16S ribosomal DNA amplification for phylogenetic study

Eco-friendly biocontrol of pine wilt disease: Enhancing tree defense with Bacillus subtilis JCK-1398 for sustainable forest management

Pine wilt disease (PWD), caused by pinewood nematodes (Bursaphelenchus xylophilus), poses a significant threat to forestry worldwide. This study introduces a novel biocontrol strategy using Bacillus subtilis JCK-1398, which was selected and identified for its resistance-induction potential after extensive screening of microbial strains from pine tissues. The bacterium was found to biostimulate resistance in Pinus densiflora. Comprehensive analyses, including transcriptomics, qPCR assays, and high-performance liquid chromatography (HPLC), revealed that B. subtilis JCK-1398 significantly upregulates defense-related genes and stimulates pinoresinol production, a compound linked to resistance against nematodes. Treatment with B. subtilis JCK-1398 suppressed nematode migration and reduced nematode populations within pine tissues, effects attributed to the enhanced tree defense response. Field trials corroborated these findings, demonstrating a 72 % decrease in PWD incidence with aerial application of JCK-1398, confirming its potential for large-scale forest application. This biocontrol strategy, leveraging the stimulation of plant defense by B. subtilis JCK-1398, presents a promising and scalable, eco-friendly solution for managing PWD. Overall, this study provides new insights into the interactions between the bioagent, the host tree, and the pest nematode, offering an effective and sustainable approach to mitigate pine wilt disease.

Spatially variable organic-matter-driven clogging in a stormwater infiltration pond: Isotopic, microbiological and hydrogeological evidence

Stormwater infiltration ponds (SIPs) are nature-based solutions which tend to decrease their infiltration capacity over time due to pore clogging. Organic matter (OM) is a well-known clogging driver, but how OM affects the physical and biochemical processes in a SIP remains largely unknown. An analysis encompassing soil organic carbon (SOC) stable isotopes, extracellular polymeric substances (EPS) of biofilms, DNA-based identification of microbiological communities and hydrogeological tests was carried out to elucidate the main clogging mechanisms in a large SIP in Italy. Open pits revealed a stratified soil composed of different textures and compositions, associated with artificial recharge sequences and on-site maintenance practices. A very different isotopic and microbiological signature of soil samples collected at different depths within the first meter of the soil surface was observed. Such diversity was linked to the spatially variable permeability of OM-enriched sediments limiting the infiltration. The isotopic signature beneath the more permeable (i.e., less clogged) OM-enriched layers was similar to that of the isotopic value of the biological surficial crust (δ13C → -27 ‰). Below the less permeable (i.e., more clogged) OM-enriched layers, isotopic values were more consistent with advanced degradation of organic matter (δ13C → -23 ‰). The selective hydraulic isolation of the analyzed trenches could lead to the formation of microbial microenvironments, with direct consequences on local composition of EPS and biofilm production. Based on this multidisciplinary approach, a new conceptual model could be proposed to the site managers and authorities dealing with the SIP's maintenance.

Halotolerant Enterobacter asburiae A103 isolated from the halophyte Salix linearistipularis: Genomic analysis and growth-promoting effects on Medicago sativa under alkali stress

Soil salinization negatively affects plant growth and threatens food security. Halotolerant plant growth-promoting bacteria (PGPB) can alleviate salt stress in plants via diverse mechanisms. In the present study, we isolated salt-tolerant bacteria with phosphate-solubilizing abilities from the rhizosphere of Salix linearistipularis, a halophyte distributed in saline-alkali soils. Strain A103 showed high phosphate solubilization activity and was identified as Enterobacter asburiae based on genome analysis. In addition, it can produce indole-3-acetic acid (IAA), siderophores, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Genome mining has also revealed the presence of several functional genes involved in the promotion of plant growth. Inoculation with A103 markedly improved alfalfa growth in the presence of 100 mM NaHCO3. Under alkali stress, the shoot and root dry weights after bacterial inoculation improved by 42.9 % and 21.9 %, respectively. Meanwhile, there was a 35.9-37.1 % increase in the shoot and root lengths after treatment with A103 compared to the NaHCO3-treated group. Soluble sugar content, peroxidase and catalase activities increased in A103-inoculated alfalfa under alkaline stress. A significant decrease in the malondialdehyde content was observed after treatment with strain A103. Metabolomic analysis indicated that strain A103 positively regulated alkali tolerance in alfalfa through the accumulation of metabolites, such as homocarnosine, panthenol, and sorbitol, which could reduce oxidative damage and act as osmolytes. These results suggest that halophytes are valuable resources for bioprospecting halotolerant beneficial bacteria and that the application of halotolerant growth-promoting bacteria is a natural and efficient strategy for developing sustainable agriculture.

Biogenic engineered zinc oxide nanoparticle for sulfur black dye removal from contaminated wastewater: comparative optimization, simulation modeling, and isotherms

This research work aimed to isolate and culture the bacterium Bacillus paramycoides for biogenic fabrication of zinc oxide nanoparticles, specifically ZnO and ZnO-ME nanoparticles (nanoparticles fabricated from bacterial extracts only - ZnO, and from bacterial cell mass including extract - ZnO-ME). SEM investigation revealed the spherical-shaped NPs with 22.33 and 39 nm in size for ZnO and ZnO-ME, respectively. The Brunauer, Emmett, and Teller (BET) studies revealed mesoporous structure with pore diameters of 13.839 and 13.88 nm and surface area of 7.617 and 33.635 m2/gm for ZnO and ZnO-ME, respectively. Various parameters for the adsorption of sulfur black dye onto both ZnO and ZnO-ME were screened and optimized using Plackett-Burman Design (PBD), Full Factorial Design (FFD) and Central Composite Design (CCD). The results of the optimization modeling study revealed that FFD yielded the most predictable and best-fitting results among all the models studied, with R2 values of 0.998 for ZnO and 0.993 for ZnO-ME. Notably, ZnO-ME exhibited a greater dye removal efficiency 80% than ZnO i.e., 71%, it may be due to the presence of amorphous carbon on the surface of ZnO-ME. Among the various isothermal models, the Freundlich model displayed the strongest correlation with the dye removal data, confirming the multilayer adsorption of dye on both nanoparticles and supporting physisorption. Therefore, ZnO and ZnO-ME nanoparticles have been proven as potential tools for mitigating environmental impacts associated with dye-containing wastewater.

Emergence of Aeromonas salmonicida subsp. masoucida MHJM250: unveiling pathological characteristics and antimicrobial susceptibility in golden mahseer, Tor putitora (Hamilton, 1822) in India

Aeromonas salmonicida subsp. masoucida, designated as laboratory strain MHJM250, was characterized from a naturally infected farmed golden mahseer, Tor putitora. The infected fish exhibited clinical signs of erosion at the caudal fin and hemorrhage onx the ventral body surface. Molecular identification through 16 S rDNA and phylogenetic analysis revealed 100% similarity with a known strain A. salmonicida subsp. masoucida (MT122821.1). MHJM250 exhibited positive reactions for oxidase, catalase, esculin, MR-VP, O/F and utilized arginine and lysine. It also demonstrated siderophore activity, thrived at various NaCl concentrations, hydrolyzed gelatinase, skimmed milk and casinase. In vitro studies exhibited its hemolytic nature, significant biofilm production in glucose-rich tryptone soya broth and beta-hemolysis. MHJM250 didn't produce slime and was non-precipitated upon boiling. It showed crystal violet binding characteristics and auto-agglutination with relatively weak hydrophobicity (25%). In the challenge assay, intraperitoneal administration of MHJM250 to T. pitutora fingerlings at 108 CFU mL-1 resulted in pathogenicity with 3% mortality and mild hemorrhagic symptoms. Histopathological analysis revealed degenerative changes in gill, kidney, liver, muscle, and intestine samples. The bacterium displayed resistance to several antibiotics (µg/disc); ampicillin (10 µg), ampicillin/ sulbactam (10/10 µg), clindamycin (2 µg), linezolid (30 µg), penicillin G (10 µg) and rifampicin (5 µg) and varied minimum inhibitory concentrations against oxytetracycline, erythromycin and florfenicol. Transmission electron microscopy showed its rod-shaped structure with single polar flagellum and lophotrichous flagella. An investigation on the molecular basis for virulence factors of A. salmonicida subsp. masoucida MHJM250 may offer crucial understandings to formulate disease prevention and control strategies in aquaculture.

