Isolation and identification of NEAU-CP5: A seed-endophytic strain of B. velezensis that controls tomato bacterial wilt.

Bacterial wilt of tomato caused by Ralstonia solanacearum is a critical soilborne disease that drastically reduces yield. In the current study, an endophytic strain NEAU-CP5 with strong antagonistic activity against R. solanacearum was isolated from tomato seeds and characterized. The strain was identified as Bacillus velezensis based on 16S rRNA gene and whole genome sequence analysis. NEAU-CP5 can secrete amylase, protease, and cellulase, and also produce known antibacterial metabolites, including cyclo (leucylprolyl), cyclo (phenylalanyl-prolyl), cyclo (Pro-Gly), 3-benzyl-2,5-piperazinedione, pentadecanoic acid, eicosane, 2-methyoic acid, isovaleric acid, dibuty phthalate, and esters of fatty acids (HFDU), which may be responsible for its strong antibacterial activity. Fourteen gene clusters associated with antibacterial properties were also identified in the whole genome sequence of NEAU-CP5. Pot experiment demonstrated that the application of 108 CFU/mL NEAU-CP5 on tomato plants significantly reduced the incidence of tomato bacterial wilt by 68.36 ± 1.67 %. NEAU-CP5 also increased the activity of defense-related enzymes (CAT, POD, PPO, SOD, and PAL) in tomato plants. This is the first report of an effective control of bacterial wilt on tomato plants by B. velezensis and highlights the potential of NEAU-CP5 as a potential biocontrol agent for the management of tomato bacterial wilt.

Phenotypic characterization for bioremediation suitability of isolates from Southern Tunisian tannery effluent.

Effluents from the leather tanning industry contain diverse pollutants, including hazardous heavy metals, posing threats to public health and the surrounding environment. Indigenous bacterial isolates can represent an eco-friendly approach for tannery wastewater treatment; however, phenotypic characterization is necessary to determine whether these strains are suitable for bioremediation. In the present study, we analyzed seven new Enterococcus faecium strains and two new Bacillus subtillis strains isolated from effluents from the Southern Tunisian Tannery (ESTT). We evaluated phenotypic features beneficial for bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities. Additionally, we examined characteristics naturally occurring in environmental bacteria but less desirable in strains selected for bioremediation, such as antibiotic resistances and pathogenicity indicators. The observed phenotypes were then compared with whole-genome analysis. We observed biofilm production in two slime-producing bacteria, B. licheniformis RLT6, and E. faecium RLT8. Hydrophobicity of E. faecium strains RLT1, RLT5, RLT8, and RLT9, as well as B. licheniformis RLT6 correlated positively with increasing ESTT concentration. Exoenzyme activities were detected in E. faecium strains RLT2, RLT4, and RLT7, as well as B. licheniformis RLT6. As anticipated, all strains exhibited common resistances to antibiotics and hemolysis, which are widespread in nature and do not hinder their application for bioremediation. Importantly, none of the strains exhibited the pathogenic hypermucoviscosity phenotype. To the best of our knowledge, this is the first report consolidating all these phenotypic characteristics concurrently, providing a complete overview of strains suitability for bioremediation. IMPORTANCE: The study evaluates the bioremediation potential of seven Enterococcus faecium strains and two Bacillus subtillis strains isolated from the effluents from the Southern Tunisian tannery (ESTT), which pose threats to public health and environmental integrity. The analysis primarily examines the phenotypic traits crucial to bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities, as well as characteristics naturally occurring in environmental bacteria related to heavy metal resistance, such as antibiotic resistances. Several strains were found to have high bioremediation potential and exhibit only antibiotic resistances commonly found in nature, ensuring their application for bioremediation remains uncompromised. The results of the exhaustive phenotypic analysis are contrasted with the whole genome sequences of the nine strains, underscoring the appropriateness of these bacterial strains for eco-friendly interventions in tannery wastewater treatment.

The potential of Bacillus species isolated from Cinnamomum camphora for biofuel production.

