristin-dalfopristin, whereas Enterobacteriaceae resistance higher than 25% was found against cefoxitin, ampicillin, and amoxicillin-clavulanic acid. Based on the species identification, the observed resistances seemed to be intrinsic both for enterococci and Enterobacteriaceae, except for some β-lactams resistance in Shigella boydii (cefoxitin and aztreonam). These could be due to transferable genetic elements. This study suggests the need for further investigations to clarify the role of edible insects in the spreading of antibiotic resistance determinants through the food chain.

Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights

Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.

Evaluation of the health of Mediterranean mussels (Mytilus galloprovincialis Lamarck, 1819) distributed in the Çanakkale strait, Turkey

The observation of mortality in Mediterranean mussels (Mytilus galloprovincialis) distributed in the Çanakkale Strait in recent years was influential in developing the research question for this study. In this study, the presence of bacteria (Vibrio spp.) and parasites (Marteilia spp. and Haplosporidium spp.) in mussels collected from Kumkale, Kepez, and Umurbey stations in the Çanakkale Strait was investigated seasonally. Microbiological findings, histopathology, oxidative stress enzymes and their gene expressions, lipid peroxidation, lysosomal membrane stability, and changes in haemolymph were examined. In summer samples, both the defence system and the extent of damage were higher in gill tissue. In winter samples, enzyme activities and lipid peroxidation were found to be predominantly higher in digestive gland tissues. Histological examinations and Hemacolor staining revealed the presence of protozoan cysts, and for bacterial examination, molecular analysis performed after culturing revealed the presence of 7 Vibrio species. While the total numbers of heterotrophic bacteria detected in all samples were at acceptable levels, the predominance of Vibrio spp. numbers among the total heterotrophic bacteria detected in almost all samples were noteworthy. The total hemocyte count was calculated as 5.810(4)±0.58 (cells/mm3) in winter and 7.210(4)±1.03 (cells/mm3) in summer. These factors are considered to be possible causes of mussel mortality.

Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells

Phage therapy is a therapeutic approach to treat multidrug-resistant (MDR) infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells (AECs) derived from a person with cystic fibrosis (CF), we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.

Assessment of the presence of Acinetobacter spp. resistant to β-lactams in commercial ready-to-eat salad samples

Acinetobacter baumannii is a well-known nosocomial infection causing agent. However, other Acinetobacter spp. have also been implicated in cases of human infection. Additionally, these bacteria are known for the development of antibiotic resistance thus making the treatment of the infections they cause, challenging. Due to their relevance in clinical setups less attention has been paid to their presence in foods, and its relation with infection/dissemination routes. In the current study commercial Ready-To-Eat (RTE) salads were analyzed seeking for antibiotic resistant Acinetobacter spp. A preliminary screening allowed us to recover Gram-negative bacteria resistant to β - lactams using cefotaxime, third generation cephalosporins, as the selective agent, and this was followed by identification with CHROMagar™ Acinetobacter and 16S rDNA sequencing. Finally, the isolates identified as Acinetobacter spp. were reanalyzed by PCR to determine the presence of nine potential Extended Spectrum β Lactamases (ESBL). Two commercial RTE salad brands were included in the study (2 batches per brand and 8 samples of each batch making a total of 32 independent samples), and compared against an organic lettuce. High concentrations of β - lactam, resistant bacteria were found in all the samples tested (5 log CFU/g). Additionally, 209 isolates were phenotypically characterized on CHROMagar Acinetobacter. Finally, PCR analysis identified the presence of different ESBL genes, being positive for blaACC, blaSHV, blaDHA and blaVEB; out of these, blaACC was the most prevalent. None of the isolates screened were positive for more than one gene. To conclude, it is important to highlight the fact that pathogenic species within the genus Acinetobacter spp., other than A. baumannii, have been identified bearing resistance genes not typically associated to these microorganisms highlight the importance of continuous surveillance.

Pitting the olive seed microbiome

BACKGROUND

The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.

RESULTS

A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.

CONCLUSIONS

This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.

Complete genome sequence of new Microbacterium sp. strain ET2, isolated from roots of leafless orchid

Whole-genome sequence of ET2 strain, isolated from the roots of leafless orchid, constitutes a single circular chromosome of 3,604,840 bp (69.44% G + C content). BLAST+-based average nucleotide identity (ANIb) and digital DNA-DNA hybridization values indicate that ET2 may be a novel Microbacterium species. Genes putatively involved in plant-microbial interactions were predicted.