Wolbachia of phylogenetic supergroup K identified in oribatid mite Nothrus anauniensis (Acari: Oribatida: Nothridae)

Heritable endosymbionts widely occur in arthropod and nematode hosts. Among these endosymbionts, Wolbachia has been extensively detected in many arthropods, such as insects and crustaceans. Maternal inheritance is the most basic and dominant mode of transmission of Wolbachia, and it might regulate the reproductive system of the host in four ways: feminization, parthenogenesis, male killing, and cytoplasmic incompatibility. There is a relatively high percentage (10%) of thelytokous species in Oribatida, a suborder under the subclass Acari of arthropods, but the study of the endosymbionts in oribatid mites is almost negligible. In this paper, we detected endosymbiotic bacteria in two parthenogenetic oribatid species, Nothrus anauniensis Canestrini and Fanzago, 1877, which has never been tested for endosymbionts, and Oppiella nova, in which Wolbachia and Cardinium have been reported before. The results showed that Wolbachia was first found in N. anauniensis with an infection rate of 100% across three populations. Phylogenetic analysis showed that Wolbachia in N. anauniensis belonged to the supergroup K, marking the second supergroup of Wolbachia found in oribatid mites. Unlike previous studies, our study did not detect Wolbachia in O. nova, leading to the exclusion of Wolbachia's role in mediating thelytoky in this species.

Characteristics and in vitro properties of potential probiotic strain Fructobacillus tropaeoli KKP 3032 isolated from orange juice

Fructobacillus, a Gram-positive, non-spore-forming, facultative anaerobic bacterium, belongs to the fructophilic lactic acid bacteria (FLAB) group. The group's name originates from fructose, the favored carbon source for its members. Fructobacillus spp. are noteworthy for their distinctive traits, captivating the interest of scientists. However, there have been relatively few publications regarding the isolation and potential utilization of these microorganisms in the industry. In recent years, F. tropaeoli has garnered interest for its promising role in the food and pharmaceutical sectors, although the availability of isolates is rather limited. A more comprehensive understanding of Fructobacillus is imperative to evaluate their functionality in the industry, given their unique and exceptional properties. Our in vitro study on Fructobacillus tropaeoli KKP 3032 confirmed its fructophilic nature and high osmotolerance. This strain thrives in a 30% sugar concentration, shows resistance to low pH and bile salts, and exhibits robust autoaggregation. Additionally, it displays significant antimicrobial activity against foodborne pathogens. Evaluating its probiotic potential, it aligns with EFSA recommendations in antibiotic resistance, except for kanamycin, to which it is resistant. Further research is necessary, but preliminary analyses confirm the high probiotic potential of F. tropaeoli KKP 3032 and its ability to thrive in the presence of high concentrations of fructose. The results indicate that the isolate F. tropaeoli KKP 3032 could potentially be used in the future as a fructophilic probiotic, protective culture, and/or active ingredient in fructose-rich food.

Emerging antibiotic and heavy metal resistance in spore-forming bacteria from pig manure, manure slurry and fertilized soil

Spore-forming bacteria (SFB), like Bacillus, are the gram-positive bacteria with broad-spectrum activity that is one of the commonly used strains of probiotics. However, these bacteria also have significant resistance. In this study, we systematically investigated pig manure, manure slurry and soil by 16S rRNA high-throughput sequencing and traditional culture techniques. We found the SFB was widespread in manure, manure slurry and soil, Firmicutes was one of the main dominant phyla in pig manure, manure slurry and soil, the relative abundance of Bacillus were 0.98%, 0.01%, and 2.57%, respectively, and metals such as copper have complex relationships with bacteria. We isolated 504 SFB from 369 samples, with the highest number identified as Bacillus subtilis. SFB strains showed varying degrees of antibiotic resistance; the greatest against erythromycin, followed by imipenem. The MICs of SFB varied greatly against different heavy metals; with high (est) resistance against Zn2+, followed by Cu2+. Second-generation whole genome sequencing (WGS) revealed that nine Bacillus strains carried different subtypes of vancomycin resistance genes, among which vanRM had the highest frequency. The strain W129 included the vanRA-vanRM-vanSA-vanZF cluster. The nine Bacillus strains also contained antibiotic genes such as aminoglycoside (ant(9)-Ia), β-lactam (bcII), and macrolide (msrE). Twenty-six Bacillus isolates carried copper resistance clusters, including csoR-copZ, copA-copZ-csoR, and copZ-copA. WGS showed that strain W166 carried 11 vancomycin resistance genes and 11 copper resistance genes. There were 4 vancomycin resistance genes and 14 copper resistance genes on the W129 chromosome. Strain W129 also harbors the plasmid pLKYM01 that contains an intact transposon consisting of insertion sequence and vancomycin resistance genes vanYF and vanRA. This study explores the potential risks of using pig manure and fertilized soil to inform safe and effective use of probiotics in agriculture. It highlights scientific evidence for concern over the safe utilization and control of animal waste products.

In vitro antimicrobial and antioxidant activities of bioactive compounds extracted from Streptomyces africanus strain E2 isolated from Moroccan soil

This study aimed to isolate Streptomyces sp. from Moroccan terrestrial ecosystems and identify bioactive compounds through GC-MS analysis. Antimicrobial activity was assessed against various pathogenic microorganisms including Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Escherichia coli ATCC 25922 and Candida albicans ATCC 60193, and multi-drug resistant strains comprising Listeria monocytogenes, Klebsiella pneumoniae 19K 929, Proteus sp. 19K1313, Klebsiella pneumoniae 20B1572, Proteus vulgaris 16C1737, and Klebsiella pneumoniae 20B1572. Based on the results of the gene sequencing of gene 16S rRNA and phylogenetic analysis, the E2 isolate belongs to the genus Streptomyces with the highest degree of resemblance (97.51%) to the Streptomyces africanus strain NBRC 101005 (NR_112600.1). The isolate exhibited broad-spectrum antibacterial activity, with maximum efficacy against Klebsiella pneumoniae 20B1572 indicated by an inhibition zone diameter of 22.5 ± 0.71mm and a minimum inhibitory concentration (MIC) of 0.0625 mg/mL. The in vitro antioxidant potential of E2 strain was determined through screening of its ethyl acetate extract against sets of antioxidant assays. The results were indicative of E2 strain displaying strong antioxidant activity against ABTS, DPPH free radicals, and FRAP. Furthermore, there was a high significant correlation (p < 0.0001) between the total phenolic and flavonoid content and antioxidant activities. The GC-MS analysis of the extract identified six volatile compounds, with Eugenol (96%) and Maltol (93%) being the most prominent. Additionally, the HPLC-UV/vis analysis revealed six phenolic compounds: gallic acid, chlorogenic acid, vanillic acid, trans-ferulic acid, ellagic acid, and cinnamic acid. Overall, the study highlights Streptomyces sp. strain E2 as a potential source of potent antimicrobial and antioxidant metabolites, offering promise in addressing antibiotic resistance and oxidative stress-related conditions.

Production of a novel cellulase by Bacillus amyloliquefaciens OKB3 isolated from soil: Purification and characterization

Microbial cellulases have become significant biocatalysts because of their complex composition and extensive industrial applications. This study aimed to isolate an efficient cellulase-producing strain, followed by molecular identification, enzyme purification, and characterization. Among 110 isolates, Bacillus amyloliquefaciens OKB3 was selected for its significant cellulase production, with optimal activity at pH 5.0 and 34 °C. The purification using ammonium sulfate and Sephadex G-100 chromatography resulted in specific activity of 2720.76 U/mg, 2.91 fold purification, and 29.44 % yield. The purified cellulase named CelB was a dimeric macromolecule of 123 kDa consisting of 67 and 54 kDa subunits. CelB was most active at 60 °C and pH 6, and it was stable at pH 5.5 to 6.0 and 0 °C to 4 °C. CelB was unaffected by metal cofactors and inhibited in the presence of divalent cations Cu2+, Hg2+, Cd2+, and Ag2+. The CelB has higher specificity of CMC compared to other substrates. The Km, Vmax, and Kcat values were 0.037 mM, 188.67 μmole/min, and 7430 S-1 respectively. The unique attributes of CelB make it a very promising candidate for various biotechnological applications.

The point mutation A1387G in the 16S rRNA gene confers aminoglycoside resistance in Campylobacter jejuni and Campylobacter coli

Thermotolerant Campylobacter spp. are the most frequent cause of foodborne bacterial diarrhea and high-priority antibiotic-resistant pathogens, according to the World Health Organization (WHO). Monitoring revealed current low prevalence of gentamicin resistance in European Campylobacter spp. isolates but substantial presence of gentamicin modifying genes circulating globally. Using a combined approach of natural transformation and whole-genome sequencing, we revealed a novel gentamicin resistance mechanism, namely the point mutation A1387G in the 16S rRNA gene, originally identified in a C. coli isolate from turkey caecal content. The transformation rate of the resistance using genomic DNA of the resistant donor to sensitive recipient C. jejuni and C. coli was ~2.5 log10 lower compared to the control rpsL-A128G point mutation conferring streptomycin resistance. Antimicrobial susceptibility tests showed cross-resistance to apramycin, kanamycin, and tobramycin, with transformants exhibiting more than 4- to 8-fold increased MICs to apramycin and tobramycin and over 64-fold higher MICs to kanamycin compared to wild-type isolates. Although transformants showed 177-1,235 variations relative to the recipient, only the A1387G point mutation in the 16S rRNA was in common. This mutation was causal for resistance, as transformation of a 16S rRNA_A1387G PCR fragment into susceptible isolates also led to resistant transformants. Sanger sequencing of the 16S rRNA genes and Oxford nanopore whole-genome sequencing of transformants identified clones harboring either all three copies with A1387G or a mixed population of wild-type and mutated 16S rRNA gene alleles. Within 15 passages on non-selective medium, transformants with mixed populations of the 16S rRNA gene copies partially reverted to wild type, both geno- and phenotypically. In contrast, transformants harboring the A1387G point mutation in all three 16S rRNA gene copies kept full resistance within at least 45 passages. We speculate that partial acquisition and rapid loss of the point mutation limited its spread among C. spp. isolates. In-depth knowledge on resistance mechanisms contributes to optimal diagnosis and preventative measures.