BACKGROUND: Increasing concerns about climate change and global petroleum supply draw attention to the urgent need for the development of alternative methods to produce fuels. Consequently, the scientific community must devise novel ways to obtain fuels that are both sustainable and eco-friendly. Bacterial alkanes have numerous potential applications in the industry sector. One significant application is biofuel production, where bacterial alkanes can serve as a sustainable eco-friendly alternative to fossil fuels. This study represents the first report on the production of alkanes by endophytic bacteria. RESULTS: In this study, three Bacillus species, namely Bacillus atrophaeus Camph.1 (OR343176.1), Bacillus spizizenii Camph.2 (OR343177.1), and Bacillus aerophilus Camph.3 (OR343178.1), were isolated from the leaves of C. camphora. The isolates were then screened to determine their ability to produce alkanes in different culture media including nutrient broth (NB), Luria-Bertani (LB) broth, and tryptic soy broth (TSB). Depending on the bacterial isolate and the culture media used, different profiles of alkanes ranging from C8 to C31 were detected. CONCLUSIONS: The endophytic B. atrophaeus Camph.1 (OR343176.1), B. spizizenii Camph.2 (OR343177.1), and B. aerophilus Camph.3 (OR343178.1), associated with C. camphora leaves, represent new eco-friendly approaches for biofuel production, aiming towards a sustainable future. Further research is needed to optimize the fermentation process and scale up alkane production by these bacterial isolates.

A rare waterborne outbreak of Bacillus paranthracis in Shandong province, China, 2020: epidemiologic survey, genomic insights, and virulence characteristics.

Bacillus paranthracis, a Gram-positive conditional pathogen of Bacillus cereus group species, is capable of causing foodborne and waterborne illnesses, leading to intestinal diseases in humans characterized by diarrhoea and vomiting. However, documented cases of B. paranthracis infection outbreaks are rare in the world, and the genomic background of outbreak strains is seldom characterized. This study retrospectively analyzed strains obtained from an outbreak in schools, as well as from water systems in peri-urban areas, China, in 2020. In total, 28 B. cereus group isolates were retrieved, comprising 6 from stool samples and 22 from water samples. Epidemiological and phylogenetic investigations indicated that the B. paranthracis isolate from drinking water as the causative agent of the outbreak. The genomic comparison revealed a high degree of consistency among 8 outbreak-related strains in terms of antimicrobial resistance gene profiles, virulence gene profiles, genomic content, and multilocus sequence typing (MLST). The strains related to the outbreak show highly similar genomic ring diagrams and close phylogenetic relationships. Additionally, this study shed light on the pathogenic potential and complexity of B. cereus group through its diversity in virulence genes and mice infection model. The findings highlight the usefulness of B. paranthracis genomes in understanding genetic diversity within specific environments and in tracing the source of pathogens during outbreak situations, thereby enabling targeted infection control interventions.

Unveiling the Biocontrol Potential of Rhizoplane Bacillus Species against Sugarcane Fusarium Wilt through Biochemical and Molecular Analysis.

BACKGROUND: Biocontrol is regarded as a viable alternate technique for managing sugarcane wilt disease caused by Fusarium sacchari. Many fungal antagonists against F. sacchari, have been reported, but the potential of bacterial antagonists was explored to a limited extent, so the present study evaluated the antagonistic potential of rhizoplane Bacillus species and their mode of action. RESULTS: A total of twenty Bacillus isolates from the rhizoplane of commercially grown sugarcane varieties were isolated. The potential isolate SRB2 had shown inhibition of 52.30, 33.33, & 44.44% and SRB20 of 35.00, 33.15, & 36.85% in direct, indirect, and remote confrontation respectively against F. sacchari. The effective strains were identified as Bacillus inaquosorum strain SRB2 and B. vallismortis strain SRB20, by PCR amplification of 16S-23S intergenic region. The biochemical studies on various direct and indirect biocontrol mechanisms revealed the production of IAA, Protease, Cellulase, Siderophores, and P solubilization. The molecular analysis revealed the presence of antimicrobial peptides biosynthetic genes like fenD (Fengycin), bmyB (Bacyllomicin) ituC (Iturin) and spaS (Subtilin) which provided a competitive edge to these isolates compared to other Bacillus strains. Under greenhouse experiments, the sett bacterization with SRB2, significantly (P < 0.001) reduced the seedling mortality by > 70% followed by SRB20 in F. sacchari inoculated pots. CONCLUSION: The study revealed that the isolates B. inaquosorum SRB2 and B. vallismortis SRB20 can be used as potential bioagents against sugarcane Fusarium wilt.