Volatile organic compounds produced by Paenibacillus polymyxa J2-4 exhibit toxic activity against Meloidogyne incognita

BACKGROUND

Root knot nematodes cause great damage to crops worldwide. Due to the negative effects of the application of fumigant and old chemical nematicides, biological nematicides have drawn increasing attention in recent years. Here we tested the fumigant activity of the volatile organic compounds (VOCs) blends emitted from Paenibacillus polymyxa and pure commercial VOCs against M. incognita.

RESULTS

In this study, we investigated whether P. polymyxa strain J2-4 could produce VOCs that exhibit nematicidal activity. In vitro assays indicated that J2-4 VOCs were highly toxic to second stage juveniles (J2s) and could inhibit egg hatching. Three-layered pot experiments showed that the number of nematodes that penetrating in cucumber roots was reduced by 69.27% after the application of J2-4 VOCs under greenhouse conditions. We identified 14 volatiles using solid-phase micro-extraction gas chromatography-mass spectrometry. The efficacy of six commercially available VOCs, namely 2-isobutyl-3-methylpyrazine, 2,4-dimethoxybenzaldoxime, 2-dodecanone, 2-tridecanol, 2-tridecanone, and 2-tetradecanol, against M. incognita were examined. Except for 2,4-dimethoxybenzaldoxime, the remaining five VOCs showed strong direct-contact nematicidal activity against J2s of M. incognita, and only 2-isobutyl-3-methylpyrazine showed strong fumigant activity against J2s of M. incognita. In pot experiments, 2-isobutyl-3-methylpyrazine and 2-dodecanone reduced the number of root galls by about 70%, and 2-tridecanone reduced the number of root galls and egg masses by about 63% compared with controls.

CONCLUSION

Paenibacillus polymyxa strain J2-4 exhibited high fumigant activity against M. incognita. Our results provide evidence for the use of J2-4 and its VOCs as biocontrol agents in the management of root-knot nematodes. © 2023 Society of Chemical Industry.

Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster

Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.

Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines

Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. We determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.

Enhanced biodegradable polyester film degradation in soil by sequential cooperation of yeast-derived esterase and microbial community

The degradation of biodegradable plastics poses a significant environmental challenge and requires effective solutions. In this study, an esterase derived from a phyllosphere yeast Pseudozyma antarctica (PaE) enhanced the degradation and mineralization of poly(butylene succinate-co-adipate) (PBSA) film in soil. PaE was found to substitute for esterases from initial degraders and activate sequential esterase production from soil microbes. The PBSA film pretreated with PaE (PBSA-E) rapidly diminished and was mineralized in soil until day 55 with high CO2 production. Soil with PBSA-E maintained higher esterase activities with enhancement of microbial abundance, whereas soil with inactivated PaE-treated PBSA film (PBSA-inact E) showed gradual degradation and time-lagged esterase activity increases. The fungal genera Arthrobotrys and Tetracladium, as possible contributors to PBSA-film degradation, increased in abundance in soil with PBSA-inact E but were less abundant in soil with PBSA-E. The dominance of the fungal genus Fusarium and the bacterial genera Arthrobacter and Azotobacter in soil with PBSA-E further supported PBSA degradation. Our study highlights the potential of PaE in addressing concerns associated with biodegradable plastic persistence in agricultural and environmental contexts.

Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model

Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.

Isolation and draft genome sequence of Enterobacter asburiae strain i6 amenable to genetic manipulation

Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.

Phyllosphere bacteria with antiquorum sensing and antibiofilm activities against fish pathogenic bacteria

OBJECTIVE

This research aims to quantify antiquorum sensing and antibiofilm activity of f phyllosphere bacteria against biofilm formed by pathogenic fish bacteria such as Aeromonas hydrophila, Streptococcus agalactiae, and Vibrio harveyi.

RESULTS

Antiquorum sensing assay using Chromobacter violaceum as indicator bacteria and antibiofilm assay showed six phyllosphere bacteria have antiquorum sensing and antibiofilm activities against tested bacteria. The highest inhibition and destruction activity was showed by metabolite of JB 3B and EJB 5 F against A. hydrophila, respectively. Determination using light microscope and scanning electron microscope performed decreaing in biomass of biofilm observed after treated with metabolite from phyllosphere bacteria.