Methane-oxidizing bacterial community dynamics in sub-alpine forest soil

Microbial activities in sub-alpine forest soil influence global cycling of the potent greenhouse gas methane. Understanding the dynamics of methane-oxidizing bacterial communities, particularly the roles of potentially active versus total microbial populations, is necessary for reducing uncertainty in global methane budget estimates. However, our understanding of the factors influencing methane cycling in forest soils is limited by our lack of knowledge about the biology of the microbes involved and how these communities are shaped by their environment. Here, we compared the composition and potential activity of microbial communities using 16S rRNA gene amplicon sequencing of total genomic DNA (gDNA) and potentially active complementary DNA (cDNA) from shallow soil in Red Butte Canyon (Salt Lake City, Utah, USA). We compared riparian and upland soils at two time points in the growing season and found distinct differences in both the community composition of the gDNA and cDNA libraries and the potential drivers of these community structures. Aerobic methane-oxidizing bacteria (methanotrophs) were detected in all samples, with cDNA libraries containing a higher average relative abundance and diversity of methanotrophs compared to gDNA libraries. Methane flux at the sample sites did not significantly correlate to the relative abundance (gDNA) or potential activity (cDNA) of methanotrophs. In the cDNA libraries, there were significant positive correlations between the abundance of Methylococcaceae family methanotrophs and several non-methanotrophic methylotrophs previously found to be associated with methane-oxidizing bacterial communities. These findings suggest a complex relationship between methane-cycling bacterial communities and methane flux and highlight the need for further in situ studies to understand the environmental and ecological influences of these microbial consortia.

IMPORTANCE

Methane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.

Fire-associated microbial shifts in soils of western conifer forests with Armillaria root disease

Fires in coniferous forests throughout the northern United States alter ecosystem processes and ecological communities, including the diversity and composition of microbial communities living in the soil. In addition to its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. Altering the microbiome composition to promote taxa that inhibit pathogenic activity has been suggested as a management strategy for forest diseases, including Armillaria root disease caused by Armillaria solidipes, which causes growth loss and mortality of conifers. These forest ecosystems are experiencing increased wildfire burn severity that could influence A. solidipes activity and interactions of the soil microbiome with Armillaria root disease. In this research, we examine changes to the soil microbiome following three levels of burn severity in a coniferous forest in northern Idaho, United States, where Armillaria root disease is prevalent. We further determine how these changes correspond to the soil microbiomes associated with the pathogen A. solidipes, and a putatively beneficial species, A. altimontana. At 15-months post-fire, we found significant differences in richness and diversity between bacterial communities associated with unburned and burned areas, yet no significant changes to these metrics were found in fungal communities following fire. However, both bacterial and fungal communities showed compositional changes associated with burn severity, including microbial taxa with altered relative abundance. Further, significant differences in the relative abundance of certain microbial taxa in communities associated with the three burn severity levels overlapped with taxa associated with various Armillaria spp. Following severe burn, we observed a decreased relative abundance of beneficial ectomycorrhizal fungi associated with the microbial communities of A. altimontana, which may contribute to the antagonistic activity of this soil microbial community. Additionally, A. solidipes and associated microbial taxa were found to dominate following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Overall, our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in similar conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

IMPORTANCE

With its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. These forest ecosystems are experiencing increased wildfire frequency and burn severity that could influence the fungal root pathogen, Armillaria solidipes, and interactions with the soil microbiome. We examined changes to the soil microbiome following three levels of burn severity, and examined how these changes correspond with A. solidipes, and a putatively beneficial species, A. altimontana. Following severe burn, there was a decreased relative abundance of ectomycorrhizal fungi associated A. altimontana. A. solidipes and associated microbial taxa dominated following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach

Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.

Microbispora maris sp. nov., a novel actinobacterium isolated from the gill of the leopard coral grouper (Plectropomus leopardus)

A novel actinomycete, designated strain ZYX-F-249T, was isolated from the gill of a leopard coral grouper in Yongxing Island, Hainan Province, China. Based on 16S rRNA gene sequence analysis, strain ZYX-F-249T belonged to the genus Microbispora, with high similarities to Microbispora rosea ATCC 12950T (98.7 %), Microbispora hainanensis 211020T (98.5 %), Microbispora clausenae CLES2T (98.4 %), Microbispora bryophytorum NEAU-TX2-2T (98.1 %) and Microbispora oryzaeRL4-1ST (98.0 %). Phylogenetic analysis of the 16S rRNA gene sequence of strain ZYX-F-249T showed that the strain formed a stable subclade with Microbispora rosea ATCC 12950T in the genus Microbispora. The cell wall of the novel isolate contained meso-diaminopimelic acid, while whole-cell sugars were madurose, glucose and ribose. The predominant menaquinones were MK-9(H6), MK-9(H4), MK-9(H2) and MK-9(H0). The characteristic phospholipids (PLs) were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, glycophospholipids and an unknown PL. The major cellular fatty acids (>10%) were iso-C16 : 0 and iso-C18 : 0. Genome sequencing showed a DNA G+C content of 71.6%. The low average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values demonstrated that strain ZYX-F-249T could be readily distinguished from closely related species. Based on data from these phylogenetic, chemotaxonomic and physiological characteristics, strain ZYX-F-249T represents a novel species of the genus Microbispora, for which the name Microbispora maris sp. nov. is proposed. The type strain is ZYX-F-249T (=CCTCC AA 2023030T =JCM 36778T).

Polyphasic identification of Vibrio species from aquatic sources using mass spectrometry, housekeeping gene sequencing and whole genome analysis

Accurate bacterial identification is essential for determining the causative agent of an infection, thus facilitating appropriate treatment and management strategies in both human and animal health contexts. Some species in the Vibrio genus are recognized pathogens, associated with a variety of infections. However, identification of these bacteria is oftentimes controversial. Therefore, we aimed to evaluate different identification approaches in terms of their reliability in distinguishing Vibrio species. To achieve this, we selected a set of 40 Vibrio isolates previously recovered from water and floating plastic samples in a large bay environment and identified them employing MALDI-TOF mass spectrometry, and rrs and pyrH gene sequencing. A subset of isolates was also submitted to whole genome sequencing. Overall, MALDI-TOF was found to be a fast-screening methodology for identification, notably at genus-level. However, for better species discrimination, pyrH gene sequencing stood out as a more reliable tool in contrast to rrs gene sequencing and MALDI-TOF, as corroborated by whole genome sequencing analysis.

Modulating the gut microbiota in Crohn's disease: a pilot study on the impact of a plant-based diet with DNA-based monitoring

Introduction

Crohn's Disease (CD) is characterized by chronic intestinal inflammation and dysbiosis. This study aimed to investigate the effects of a plant-based diet (PBD) on gut microbiota composition and inflammation in CD patients and assess the utility of trnL gene sequencing for monitoring dietary adherence.

Methods

Fourteen CD patients participated in a 12-week PBD intervention. Dietary adherence was monitored through self-reported food diaries and trnL sequencing, which detects plant residues in fecal samples. Gut microbiota was analyzed using 16S rRNA sequencing, and fecal calprotectin levels were measured as an indicator of intestinal inflammation.

Results

TrnL sequencing identified 55 plant genera in fecal samples, compared to 41 reported in food diaries, highlighting its accuracy in assessing plant residue diversity. By week 4, participants demonstrated a 1.4-fold increase in plant intake, correlating with a significant increase in microbial diversity. Key genera associated with gut health, such as Faecalibacterium and Bacteroides, increased in abundance. Additionally, fecal calprotectin levels decreased from 472 mg/kg at baseline to 207 mg/kg at week 12, indicating reduced intestinal inflammation.

Discussion

A PBD positively influenced gut microbiota composition and decreased intestinal inflammation in CD patients. The study also demonstrated that trnL sequencing is an effective tool for assessing dietary adherence in clinical settings, offering a more objective measure than self-reported food diaries.

Large-scale genomic analysis of Elizabethkingia anophelis

The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.