Genome-wide transformation reveals extensive exchange across closely related Bacillus species.

Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.

Bacillus coagulans (Weizmannia coagulans) XY2 attenuates Cu-induced oxidative stress via DAF-16/FoxO and SKN-1/Nrf2 pathways and gut microbiota regulation.

Copper (Cu) pollution has become a serious environmental problem especially in recent decades. In this study, the mechanisms of Bacillus coagulans (Weizmannia coagulans) XY2 against Cu-induced oxidative stress were explored through a dual model. In mice, Cu disturbed microbial community structure, revealing an increased level of Enterorhabdus abundance and decreased levels of Intestinimonas, Faecalibaculu, Ruminococcaceae and Coriobacteriaceae_UCG-002 abundance. Meanwhile, B. coagulans (W. coagulans) XY2 intervention reversed this trend along with alleviated Cu-induced metabolic disturbances by increasing levels of hypotaurine and L-glutamate and declining levels of phosphatidylcholine and phosphatidylethanolamine. In Caenorhabditis elegans, nuclear translocation of DAF-16 and SKN-1 was inhibited by Cu, which in turn suppressed antioxidant-related enzymes activities. XY2 mitigated biotoxicity associated with oxidative damage caused by Cu exposure via regulating DAF-16/FoxO and SKN-1/Nrf2 pathways and intestinal flora to eliminate excess ROS. Our study provides a theoretical basis formulating future strategy of probiotics against heavy metal contamination.

Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects.

Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture. IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination.

In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction-modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

Bioscouring of wool fibres using immobilized thermophilic lipase.

The hydrophobic nature of wool induced by its surface lipid barrier hinders its wettability during processing. Scouring of wool is conducted to remove this lipid barrier and facilitate any wet processes. Scouring of wool is conducted using soda ash followed by rinsing with huge amount of water to ensure complete removal of alkali. This work aimed at utilization of thermophilic lipase enzyme for removal of wool surface lipid barrier without deterioration on the fibre interior. A thermally stable lipase enzyme was produced from thermophilic microorganism; namely Bacillus aryabhattai B8W22, and was utilized in bio-scouring of wool. The produced enzyme was immobilized on sericin-based discs to enhance its stability and to make it reusable. The activity of both free and immobilized lipase enzymes at different conditions was assessed. The effects of bio-scouring of wool on its dyeability with acid, basic, and reactive dyes, as well as on some of its inherent properties, were monitored. Results showed that the bio-scoured wool exhibits enhanced dyeability with the said classes of dyes more than that of conventionally scoured samples. One-bath scouring and dyeing of wool fibres in two successive steps was conducted to reduce consumption of water and energy during wet processing of wool.

A Novel Rhizospheric Bacterium: Bacillus velezensis NKMV-3 as a Biocontrol Agent Against Alternaria Leaf Blight in Tomato.

A novel strain of Bacillus isolated from rhizosphere has shown to be an excellent biocontrol agent against various plant pathogens. In this study, a first report of a Bacillus strain NKMV-3 which effectively controls Alternaria solani, which cause the early blight disease in tomato. Based on the cultural and molecular sequencing of 16S rRNA gene sequence, the identity of the strain was confirmed as Bacillus velezensis NKMV-3. The presence of the lipopeptide which are antibiotic synthesis genes, namely iturin C, surfactin A and fengycin B and D, was confirmed through gene amplification. In addition, lipopeptides were also confirmed through liquid chromatography. The extract showed inhibitory effect against A. solani in vitro and detached tomato leaf assays. Bacillus velezensis strain NKMV-3-based formulations may provide an effective solution in controlling early blight disease in tomato and other crops.

Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species.

The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the "culinary preferences" of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.

Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome.

Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites. This study recruited 74 IBS-D patients and 20 healthy controls (HC). 22.34%, 8.51%, 14.89%, and 54.26% of them contributed to one, two, three, and four sites: duodenal mucosa (DM), duodenal lumen (DL), rectal mucosa (RM), and rectal lumen (RL) of intestinal samples, respectively. Then 16S rRNA gene analysis was performed on these 283 samples. The result showed that IBS-D microbial communities have specific patterns at each intestinal site differing from that of HC. Across hosts and sites, Bacillus, Burkholderia, and Faecalibacterium were the representative genera in duodenum of IBS-D, duodenum of HC, and rectum of HC, respectively. Samples from mucosa and lumen in rectum were highly distinguishable, regardless of IBS-D and HC. Additionally, IBS-D patients have lower microbial co-abundance network connectivity. Moreover, RM site-specific biomarker: Bacteroides used alone or together with Prevotella and Oscillospira in RM showed outstanding performance in IBS-D diagnosis. Furthermore, Bacteroides and Prevotella in RM were strongly related to the severity of abdominal pain, abdominal discomfort, and bloating in IBS-D patients. In summary, this study also confirmed fecal microbial community could not fully characterize intestinal microbial communities. Among these site-specific microbial communities, RM microbial community would be more applicable in the diagnosis of IBS-D. IMPORTANCE Microbial community varied from one site to another along the gastrointestinal tract, but current studies about intestinal microbial community in IBS-D were mainly based on fecal samples. Based on 283 intestinal samples collected from DM, DL, RM, and RL of HC and IBS-D, we found different intestinal sites had their site-specific microbial patterns in IBS-D. Notably, RM site-specific microbes Bacteroides, Prevotella, and Oscillospira could be used to discriminate IBS-D from HC accurately. Our findings could help clinicians realize the great potential of the intestinal microbial community in RM for better diagnosis of IBS-D patients.

Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea.

BACKGROUND: Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. RESULTS: Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. CONCLUSIONS: Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates' genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-ß-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.

Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere.

Bacillus species genomes are rich in plant growth-promoting genetic elements. Bacillus subtilis and Bacillus velezensis are important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using ten Bacillus species. From the analysis, pan-genome of Bacillus subtilis and Bacillus velezensis are still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

Profiles of Bacillus spp. Isolated from the Rhizosphere of Suaeda glauca and Their Potential to Promote Plant Growth and Suppress Fungal Phytopathogens.

Members of the genus Bacillus are known to play an important role in promoting plant growth and protecting plants against phytopathogenic microorganisms. In this study, 21 isolates of Bacillus spp. were obtained from the root micro-ecosystem of Suaeda glauca. Analysis of the 16S rRNA genes indicated that the isolates belong to the species Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus subtilis, Bacillus pumilus, Bacillus aryabhattai and Brevibacterium frigoritolerans. One of the interesting findings of this study is that the four strains B1, B5, B16 and B21 are dominant in rhizosphere soil. Based on gyrA, gyrB, and rpoB gene analyses, B1, B5, and B21 were identified as B. amyloliquefaciens and B16 was identified as B. velezensis. Estimation of antifungal activity showed that the isolate B1 had a significant inhibitory effect on Fusarium verticillioides, B5 and B16 on Colletotrichum capsici (syd.) Butl, and B21 on Rhizoctonia cerealis van der Hoeven. The four strains grew well in medium with 1-10% NaCl, a pH value of 5-8, and promoted the growth of Arabidopsis thaliana. Our results indicate that these strains may be promising agents for the biocontrol and promotion of plant growth and further study of the relevant bacteria will provide a useful reference for the development of microbial resources.

Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution.

Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Bialowieza National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions. IMPORTANCE This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.

Bacillus velezensis strain MBY2, a potential agent for the management of crown gall disease.