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize (Zea mays)

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Biotransformation of Sclareol by a Fungal Endophyte of Salvia sclarea

Microbial endophytes are known as versatile producers of useful metabolites, which have extensive applications in pharmacy, fragrance, agriculture and food. This study aims to screen sclareol-biotransforming microorganisms from Salvia sclarea, an untapped source of diverse endophytes. In this study, 50 culturable endophytes were isolated from S. sclarea grown in Xinjiang using sclareol as the sole carbon source and screened for their potential to transform sclareol into analogues. A fungal endophyte, identified as the generally recognized as safe (GRAS) strain Aspergillus tubingensis, can produce labd-14-ene-3β,8α,13β-triol and 8α,13β-dihydroxylabd-14-en-3-one from sclareol, involving hydroxylation and carbonylation at the C3 site. Structures of the two metabolites were elucidated by HR-ESI-MS and NMR analysis. S. sclarea was proven to be a good source of endophytes that are prospective producers of secondary metabolites with valuable chemical and biological properties. This study is the first report regarding the isolation of endophytes from S. sclarea.

In Vitro Efficacy of Isobutyl Cyanoacrylate Nanoparticles against Fish Bacterial Pathogens and Selection Preference by Rainbow Trout (Oncorhynchus mykiss)

The upsurge in havoc being wreaked by antibiotic-resistant bacteria has led to an urgent need for efficacious alternatives to antibiotics. This study assessed the antibacterial efficacy of two isobutyl cyanoacrylate nanoparticles (iBCA-NPs), D6O and NP30, against major bacterial pathogens of fish. In vivo tests on rainbow trout were preceded by in vitro tests of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). NP30 exhibited higher efficacy than D60, but both iBCA-NPs demonstrated dose-dependent and species-specific in vitro antibacterial properties against the bacterial isolates. Generally, Gram-negative bacteria were more resistant to the iBCA-NPs. Streptococcus iniae, Tenacibaculum maritimum, and Photobacterium damselae were particularly sensitive to both iBCA-NPs. Administered to rainbow trout at 3571.4 mg (iBCA-NP)/kg feed, the iBCA-NPs produced a relative gain rate and survival rates comparable to the control (p > 0.05). The condition factor and the hepatosomatic and viscerosomatic indices of fish were indifferentiable (p > 0.05) between the iBCA-NP groups and the control. The iBCA-NPs caused no alteration in stress, oxidative stress (superoxide dismutase, SOD), plasma complement titer, or lysozyme activity. This study presents the first report of antibacterial activity of iBCA-NPs against Gram-negative bacteria. The results of this study suggest that D60 and NP30 may contribute to reducing the amounts of antibiotics and chemotherapeutic agents used in aquaculture.

Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress

Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.

Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities

Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

The Antibacterial and Antibiofilm Activities of the Endophytic Bacteria Associated with Archidendron pauciflorum against Multidrug-Resistant Strains

Endophytes associated with medicinal plants are a potential source of valuable natural products. This study aimed to evaluate the antibacterial and antibiofilm activities of endophytic bacteria from Archidendron pauciflorum against multidrug-resistant (MDR) strains. A total of 24 endophytic bacteria were isolated from the leaf, root, and stem of A. pauciflorum. Seven isolates showed antibacterial activity with different spectra against four MDR strains. Extracts derived from four selected isolates (1 mg/mL) also displayed antibacterial activity. Among four selected isolates, DJ4 and DJ9 isolates exhibited the strongest antibacterial activity against P. aeruginosa strain M18, as indicated by the lowest minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) (DJ4 and DJ9 MIC: 7.81 µg/mL; DJ4 and DJ9 MBC: 31.25 µg/mL). 2 × MIC of DJ4 and DJ9 extracts was found to be the most effective concentration to inhibit more than 52% of biofilm formation and eradicate more than 42% of established biofilm against all MDR strains. 16S rRNA-based identification revealed four selected isolates belong to the genus Bacillus. DJ9 isolate possessed nonribosomal peptide synthetase (NRPS) gene, and DJ4 isolate possessed NRPS and polyketide synthase type I (PKS I) gene. Both these genes are commonly responsible for secondary metabolites synthesis. Several antimicrobial compounds, including 1,4-dihydroxy-2-methyl-anthraquinone and paenilamicin A1, were detected in the bacterial extracts. This study highlights endophytic bacteria isolated from A. pauciflorum provide a great source of novel antibacterial compounds.

Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking

The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.

Bacterial Metal-Scavengers Newly Isolated from Indonesian Gold Mine-Impacted Area: Bacillus altitudinis MIM12 as Novel Tools for Bio-Transformation of Mercury

Selikat river, located in the north part of Bengkulu Province, Indonesia, has critical environmental and ecological issues of contamination by mercury due to artisanal small-scale gold mining (ASGM) activities. The present study focused on the identification and bioremediation efficiency of the mercury-resistant bacteria (MRB) isolated from ASGM-impacted areas in Lebong Tambang village, Bengkulu Province, and analyzed their merA gene function in transforming Hg2+ to Hg0. Thirty-four MRB isolates were isolated, and four out of the 34 isolates exhibited not only the highest degree of resistance to Hg (up to 200 ppm) but also to cadmium (Cd), chromium (Cr), copper (Cu), and lead (Pb). Further analysis shows that all four selected isolates harbor a merA operon-encoded mercuric ion (Hg2+) reductase enzyme, with the Hg bioremediation efficiency varying from 71.60 to 91.30%. Additionally, the bioremediation efficiency for Cd, Cr, Cu, and Pb ranged from 54.36 to 98.37%. Among the 34, two isolates identified as Bacillus altitudinis possess effective and superior multi-metal degrading capacity up to 91.30% for Hg, 98.07% for Cu, and 54.36% for Cr. A pilot-scale study exhibited significant in situ bioremediation of Hg from gold mine tailings of 82.10 and 95.16% at 4- and 8-day intervals, respectively. Interestingly, translated nucleotide blast against bacteria and Bacilli merA sequence databases suggested that B. altitudinis harbor merA gene is the first case among Bacilli with the possibility exhibits a novel mechanism of bioremediation, considering our new finding. This study is the first to report the structural and functional Hg-resistant bacterial diversity of unexplored ASGM-impacted areas, emphasizing their biotechnological potential as novel tools for the biological transformation and adsorption of mercury and other toxic metals.

Multi-omic profiling of a novel activated sludge strain Sphingobacterium sp. WM1 reveals the mechanism of tetracycline biodegradation and its merits of potential application

As an emerging pollutant, the antibiotic tetracycline (TC) has been consistently detected in wastewater and activated sludge. Biodegradation represents a potentially crucial pathway to dissipate TC contamination. However, few efficient TC-degrading bacteria have been isolated and a comprehensive understanding of the molecular mechanisms underlying TC degradation is still lacking. In this study, a novel TC-degrading bacterium, designated as Sphingobacterium sp. WM1, was successfully isolated from activated sludge. Strain WM1 exhibited a remarkable performance in degrading 50 mg/L TC within 1 day under co-metabolic conditions. Genomic analysis of the strain WM1 unveiled the presence of three functional tetX genes. Unraveling the complex molecular mechanisms, transcriptome analysis highlighted the role of upregulated transmembrane transport and accelerated electron transport in facilitating TC degradation. Proteomics confirmed the up-regulation of proteins involved in cellular biosynthesis/metabolism and ribosomal processes. Crucially, the tetX gene-encoding protein showed a significant upregulation, indicating its role in TC degradation. Heterologous expression of the tetX gene resulted in TC dissipation from an initial 51.9 mg/L to 4.2 mg/L within 24 h. The degradation pathway encompassed TC hydroxylation, transforming into TP461 and subsequent metabolites, which effectively depleted TC's inhibitory activity. Notably, the tetX genes in strain WM1 showed limited potential for horizontal gene transfer. Collectively, strain WM1's potent TC degradation capacity signals a promise for enhancing TC clean-up strategies.