Comparative genomic analysis of two putative novel Idiomarina species from hypersaline miocene deposits

BACKGROUND

Hypersaline habitats, as extreme environments, are a great source of well-adapted organisms with unique properties as they have evolved various strategies to cope with these extreme conditions. Bioinformatics and genomic mining may shed light on evolutionary relationships among them. Therefore, the aim of this study was to assess the biodiversity and especially the strategies evolved within the Idiomarina genus, with the primary focus on the taxonomy and genomic adaptations of two novel strains affiliated with Idiomarina genus isolated from unique environment - brines of two Early Miocene salt deposits.

RESULTS

Both analyzed species belonged to the Idiomarina loihiensis cluster with similarity levels of 16S rRNA gene sequences as high as 99.5% and showed a significant genome size reduction, known characteristic of Idiomarina genomes, though within the genome of Sol25 strain the lowest extent of the carbohydrate utilization genes reduction was observed t among the Idiomarina species. Moreover, the comparative genome analyses indicated that despite both strains being isolated from geographically and geologically similar environments (brines from at least 12 Ma), the species showed higher relatedness to other Idiomarina species than to each other.

CONCLUSION

The present findings highlighted the importance of genomic data in resolving taxonomic uncertainties and understanding of adaptation strategies of extremophiles. Geographic isolation likely contributed to population divergence of the Idiomarina genus, and the recent study offered insights into biogeographic patterns and allopatric speciation of this bacterial group.

In-vitro and in-vivo assessment of the bactericidal potential of peracetic acid and hydrogen peroxide disinfectants against A. hydrophila infection in Nile tilapia and their effect on water quality indices and fish stress biomarkers

This study aimed to assess the in vitro and in vivo disinfectant potential of peracetic acid (PAA) (1 mg/L) and hydrogen peroxide (H2O2) (20 mg/L) on the physicochemical and microbiological water quality parameters of fish aquaria, the microbial density of Nile tilapia muscular tissue, fish hepatic cortisol levels, and antioxidant biomarkers. In vitro, PAA and H2O2 reduced A. hydrophila colony viability by 5 log units after 30 and 5 min of contact time, respectively. PAA and H2O2 were added to aquaria water twice a week for the three-week experiment. Increased fish escape reflexes were observed only in the PAA group, which returned to normal within 10 min. No mortalities were reported in either the PAA or H2O2 groups. An in vivo experimental challenge with a pathogenic strain of A. hydrophila revealed a 20% reduction in mortality in the PAA group, with no mortalities in the H2O2 group. Cortisol levels and antioxidant markers were measured to assess the impact of PAA and H2O2 on fish health. Cortisol levels in the PAA and H2O2 groups were significantly higher than in the control group after disinfectant exposure, but they progressively returned to normal. A significant reduction in superoxide dismutase (SOD) and catalase (CAT) activity, along with considerably higher glutathione peroxidase (GPx) and malondialdehyde (MDA) enzymatic activity, was observed in the PAA and H2O2 groups compared to the control group. A substantial increase in total antioxidant capacity (TAC) was recorded in the PAA group. Physicochemical analyses revealed reduced pH and increased dissolved oxygen levels in the PAA and H2O2 groups. Microbiological analyses showed a significant reduction in bacterial density in water by 64% and 76% after 30 min of exposure to PAA and H2O2, respectively, with a non-significant increase in microbial count after bacterial challenge. Additionally, aerobic bacterial count, Aeromonas spp., and psychotropic bacterial count in fish muscle showed a significant reduction in the H2O2 group compared to the PAA and control groups before and after infection. The study concludes that regular application of PAA and H2O2 can temporarily reduce bacterial load in aquaria and fish muscle, regulate stress responses, and improve fish health by reducing A. hydrophila-induced infections and improving survival.

A Novel Strain Burkholderia theae GS2Y Exhibits Strong Biocontrol Potential Against Fungal Diseases in Tea Plants (Camellia sinensis)

BACKGROUND

Tea plants (Camellia sinensis) are widely cultivated cash crops. However, fungal diseases lead to significant reductions in both the yield and quality of tea. Therefore, searching for economical, eco-friendly, and efficient biological control measures is crucial for protecting tea plants from pathogenic fungi.

METHODS

The confrontation assays were performed to identify the antagonistic bacteria against tea pathogenic fungi and evaluate the antifungal activity of these bacteria.

RESULTS

Here, three tea pathogenic fungi were identified: Colletotrichum siamense HT-1, Diaporthe phaseolorum HT-3, and Fusarium fujikuroi HT-4. Notably, D. phaseolorum was the first to be reported in tea plants in China. Some tea pathogenic fungi showed a high relative abundance, suggesting a potential disease risk in tea plantations. Strain GS2Y, isolated from tea rhizosphere soil, exhibited strong antifungal activity against tea pathogenic fungi and represented a novel species within the genus Burkholderia, designated as Burkholderia theae. GS2Y could directly inhibit tea pathogenic fungi by disrupting the cellular structures and protect tea plants from fungal diseases caused by C. siamense HT-1 and D. phaseolorum HT-3.

CONCLUSIONS

B. theae GS2Y might function as a potentially valuable resource for biocontrol agents, laying the foundation for the development of strategies to manage fungal diseases in tea plants.

Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea

Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.

Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation

Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.

IMPORTANCE

Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.

Comparative genomic analyses of the genus Robertmurraya and proposal of the novel species Robertmurraya mangrovi sp. nov., isolated from mangrove soil

A Gram-positive, aerobic, motile, rod-shaped bacterial strain, designated 31A1RT, was isolated from the mangrove soil of Xilian village, Zhanjiang, China. Strain 31A1RT thrives at temperatures ranging from 15 to 45 °C (optimum at 30 °C), pH 6.5-10 (optimum at 8.5), and in the presence of 0-5% (w/v) NaCl (optimum at 1.5%). The strain shares the highest 16S rRNA gene sequence similarity with Robertmurraya crescens (97.24%) and Robertmurraya dakarensis (97.18%). The complete genome of strain 31A1RT spans 4.71 Mbp with a genomic DNA G + C content of 35.9 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain 31A1RT and type strains of other species of the genus Robertmurraya were 71.24-72.11% and 19.90-21.40%, respectively. The amino acid identity values and percentage of conserved proteins ranged from 66.94 to 68.10% and from 58.34 to 61.62%, respectively, aligning with intrageneric cutoff values. The major fatty acids (≥ 5.0%) were iso-C14:0 (5.0%), iso-C15:0 (41.4%), iso-C16:0 (12.6%), C16:1ω7c alcohol (12.2%), and iso-C17:1 ω10c (6.5%). The polar lipids profile was mainly composed of diphosphatidyl glycerol, phosphatidyl glycerol, and phosphatidyl ethanolamine. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Robertmurraya, which indicated functional capacities and metabolic similarities. Consequently, we propose that strain 31A1RT represents a new species in the genus Robertmurraya, for which the name Robertmurraya mangrovi sp. nov. is proposed, with the type strain being 31A1RT (= GDMCC 1.4378T = JCM 36937T).

Gut microbiota-derived gamma-aminobutyric acid improves host appetite by inhibiting satiety hormone secretion

Globally, appetite disorders have become an increasingly prominent public health issue. While short-term appetite loss may seem relatively harmless, prolonged instances can lead to serious physical and mental damage. In recent years, numerous studies have highlighted the significant role of the "microbiota-gut-brain" axis in the regulation of feeding behavior in organisms, suggesting that targeting the gut microbiota may be a novel therapeutic strategy for appetite disorders. However, the molecular mechanisms through which the gut microbiota mediates the increase in host appetite and the causal relationship between the two remain unclear. Based on this, we conducted 16S rRNA sequencing to analyze the gut microbiota of rabbits with high and low feed intake, followed by fecal microbiota transplantation (FMT) and metabolite gavage experiments to elucidate the underlying mechanisms. Our research indicates that the high feed intake group exhibited significant enrichment of the g__Bacteroides and gamma-aminobutyric acid (GABA), and intragastric administration of GABA effectively promoted the host's feeding behavior. The underlying mechanism involves GABA derived from the gut microbiota inhibiting the secretion of satiety hormones to enhance the host's feeding behavior. Furthermore, the results of FMT suggest that differences in gut microbiota composition may be a contributing factor to varying levels of feed intake in the host. In conclusion, these findings emphasize the role of the gut microbiota-derived GABA, in increasing host feed intake, offering a new target for the treatment of appetite disorders from the perspective of gut microbiota.IMPORTANCEThe incidence of anorexia is rapidly increasing and has become a global burden. Gut microbiota can participate in the regulation of host feeding behavior, yet the molecular mechanisms through which the gut microbiota mediates the increase in host appetite and the causal relationship between them remain unclear. In this study, we utilized 16S rRNA sequencing to investigate the composition of the gut microbiota in rabbits with varying levels of feed intake and employed fecal microbiota transplantation and gastric infusion experiments with gamma-aminobutyric acid (GABA) to elucidate the potential mechanisms involved. GABA derived from the gut microbiota can effectively enhance the host's feeding behavior by inhibiting the secretion of satiety hormones. This discovery underscores the pivotal role of the gut microbiota in modulating host appetite, offering novel research avenues and therapeutic targets for appetite disorders.

Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral

Coral diseases contribute to the worldwide loss of coral reefs, with the Black Band Disease (BBD) being a prominent example. BBD is an infectious condition with lesions with a pigmented mat composed of cyanobacteria, sulphate-reducing, sulphide-oxidizing, and heterotrophic bacteria. We compared the heterotrophic bacterial communities of healthy and BBD-affected colonies of the Caribbean coral Orbicella faveolata using culture-dependent and -independent techniques. Twenty and 23 bacterial isolates were identified from healthy and diseased tissues, respectively, which differed in their capacities to metabolize carbohydrates and citrate, either anaerobically or aerobically. They also differed in their quorum-sensing (QS) activity, as QS signaling molecules were found exclusively, and QS-inhibition was found primarily, in isolates from diseased tissues. Screening of bacterial diversity by 16SrDNA metabarcoding showed that members of the bacterial genera Muricauda and Maritimimonas were dominant in healthy tissues whereas members of the cyanobacterial genus Roseofilum were dominant in diseased tissues. These results suggest that bacterial dysbiosis can be linked with altered bacterial communication, likely leading to diachrony and imbalance that may participate in the progression of BBD. Investigating physiological traits and QS-based communication offers insights into the onset and progression of coral infections, paving the way for novel strategies to mitigate their impact.

Cell immobilization for enhanced milk clotting enzyme production from Bacillus amyloliquefacien and cheese quality

BACKGROUND

Milk clotting enzymes, essential for milk coagulation in cheese production, are obtained from the stomach of young ruminants, an expensive and limited source. This study was accomplished by finding a suitable alternative. Bacterial isolates recovered from honey were screened for milk clotting enzyme activity. and further, by immobilization of the microorganisms to enhance stability and facilitate their repeated use.

RESULT

The most effective enzyme was produced by a microbe identified as Bacillus amyloliquefaciens based on 16 S rRNA sequencing. The cells were encapsulated in Ca2+ alginate beads. These beads retained complete enzyme production after being used five times. Glucose and Soybean were selected as the most favorable carbon and nitrogen sources, respectively. The optimum temperature for activity was 35 ℃ for both free and immobilized cells but as the temperature was increased to 55 °C and above, the encapsulated form retained more activity than the free cells. The pH optimum shifted from 6.5 to 7 for the free cells to 7-7.5 for the immobilized cells. The immobilization process decreased the activation energy for enzyme production and activity, prolonged the enzyme half-life, and increased the deactivation energy. Enzyme produced by immobilized cells generated a more compact cheese.

CONCLUSIONS

The finding of this study was to identify a less expensive source of milk-clotting enzymes and confirm the success of cell immobilization in improving cell rigidity and stability. Also, immobilization of this B. amyloliquefaciens strain offers an enzyme source of value for industrial production of cheese.

2,4-Di-Tert-Butylphenol of Streptomyces luridiscabiei MMS-10 Inhibits Biofilm Forming Cariogenic Streptococcus mutans ULSP-2

Dental caries is a common chronic infectious disease of the oral cavity that affects the overall oral health of the individual. Cariogenic bacteria have long been recognized for their role in developing chronic dental infections. Drug-resistant bacteria represent a global challenge to effective pathogen control in caries. The present study aimed to isolate and identify soil actinomycetes for their antibacterial and anti-biofilm activities against antibiotic-resistant and biofilm-forming cariogenic bacteria. Thirteen caries bacteria isolated from infected tooth samples were evaluated for antibiotic resistance and biofilm formation. The isolate ULSP-2 showed the highest antibiotic resistance score (0.714) and was found to be a strong biofilm producer when tested by congo red agar and microtiter plate assays. The bacterium was identified as Streptococcus mutans based on morphological, biochemical, and molecular characterization. The effect of ethyl acetate extracts from 20 soil actinomycetes on the growth and biofilm formation ability of S. mutans was evaluated. The MMS-10 extract strongly inhibited growth (18.5 ± 0.5 mm) and biofilm formation (56.46 ± 0.32%) of S. mutans at 100 µg/mL. The isolate MMS-10 was identified at the molecular level as Streptomyces luridiscabiei. Based on FTIR, NMR, and GC-MS analysis, the purified MMS-10 extract was characterized and identified as 2,4-Di-tert-butylphenol. The metabolite's physiological, physicochemical, and pharmacokinetic properties were analyzed using the Swiss ADME web server and found to satisfy the criteria of drug-likenessof a molecule. The study revealed the significance of soil actinomycetes in controlling growth and biofilm formation in cariogenic S. mutans.

Burkholderia pseudomallei produces 2-alkylquinolone derivatives important for host virulence and competition with bacteria that employ naphthoquinones for aerobic respiration

Melioidosis is caused by Burkholderia pseudomallei, an opportunistic Gram-negative pathogen that inhabits soil and water in tropical and subtropical regions. B. pseudomallei infections often occur following contact with contaminated water or soil or by inhalation of contaminated dust and water droplets. There is limited knowledge about how B. pseudomallei is able to survive in harsh environmental conditions and compete with the microbes that inhabit these niches. Previous research demonstrated that 3-methyl-2-alkylquinolones (MAQs), and their corresponding N-oxides (MAQNOs), are produced by B. pseudomallei and provide a competitive advantage when grown in the presence of Gram-positive bacteria. In this study, 39 Gram-negative environmental bacteria in the Pseudomonadota and Bacteroidota phyla were isolated and characterized. Intriguingly, B. pseudomallei inhibited 71% of bacteria in the phylum Bacteroidota in zone of inhibition and coculture competition assays, but no Pseudomonadota isolates were similarly inhibited. Transposon mutagenesis was utilized to identify B. pseudomallei genes required for the inhibition of Sphingobacterium sp. ST4, a representative member of the Bacteroidota. Three mutations mapped to hmqA-G, the locus encoding 2-alkylquinolone derivatives, and two mutations were identified in scmR, a gene encoding a quorum-sensing controlled LysR-type transcriptional regulator. B. pseudomallei strains with deletion mutations in hmqD and scmR were unable to produce 2-alkylquinolone derivatives or inhibit Bacteroidota isolates in competition assays. RAW264.7 murine macrophage cells were infected with B. pseudomallei 1026b and 1026b ΔhmqD and there was a 94-fold reduction in the number of intracellular 1026b ΔhmqD bacteria relative to 1026b. The 50% lethal dose (LD50) of 1026b and 1026b ΔhmqD in BALB/c mice was determined to be 3 x 105 colony forming units (CFU) and > 1 x 106 CFU, respectively. Taken together, the results indicate that the products of the B. pseudomallei hmqA-G locus are important for intracellular replication in murine macrophages, virulence in a mouse model of melioidosis, and competition with bacteria that utilize naphthoquinones for aerobic respiration.

First draft genome sequence of a Pectobacterium polaris strain isolated in South Africa from potato tuber affected by soft rot

A phytopathogenic strain of Pectobacterium polaris (designated SRB2) was isolated for the first time in South Africa from a potato tuber affected by soft rot. The draft genome of strain SRB2 encodes various plant cell wall-degrading enzymes and genes associated with biofilm formation and virulence. Antibiotic resistance genes were not detected.

Trifolium repens L. recruits root-associated Microbacterium species to adapt to heavy metal stress in an abandoned Pb-Zn mining area

Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction between heavy metal-stressed plants and the microbiota are poorly understood. In this study, we screened and isolated representative amplicon sequence variants (strain M4) from rhizosphere soil samples of Trifolium repens L. growing in areas with high concentrations of heavy metals. To investigate the microecological mechanisms by which T. repens adapts to heavy metal stress in abandoned mining areas, we conducted potting experiments, bacterial growth promotion experiments, biofilm formation experiments, and chemotaxis experiments. The results showed that high concentrations of heavy metals significantly altered the rhizosphere bacterial community structure of T. repens and significantly enriched Microbacterium sp. Strain M4 was demonstrated to significantly increased the biomass and root length of T. repens under heavy metal stress. Additionally, L-proline and stigmasterol could promote bacterial growth and biofilm formation and induce chemotaxis for strain M4, suggesting that they are key rhizosphere secretions of T. repens for Microbacterium sp. recruitment. Our results suggested that T. repens adapted the heavy metal stress by reshaping rhizosphere secretions to modify the rhizosphere microbiota.

Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil

Strains M29T and ASUV-10-1T, which are aerobic, non-flagellated, and Gram-stain-negative, were isolated from soil samples collected in Inje (37°57'49.1"N 128°19'53.7"E) and Cheonan City (36°48'47.1"N 127°05'22.4"E), South Korea. Phylogenetic analyses based on rRNA gene sequences revealed that strains M29T and ASUV-10-1T form a distinct branch within the family Hymenobacter (order Cytophagales, class Cytophagia). Strain M29T is most closely related to Hymenobacter rubidus DG7BT with a 16 S rRNA gene sequence similarity of 97.05%. Strain ASUV-10-1T shows closest genetic similarity to Hymenobacter frigidus B1789T (96.42%), Hymenobacter jeongseonensis BT683T (95.97%), and Hymenobacter terricola 3F2TT (95.65%). The optimal growth conditions for these strains are pH 7.0, no NaCl, and a temperature of 25 °C. The dominant cellular fatty acids identified in these strains are iso-C15:0, anteiso-C15:0, and Summed Feature 3 (C16:1ω 7c / C16:1ω 6c). Both strains predominantly contain MK-7 as the respiratory quinone. The major polar lipids in strains M29T and ASUV-10-1T are phosphatidylethanolamine, aminophospholipid, and aminolipid. Based on biochemical, chemotaxonomic, and phylogenetic data, it is evident that M29T and ASUV-10-1T represent new species within the genus Hymenobacter. The new species were classified based on biochemical and chemotaxonomic characteristics. The taxonomic classification of these species was conducted following the guidelines and protocols outlined in Bergey's Manual of Systematic Bacteriology. We followed the methods for determining physiological and biochemical characteristics, as well as chemotaxonomic markers such as fatty acid profiles, quinone types, and polar lipid compositions. We also compared with the results of carbohydrate utilization and enzyme activities results [Bergey 1994]. Therefore, we propose the names Hymenobacter mellowenesis for strain M29T (= KCTC 102056T = NBRC 116578T) and Hymenobacter aranciens for strain ASUV-10-1T (= KCTC 92969T = NBRC 116575T).

Insights into the methodological perspectives for screening polyunsaturated fatty acids-containing bacteria

Polyunsaturated fatty acids (PUFA) are vital molecules in the pharmaceutical, medical, and nutritional industries. Exploration of bacterial strains capable of producing significant amounts of PUFAs offers a promising avenue for biotechnological applications and industrial-scale production. However, an extensive screening of several samples from diverse sources is highly needed to identify a potential strain. The present study provides the results of the evaluation of 15 different screening methodologies (including changes in existing protocols in terms of reagent concentration, incubation temperature and time) for identifying PUFA-producing bacteria in comparison to the gold standard method (Gas chromatography-mass spectrometry), for the first time. The results determined the most effective techniques for each critical PUFA, leading to an optimized screening process that saves time and resources. The H2O2 plate assay using 0.5% or 1% H2O2 for 72 & 96 h of incubation at 15 °C consistently outperformed others for finding bacteria containing total nutritionally important long chain-PUFA (LC-PUFA), linoleic acid, and arachidonic acid. Whereas the 2,3,5-triphenyl tetrazolium chloride broth assay at 10-15 °C was the most effective and semiquantitative screening methodology for eicosapentaenoic acid (EPA) and alpha-linolenic acid-containing bacteria. Apart from the methodological perspectives, the study also revealed certain potential strains to be targeted in the ongoing research on PUFA-containing bacteria. Further, the manuscript forms the first report on the presence of docosahexaenoic acid (DHA) in Shewanella decolorationis, EPA in Psychrobacter maritimus and Micrococcus aloeverae, and both EPA and DHA in Arthrobacter rhombi. Altogether, the paper generates several thought-provoking insights on the methodological perspectives and identifies potential PUFA-containing bacteria with practical applications in future bacteria-based PUFA research.

Hohaiivirga grylli gen. nov., sp. nov., a New Member of the Family Methylobacteriaceae, Isolated from Cricket (Gryllus chinensis)

A Gram-staining negative, non-motile, rod-shaped, oxidase negative and catalase positive strain WL0021T was isolated from cricket (Gryllus chinensis) living in the campus of Hohai University. Strain WL0021T was characterized utilizing a polyphasic taxonomy approach. The major fatty acids (> 5%) for strain WL0021T were C16:0 and summed feature 8, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, two aminolipids, and an unidentified polar lipid. Ubiquinone-10 was detected as the predominant respiratory quinone. The results of 16S rRNA gene phylogenetic analyses revealed that strain WL0021T had the highest sequence similarity of 95.3% to Microvirga flavescens c27j1T and strain WL0021T formed a distinct linage within the family Methylobacteriaceae in the phylogenetic trees. Whole genomic DNA G+C content was 48.3%. Combined with the results from this study, strain WL0021T should represent a novel genus in the family Methylobacteriaceae, for which the name Hohaiivirga grylli gen. nov., sp. nov. (type strain WL0021T=GDMCC 1.2420T =JCM 34655T=MCCC 1K05886T) is proposed.

Optimizing nitrogen fertilization in maize: the impact of nitrification inhibitors, phosphorus application, and microbial interactions on enhancing nutrient efficiency and crop performance

Despite the essential role of nitrogen fertilizers in achieving high crop yields, current application practices often exhibit low efficiency. Optimizing nitrogen (N) fertilization in agriculture is, therefore, critical for enhancing crop productivity while ensuring sustainable food production. This study investigates the effects of nitrification inhibitors (Nis) such as Dimethyl Pyrazole Phosphate (DMPP) and Dimethyl Pyrazole Fulvic Acid (DMPFA), plant growth-promoting bacteria inoculation, and phosphorus (P) application on the soil-plant-microbe system in maize. DMPFA is an organic nitrification inhibitor that combines DMP and fulvic acid for the benefits of both compounds as a chelator. A comprehensive rhizobox experiment was conducted, employing varying levels of P, inoculant types, and Nis, to analyze the influence of these factors on various soil properties, maize fitness, and phenotypic traits, including root architecture and exudate profile. Additionally, the experiment examined the effects of treatments on the bacterial and fungal communities within the rhizosphere and maize roots. Our results showed that the use of Nis improved plant nutrition and biomass. For example, the use of DMPFA as a nitrification inhibitor significantly improved phosphorus use efficiency by up to 29%, increased P content to 37%, and raised P concentration in the shoot by 26%, compared to traditional ammonium treatments. The microbial communities inhabiting maize rhizosphere and roots were also highly influenced by the different treatments. Among them, the N treatment was the major driver in shaping bacterial and fungal communities in both plant compartments. Notably, Nis reduced significantly the abundance of bacterial groups involved in the nitrification process. Moreover, we observed that each experimental treatment employed in this investigation could select, promote, or reduce specific groups of beneficial or detrimental soil microorganisms. Overall, our results highlight the intricate interplay between soil amendments, microbial communities, and plant nutrient dynamics, suggesting that Nis, particularly DMPFA, could be pivotal in bolstering agricultural sustainability by optimizing nutrient utilization.

Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment

The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.

Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov., novel carotenoid-producing bacterial species isolated from farm soil

Two yellow-pigmented novel strains, designated HF-S3T and HF-S4T, were isolated from farm soil in Paju, Republic of Korea. Cells of the two strains are characteristically Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and rod-shaped. Strain HF-S3T grew at 10-37 °C, while HF-S4T grew at 15-35 °C. Both strains grew at pH 5.0-12.0 and in NaCl concentrations (w/v) of 0-2.0%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that HF-S3T and HF-S4T belong to the genus Sphingomonas, with HF-S3T exhibiting 97.7, 97.6 and 97.4% similarity to Sphingomonas cannabina DM2-R-LB4T, Sphingomonas leidyi DSM 4733T and Sphingomonas canadensis FWC47T, respectively. Strain HF-S4T displayed 97.9, 97.7 and 97.6% similarity to Sphingomonas psychrotolerans Cra20T, Sphingomonas gei ZFGT-11T and Sphingomonas naasensis KIS18-15T, respectively. The DNA G+C contents of HF-S3T and HF-S4T were 67.0 and 66.5 mol%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values among the novel and related type strains were 20.2-28.2% and 75.9-84.3%, respectively. They all contained C14:0 2-OH and C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) as the major fatty acids and ubiquinone-10 as the predominant respiratory quinone. Strains HF-S3T and HF-S4T were found to produce carotenoid-type pigments. Based on polyphasic taxonomic analysis, the new isolates ostensibly represent two novel species of the genus Sphingomonas, with the proposed names Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov. for strains HF-S3T and HF-S4T, respectively. The S. rustica and S. agrestis type strains are HF-S3T (=KACC 23554T =TBRC 18352T) and HF-S4T (=KACC 23386T =TBRC 17899T), respectively.

In vitro efficacy of aquaculture antimicrobials and genetic determinants of resistance in bacterial isolates from tropical aquaculture disease outbreaks

Understanding the efficacy of antimicrobials against pathogens from clinical samples is critical for their responsible use. The manuscript presents in vitro efficacy and antimicrobial resistance (AMR) genes in seven species of fish pathogens from the disease outbreaks of Indian aquaculture against oxytetracycline, florfenicol, oxolinic acid, and enrofloxacin. In vitro efficacy was evaluated by minimum inhibitory concentration and minimum bactericidal concentration. The gene-specific PCR screened AMR genes against quinolones (qnrA, qnrB, and qnrS) and tetracyclines (tetM, tetS, tetA, tetC, tetB, tetD, tetE, tetH, tetJ, tetG, and tetY). The results showed that Aeromonas veronii (45%) showed the maximum resistance phenotype, followed by Streptococcus agalactiae (40%), Photobacterium damselae (15%), Vibrio parahaemolyticus (10%), and Vibrio vulnificus (5%). There was no resistance among Vibrio harveyi and Vibrio alginolyticus against the tested antimicrobials. The positive association between tetA, tetB, tetC, tetM, or a combination of these genes to oxytetracycline resistance and qnrS to quinolone resistance indicated their potential in surveillance studies. The prevalence of resistance phenotypes (16.43%) and evaluated AMR genes (2.65%) against aquaculture antimicrobials was low. The resistance phenotype pattern abundance was 0.143. All the isolates showed susceptibility to florfenicol. The results help with the appropriate drug selection against each species in aquaculture practices.