The reduction of the use chemical pesticides in agriculture is gaining importance as an objective of decision-makers in both politics and economics. Consequently, the development of technically efficient and economically affordable alternatives as, e.g., biological control agents or practices is highly solicited. Crown gall disease of dicotyledonous plants is caused by ubiquitous soil borne pathogenic bacteria of the Agrobacterium tumefaciens species complex, that comprises the species Agrobacterium fabrum and represents a globally relevant plant protection problem. Within the framework of a screening program for bacterial Agrobacterium antagonists a total of 14 strains were isolated from Tunisian soil samples and assayed for antagonistic activity against pathogenic agrobacteria. One particularly promising isolate, termed strain MBY2, was studied more in depth. Using a Multilocus Sequence Analysis (MLSA) approach, the isolate was assigned to the taxonomic species Bacillus velezensis. Strain MBY2 was shown to display antagonistic effects against the pathogenic A. fabrum strain C58 in vitro and to significantly decrease pathogen populations under sterile and non-sterile soil conditions as well as in the rhizosphere of maize and, to a lower extent, tomato plants. Moreover, the ability of B. velezensis MBY2 to reduce C58-induced gall development has been demonstrated in vivo on stems of tomato and almond plants. The present study describes B. velezensis MBY2 as a newly discovered strain holding potential as a biological agent for crown gall disease management.

Tyrosinase and laccase-producing Bacillus aryabhattai TFG5 and its role in the polymerization of phenols.

BACKGROUND: Tyrosinases and laccases are oxidoreductase enzymes that are used widely in the food, feed, textile, and biofuel industries. The rapidly growing industrial demand for bacterial oxido-reductases has encouraged research on this enzyme worldwide. These enzymes also play a key role in the formation of humic substances (HS) that are involved in controlling the biogeochemical carbon cycle, providing nutrients and bio-stimulants for plant growth, and interacting with inorganic and organic pollutants besides increasing carbon sequestration and mitigating greenhouse gas emission in the environment. The present study aimed to screen and characterize extracellular tyrosinase and laccase-producing soil bacteria that could be utilized in the polymerization of phenols. RESULTS: Twenty isolates from different soil samples collected from forest ecosystems were characterized through ARDRA using restriction digestion with AluI, HpaII, and HaeIII restriction enzymes. The results of Hierarchical Cluster Analysis (HCA) revealed a 60 % similarity coefficient among 13 out of 20 isolates, of which, the isolate TFG5 exhibited only 10 % similarity when compared to all the other isolates. The isolate TFG5 exhibited both tyrosinase (1.34 U.mL- 1) and laccase (2.01 U.mL- 1) activity and was identified as Bacillus aryabhattai. The increased polymerization activity was observed when B. aryabhattai TFG5 was treated with phenols. The monomers such as catechol, p-Hydroxy benzoic acid, ferulic acid, and salicylic acid were polymerized efficiently, as evidenced by their FT-IR spectra depicting increased functional groups compared to the standard mushroom tyrosinase. CONCLUSIONS: The polymerization ability of B. aryabhattai TFG5 could be applied to phenol-rich wastewater treatment for efficient precipitation of phenols. Furthermore, tyrosinases can be used for enhancing the synthesis of HS in soil.

Bacillus fonticola sp. nov., isolated from deep sea cold seep sediment.

In this study, we report a novel Gram-positive bacterium, designated as strain CS13T, isolated from deep-sea sediment collected in the cold seep area of the South China Sea. Growth of strain CS13T occurred at 16-37 °C (optimum 25-28 °C), pH 7.0-9.0 (optimum, 7.0), and 0-8% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CS13T belonged to the genus Bacillus. The closest phylogenetic neighbors of strain CS13T are Bacillus carboniphilus JCM 9731T (96.0%), Bacillus pakistanensis NCCP-168T (95.7%) and Bacillus acidicola 105-2T (95.6%). The genomic DNA G + C content of strain CS13T is 43.7 mol%. The principal respiratory quinone was menaquinone 7 (MK-7). The polar lipids of CS13T contained diphosphatidylglycerol, phosphatidylglycerol, phospholipid, and glycolipid. The major fatty acids of CS13T contained anteiso-C15:0, anteiso-C17:0, C16:0 and C18:0. Strain CS13T harboured meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic, physiological, biochemical, and morphological analyses suggested that strain CS13T represents a novel species of genus Bacillus, and the name Bacillus fonticola sp. nov. is proposed for the type species CS13T (= CCTCC AB 2019194T = JCM 33663T).