Natural Products from Singapore Soil-Derived Streptomycetaceae Family and Evaluation of Their Biological Activities

Natural products have long been used as a source of antimicrobial agents against various microorganisms. Actinobacteria are a group of bacteria best known to produce a wide variety of bioactive secondary metabolites, including many antimicrobial agents. In this study, four actinobacterial strains found in Singapore terrestrial soil were investigated as potential sources of new antimicrobial compounds. Large-scale cultivation, chemical, and biological investigation led to the isolation of a previously undescribed tetronomycin A (1) that demonstrated inhibitory activities against both Gram-positive bacteria Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) (i.e., MIC90 of 2-4 μM and MBC90 of 9-12 μM), and several known antimicrobial compounds, namely nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin, and naphthomevalin. Tetronomycin showed a two- to six-fold increase in antibacterial activity (i.e., MIC90 and MBC90 of 1-2 μM) as compared to tetronomycin A (1), indicating the presence of an oxy-methyl group at the C-27 position is important for antibacterial activity.

Physiological and biochemical characterization of biochar-induced resistance against bacterial wilt of eggplants

The abrupt variation in climatic patterns has become a global concern in terms of food security. Biochar, known to ameliorate climatic adversities by sequestering carbon and activating systemic resistance pathways in plants, has become increasingly relevant. Therefore, the study was aimed to characterize leaf waste biochar (LWB) by Fourier-transform infrared spectroscopy, scanning electron microscopy with energy dispersive X-ray (SEM-EDX) and X-ray diffraction analytical techniques as well as determination of its impact on the development of bacterial wilt (BW) in eggplant (Solanum melongena) caused by Ralstonia solanacearum (RS). The effect of LWB on the physiology and defence-associated biochemistry of eggplants was investigated thoroughly. Eggplants either inoculated (+RS) or uninoculated (-RS) were cultivated in potting mixture containing 3 and 6% (v/v) LWB separately. In comparison with substrate (soil only), percentage disease index was significantly reduced (71%) in plants grown in 6% LWB-amended treatments. Biochar-induced increase in level of total chlorophyll content as well as in biochemicals such as phenolics, flavonoids and peroxidases were evident on plants in terms of resistance response against BW. Moreover, biochar also significantly affected the level of NPK in the eggplants. In conclusion, biochar-triggered biochemical alterations played a pivotal role in the management of BW along with the curing of the disease-infested soils.

Xenorhabdus aichiensis sp. nov., Xenorhabdus anantnagensis sp. nov., and Xenorhabdus yunnanensis sp. nov., Isolated from Steinernema Entomopathogenic Nematodes

Three bacterial strains, XENO-2T, XENO-7T, and XENO-10T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel Xenorhabdus species. In this study, we describe these new species by whole-genome and whole-proteome phylogenomic reconstructions, by calculating sequence identity scores using core genome sequences, and by phenotypic characterization. Phylogenomic reconstructions using ribosomal and house-keeping genes, and whole-genome and whole-proteome sequences show that XENO-2T and XENO-10T are closely related to Xenorhabdus japonica DSM 16522T and that XENO-7T is closely related to Xenorhabdus bovienii subsp. africana XENO-1T and to X. bovienii subsp. bovienii T228T. The dDDH values between XENO-2T and XENO-10T and between XENO-2T and X. japonica DSM 16522T are 56.4 and 51.8%, respectively. The dDDH value between XENO-10T and X. japonica DSM 16522T is 53.4%. The dDDH values between XENO-7T and X. bovienii subsp. africana XENO-1T and between XENO-7T and X. bovienii subsp. bovienii T228T are 63.6 and 69.4%, respectively. These dDDH values are below the 70% divergence threshold for prokaryotic species delineation. The newly described species are highly pathogenic to G. mellonella larvae, grow at pH between 5 and 9 (optimum 5-7), at salt concentrations of 1-3% (optimum 1-2%), and temperatures between 20 and 37 °C (optimum 28-30 °C). Biochemical tests such as lysine decarboxylase, ornithine decarboxylase, urease, gelatinase, citrate utilization, indole and acetoin production, and cytochrome oxidase tests allow to differentiate the novel species from their more closely related species. Considering these genetic and phenotypic divergencies, we propose the following new species: Xenorhabdus aichiensis sp. nov. with XENO-7T (= CCM 9233T = CCOS 2024T) as the type strain, Xenorhabdus anantnagensis sp. nov., with XENO-2T (= CCM 9237T = CCOS 2023T) as the type strain, and Xenorhabdus yunnanensis sp. nov., with XENO-10T (= CCM 9322T = CCOS 2071T) as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.