Description of Rhodobacter flavimaris sp. nov. and proposal of the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter as synonyms of Rhodobacter

Two Gram-stain-negative, aerobic, ovoid to short rod-shaped bacterial strains, designated as WL0062T and WL0115, were isolated from coastal zone of the Yellow Sea, Jiangsu Province, PR China, respectively. Strain WL0062T grew optimally at 28 °C, pH 7.0-8.0 and with 1.0-3.0% (w/v) NaCl. Strain WL0115 grew optimally at 28 °C, pH 6.0-7.0 and with 1.0-3.0% (w/v) NaCl. In the bac120 tree, strains WL0062T and WL0115 clustered together with Sedimentimonas flavescens B57T. The respiratory quinone of both strains was ubiquinone-10. The major polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, glycolipid, phosphatidylmonomethylethanolamine, and one unidentified polar lipid. The major fatty acids of strain WL0062T were summed features 8 (C18 : 1  ω6c and/or C18 : 1  ω7c). The major fatty acids of strain WL0115 were summed features 8 (C18 : 1  ω6c and/or C18 : 1  ω7c), C18 : 0, iso-C17 : 1  ω5c and C20 : 4  ω6/9/12/15c (arachidonic acid). The G+C content of genomic DNA of strains WL0062T and WL0115 was 64.0 mol% in both of them. Combined with the analysis of average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization, strain WL0062T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter flavimaris sp. nov is proposed. The type strain is WL0062T (=MCCC 1K06014T=JCM 34676T=GDMCC 1.2427T). Strain WL0115 (=MCCC 1K07531=JCM 35568=GDMCC 1.3088) should belong to the same species as Sedimentimonas flavescens B57T. In addition, on the basis of phylogenomic relationship and phenotypical characteristics, the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter are proposed as synonyms of Rhodobacter.

Alleviating Coral Thermal Stress via Inoculation with Quorum Quenching Bacteria

In the background of global warming, coral bleaching induced by elevated seawater temperature is the primary cause of coral reef degradation. Coral microbiome engineering using the beneficial microorganisms for corals (BMCs) has become a hot spot in the field of coral reef conservation and restoration. Investigating the potential of alleviating thermal stress by quorum quenching (QQ) bacteria may provide more tools for coral microbial engineering remediation. In this study, QQ bacteria strain Pseudoalteromonas piscicida SCSIO 43740 was screened among 75 coral-derived bacterial strains, and its quorum sensing inhibitor (QSI) compound was isolated and identified as 2,4-di-tert-butylphenol (2,4-DTBP). Then, the thermal stress alleviating potential of QQ bacteria on coral Pocillopora damicornis was tested by a 30-day controlled experiment with three different treatments: control group (Con: 29 °C), high temperature group (HT: 31 °C), and the group of high temperature with QQ bacteria inoculation (HTQQ: 31 °C + QQ bacteria). The results showed that QQ bacteria SCSIO 43740 inoculation can significantly mitigate the loss of symbiotic algae and impairment of photosynthesis efficiency of coral P. damicornis under thermal stress. Significant difference in superoxide dismutase (SOD) and catalase (CAT) enzyme activities between HT and HTQQ was not observed. In addition, QQ bacteria inoculation suppressed the coral microbial community beta-dispersion and improved the stability of microbial co-occurrence network under thermal stress. It was suggested that QQ bacteria inoculation can alleviate coral thermal stress via reshaping microbial interaction and maintain community stability of coral microbiome. This study provided new evidence for the probiotic function of QQ bacteria in corals, which shedding light on the development of new microbiological tools for coral reef conservation.

Paracoccus actinidiae sp.nov., a novel bacterium isolated from kiwi tree rhizosphere soil

Strain M09T was isolated from the rhizoshere of kiwi fruit trees from an orchard located in Fangshan, Beijing, PR China (39° 49' 25.1″ N, 116° 4' 44.5″ E,). It is a short rod-shaped, Gram-stain-negative, facultatively anaerobic bacterium that tests positive for both oxidase and catalase. The strain exhibited growth within the temperature range of 15-45 °C (optimal growth at 30 °C) and the pH range of 4.0-10.0 (optimal growth at pH 7.0) and without NaCl. It also grew in a sodium chloride-free nutrient agar (NA) medium. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that M09T represents a member of the genus Paracoccus and shares high similarity with Paracoccus everestensis S8-55T (98.46%) and Paracoccus aerius 011410T (97.58%). The average nucleotide identity values between M09T and P. everestensis S8-55T, P. aerius 011410T, Paracoccus marinaquae X HP0099T and Paracoccus fontiphilus MVW-1T were 95.56, 84.51, 79.83 and 83.68%, respectively. The digital DNA-DNA hybridisation values between between M09T and P. everestensis S8-55T, P. aerius 011410T, P. marinaquae X HP0099T and P. fontiphilus MVW-1T were 56.40, 29.30, 21.60 and 28.60%, respectively. The major fatty acids identified were C10 : 0 3-OH (51.8%) and C18 : 1ω7c (35.5%). The major respiratory quinone was Q-10, with Q-8 present as a minor component. Polar lipids were mainly comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Genome sequencing revealed that the strain has a DNA G+C content of 64.31 mol%. On the basis of this comprehensive taxonomic characterisation data, M09T represents a novel species within the genus Paracoccus and has been named Paracoccus actinidiae sp. nov. The type strain is designated as M09T (=GDMCC 1.4157T=KCTC 8143T).

PGPR isolated from hot spring imparts resilience to drought stress in wheat (Triticum aestivum L.)

Drought is a major abiotic stress that occurs frequently due to climate change, severely hampers agricultural production, and threatens food security. In this study, the effect of drought-tolerant PGPRs, i.e., PGPR-FS2 and PGPR-VHH4, was assessed on wheat by withholding water. The results indicate that drought-stressed wheat seedlings treated with PGPRs-FS2 and PGPR-VHH4 had a significantly higher shoot and root length, number of roots, higher chlorophyll, and antioxidant enzymatic activities of guaiacol peroxidase (GPX) compared to without PGPR treatment. The expression study of wheat genes related to tryptophan auxin-responsive (TaTAR), drought-responsive (TaWRKY10, TaWRKY51, TaDREB3, and TaDREB4) and auxin-regulated gene organ size (TaARGOS-A, TaARGOS-B, and TaARGOS-D) exhibited significantly higher expression in the PGPR-FS2 and PGPR-VHH4 treated wheat under drought as compared to without PGPR treatment. The results of this study illustrate that PGPR-FS2 and PGPR-VHH4 mitigate the drought stress in wheat and pave the way for imparting drought in wheat under water deficit conditions. Among the two PGPRs, PGPR-VHH4 more efficiently altered the root architecture to withstand drought stress.

Actinoplanes kirromycinicus sp. nov., isolated from soil

A novel actinomycete, designated as TPMA0078T, was isolated from a soil sample collected in Shinjuku, Tokyo, Japan. 16S rRNA gene sequence analysis indicated that strain TPMA0078T belongs to the genus Actinoplanes and is closely related to Actinoplanes regularis IFO 12514T (99.86% 16S rRNA gene sequence similarity). The spores of strain TPMA0078T were motile, and the sporangia were cylindrical. The diamino acids in the cell wall peptidoglycan of strain TPMA0078T were meso-diaminopimelic acid and 3OH-meso-diaminopimelic acid. Whole-cell sugars were glucose and mannose, with galactose as a minor component. The major cellular fatty acids identified were iso-C15:0, iso-C16:0, and anteiso-C17:0. The predominant menaquinone was MK-9(H4), and the principal polar lipid was phosphatidylethanolamine. These chemotaxonomic properties of strain TPMA0078T were consistent with those of Actinoplanes. Meanwhile, digital DNA-DNA hybridization and average nucleotide identity values showed low relatedness between strain TPMA0078T and A. regularis NBRC 12514T. Furthermore, several phenotypic properties of strain TPMA0078T distinguished it from those of closely related species. Based on its genotypic and phenotypic characteristics, strain TPMA0078T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes kirromycinicus sp. nov. is proposed. The type strain is TPMA0078T (=NBRC 116422T = TBRC 18262T).

Development of a One-Step Multiplex qPCR Assay for Detection of Methicillin and Vancomycin Drug Resistance Genes in Antibiotic-Resistant Bacteria

The most common antibiotic-resistant bacteria in Korea are methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Pathogen identification in clinical laboratories can be divided into traditional phenotype- and genotype-based methods, both of which are complementary to each other. The genotype-based method using multiplex real-time polymerase chain reaction (PCR) is a rapid and accurate technique that analyzes material at the genetic level by targeting genes simultaneously. Accordingly, we aimed to develop a rapid method for studying the genetic characteristics of antibiotic-resistant bacteria and to provide an experimental guide for the efficient antibiotic resistance gene analysis of mecA detection for MRSA and vanA or vanB detection for VRE using a one-step multiplex qPCR assay at an early stage of infection. As a result, the sensitivity and specificity of the mecA gene for clinical S. aureus isolates, including MRSA and methicillin-susceptible S. aureus, were 97.44% (95% CI, 86.82-99.87%) and 96.15% (95% CI, 87.02-99.32%), respectively. The receiver operating characteristic area under the curve for the diagnosis of MRSA was 0.9798 (*** p < 0.0001). Therefore, the molecular diagnostic method using this newly developed one-step multiplex qPCR assay can provide accurate and rapid results for the treatment of patients with MRSA and VRE infections.

The biogeographic patterns of the olive fly and its primary symbiont Candidatus Erwinia dacicola across the distribution area of the olive tree

The olive fly, Bactrocera oleae (Rossi, 1790), is the major insect pest of olives attacking both cultivated and wild olive. Bactrocera oleae carries a primary and vertically transmitted symbiont, the bacterium Candidatus Erwinia dacicola. As any primary symbiont, it plays an important role in the reproduction and lifespan of the fly. The genetic 16S rRNA diversity of the primary symbiont and the mitochondrial haplotype variation of the insect host were simultaneously examined in 54 olive fly populations. The aim was to unravel the biogeographic patterns of this economically relevant host-bacteria interaction across a wide distribution area. Three symbiont haplotypes were identified. The primary symbiont showed a lower haplotype diversity than that of its host, a characteristic indicative of a long-term interaction. A significant genetic and geographic association between host and primary symbiont was observed, with an East-West genetic differentiation pattern in the Mediterranean basin, coinciding with the historical genetic distribution of the olive tree. The study shows promise, informing and aiding the development of future tools for the control of the olive fly.

Genetic diversity, stress tolerance and phytobeneficial potential in rhizobacteria of Vachellia tortilis subsp. raddiana

BACKGROUND

Soil bacteria often form close associations with their host plants, particularly within the root compartment, playing a significant role in plant growth and stress resilience. Vachellia tortilis subsp. raddiana, (V. tortilis subsp. raddiana)a leguminous tree, naturally thrives in the harsh, arid climate of the Guelmim region in southern Morocco. This study aims to explore the diversity and potential plant growth-promoting (PGP) activities of bacteria associated with this tree.

RESULTS

A total of 152 bacterial isolates were obtained from the rhizosphere of V. tortilis subsp. raddiana. Rep-PCR fingerprinting revealed 25 distinct genomic groups, leading to the selection of 84 representative strains for further molecular identification via 16 S rRNA gene sequencing. Seventeen genera were identified, with Bacillus and Pseudomonas being predominant. Bacillus strains demonstrated significant tolerance to water stress (up to 30% PEG), while Pseudomonas strains showed high salinity tolerance (up to 14% NaCl). In vitro studies indicated variability in PGP activities among the strains, including mineral solubilization, biological nitrogen fixation, ACC deaminase activity, and production of auxin, siderophores, ammonia, lytic enzymes, and HCN. Three elite strains were selected for greenhouse inoculation trials with V. tortilis subsp. raddiana. Strain LMR725 notably enhanced various plant growth parameters compared to uninoculated control plants.

CONCLUSIONS

The findings underscore the potential of Bacillus and Pseudomonas strains as biofertilizers, with strain LMR725 showing particular promise in enhancing the growth of V. tortilis subsp. raddiana. This strain emerges as a strong candidate for biofertilizer formulation aimed at improving plant growth and resilience in arid environments.

Prospection of strains of Bacillus sporogenes in the digestive tract of native crustaceans and characterization of the probiotic potential

The cultivation of marine shrimp is one of the fastest growing activities in the world. However, the emergence of diseases has resulted in a decrease in production and losses for the sector. Probiotics emerged as an option to the use of antibiotics to control these pathogens. The efficiency of applying this technology depends on the characteristics of the bacterial agents and their bioavailability in the shrimp intestine. The objective is to evaluate the viability and efficiency of bacteria isolated from the digestive tract of healthy crustaceans as probiotic agents in the cultivation of shrimp Litopenaeus vannamei. Eighteen strains of the genus Bacillus belonging to the following species were tested: Bacillus sp., B. cereus, B. thuringiensis, B. circulans, B. megaterium, B. subtilis and B. agaridevorans. Bacterial isolates were subjected to characterization as potential probiotics. The test results were considered satisfactory; thus, the tested strains have potential for use as probiotics in shrimp culture. Treatments that used of the genus Bacillus had reduced growth of the genus Vibrio after infection, both in the intestinal contents and in the intestine. With the results obtained, it can be suggested that further research be carried out on the probiotic potential of Bacillus sp.

Isolation of Pathogenic Cronobacter Species as Bacteriological Risks Indicator in Powdered Infant Formula Available to Deprived Infants in Lagos Metropolis, Nigeria

Powdered infant formula (PIF) is rich in nutrients that support the survival and growth of bacteria that trigger food safety disorders in deprived infants through life-threatening illnesses. The study aims to examine and identify the incidence of pathogenic bacteria of concern in PIF upon reconstitution in lukewarm water. A total of 172 samples consisting of 38 brands of PIF available in the Lagos metropolis were sampled, suspended in water (10 g in 100 mL), and bacteria strains were isolated using combinational enrichment and selective culture techniques. Pure bacterial strains were characterized and identified based on their physiology and 16S rRNA gene sequence homology. While 85 bacterial strains were isolated from the enriched culture system, 20 strains were selectively isolated based on tolerance to sodium deoxycholate. Approximately 13% of the selected bacteria were identified as Cronobacter spp., exhibiting virulence traits including extracellular protease production, coagulation and proteolysis of casein, haem-agglutination, and β-haemolysis of human blood. Approximately 82% of the Cronobacter strains tolerated NaCl (10%) and bile salt; and exhibited resistance to cefotaxime, ceftriaxone, gentamicin, and Amoxicillin-clavulanic acid antibiotics. The presence of Cronobacter spp. in 13% of the PIF brands available to infants calls for concern about the safety of deprived infants that might be fed with such PIF. Consequently, PIF safety alerts need to be activate while further studies on critical points at which the pathogens get introduced to the PIFs need to be identified.

In Vitro Utilization of Prebiotics by Listeria monocytogenes

Listeria monocytognes is an emerging pathogen responsible for the serious foodborne disease, listeriosis. The commensal gut microbiota is the first line of defense against pathogen internalization. The gut microbiome can be modified by prebiotic substrates, which are frequently added to food products and dietary supplements. Prebiotics should selectively support the growth of beneficial microbes and thus improve host health. Nevertheless, little is known about their effect on the growth of L. monocytogenes. The aim of this study was to evaluate the growth ability of four L. monocytogenes strains, representing the most common serotypes, on prebiotic oligosaccharides (beta-(1,3)-D-glucan, inulin, fructooligosaccharides, galactooligosaccharides, lactulose, raffinose, stachyose and 2'-fucosyllactose and a mixture of human milk oligosaccharides) as a sole carbon source. The results showed that only beta-(1,3)-D-glucan was metabolized by L. monocytogenes. These cell culture data suggest that beta-(1,3)-D-glucan may not be selectively utilized by healthy commensal bacteria, and its role in intestinal pathogen growth warrants further exploration in vivo.

Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System

A high cell-surface hydrophobic bacterium, strain A18T, was isolated from a waste digestion system in Chaozhou, China. Cells of strain A18T were Gram-stain-positive, aerobic, non-spore-forming, non-motile, and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene showed that strain A18T shared less than 94.2% sequence similarity to all validated species in the family Chitinophagaceae, and formed a distinct lineage close to genera Niabella and Terrimonas in the neighbor-joining tree, indicating that strain A18T is a novel species. Genome-based phylogenetic analyses revealed that strain A18T is affiliated to the genus Niabella. The cellular components, including iso-C15:0 and iso-C15:1 G as the major fatty acids, menaquinone-7 as the respiratory quinone and a DNA G + C content of 40.54% supported strain A18T as a member of the genus Niabella. However, the physiological and biochemical properties, such as enzyme activities, carbon source utilization and C18:0 3-OH as another major fatty acids, distinguished strain A18T from its close related species. Therefore, the name Niabella digestorum sp. nov. is proposed for this novel species. The type strain is A18T (= GDMCC 1.3242 T = KCTC 92386 T).