Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces

ACUTE POST-TRAUMATIC ENDOPHTHALMITIS SECONDARY TO BACILLUS PUMILUS / SAFENSIS

PURPOSE

To report a case of post-traumatic endophthalmitis secondary to Bacillus pumilus/safensis .

METHODS

Observational case report of a single patient.

RESULTS

A 62-year-old man presented with a traumatic corneal laceration because of baling wire while working on a sheep farm. Appropriate corneal laceration repair with injection of intravitreal antibiotics (ceftazidime, clindamycin, and vancomycin) was performed. A single organism, identified as B. pumilus or Bacillus safensis, was isolated from the vitreous aspirate. A subsequent pars plana vitrectomy, pars plana lensectomy, anterior capsulotomy, and fluid-air exchange was required because of severe inflammatory reaction from retained lens material, retinal edema, and vitreous opacities. Vision improved from hand motion to 20/60 at the three-month follow-up visit.

CONCLUSION

We describe a case of acute post-traumatic endophthalmitis secondary to B. pumilus/safensis.

Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species

Microorganisms are important sources of bioactive natural products. However, the complexity of microbial metabolites and the low abundance of active compounds render the isolation and purification process laborious and inefficient. During our search for active substances capable of inhibiting the newly discovered highly lethal Vibrio strain vp-HL, we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics, molecular networking (MN), and the Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) were employed in conjunction with bioactivity screening to predict the antibacterial compounds from Bacillus strains. The analysis of fractions, and their isolation, NMR-based annotation, and bioactivity evaluation of an amicoumacin compound partially confirmed the prediction from these statistical analyses. This work presents the potential of marine Bacillus in producing active substances against Vibrio species. Additionally, it highlighted the significance and feasibility of metabolomics and MN in the dereplication of compounds and the determination of isolation targets.

Isolation and characterization of novel Bacillus strains with superior probiotic potential: comparative analysis and safety evaluation

Despite the current use of some Bacillus spp. as probiotics, looking for and introducing new efficient and safe potential probiotic strains is one of the most important topics in both microbiology and food industry. This study aimed to isolate, identify, and evaluate the probiotic characteristics and safety of some Bacillus spp. from natural sources. Thirty-six spore-forming, Gram-positive, and catalase-positive Bacillus isolates were identified in 54 samples of soil, feces and dairy products. Bacterial identification was performed using 16S rDNA sequencing. To evaluate the probiotic potential of isolates, the resistance of bacterial cells to simulated gastrointestinal tract (GIT) conditions, the presence of enterotoxin genes, their susceptibility to antibiotics, antimicrobial and hemolytic activities and biochemical profiles were investigated. The results revealed that eight sporulating Bacillus spp. isolates fulfilled all tested probiotic criteria. They showed a high growth rate, non-hemolytic and lecithinase activity, and resistance to simulated GIT conditions. These strains exhibited broad-spectrum antibacterial activity against pathogenic bacteria. In addition, they did not exhibit antibacterial resistance to the 12 tested antibiotics. The results of this study suggest that these isolates can be considered as candidates for functional foods and as safe additives to improve diet quality.

Phytohormone Production by the Endophyte Bacillus safensis TS3 Increases Plant Yield and Alleviates Salt Stress

Endophytic bacteria can be used to overcome the effect of salinity stress and promote plant growth and nutrient uptake. Bacillus safensis colonizes a wide range of habitats due to survival in extreme environments and unique physiological characteristics, such as a high tolerance for salt, heavy metals, and ultraviolet and gamma radiations. The aim of our study was to examine the salt resistance of the endophytic strain TS3 B. safensis and its ability to produce phytohormones and verify its effect on plant yield in field trials and the alleviation of salt stress in pot experiments. We demonstrate that the strain TS3 is capable of producing enzymes and phytohormones such as IAA, ABA and tZ. In pot experiments with radish and oat plants in salinization, the strain TS3 contributed to the partial removal of the negative effect of salinization. The compensatory effect of the strain TS3 on radish plants during salinization was 46.7%, and for oats, it was 108%. We suppose that such a pronounced effect on the plants grown and the salt stress is connected with its ability to produce phytohormones. Genome analysis of the strain TS3 showed the presence of the necessary genes for the synthesis of compounds responsible for the alleviation of the salt stress. Strain B. safensis TS3 can be considered a promising candidate for developing biofertilizer to alleviate salt stress and increase plant yield.

Antimicrobial and quorum sensing inhibitory activity of epiphytic bacteria isolated from the red alga Halymenia durvillei

Halymenia durvillei is a red alga that is commonly utilized in the Philippines as food and as a source of high-value natural products for industrial applications. However, there are no studies regarding the microbial community associated with H. durvillei and its potential applications. This study aimed to isolate and identify the epiphytic bacteria of H. durvillei and determine their antimicrobial and quorum sensing inhibitory (QSI) effects. The thalli of H. durvillei were collected at the shores of Santa Fe, Bantayan, Cebu, Philippines. Bacterial isolates were identified using 16S rRNA, and their ethyl acetate (EtOAc) extracts were subjected to antimicrobial susceptibility tests against representative species of yeast and Gram-negative and Gram-positive bacteria. Their QSI activity against Chromobacterium violaceum was also determined. Fourteen distinct bacterial colonies belonging to four genera, namely Alteromonas (3), Bacillus (5), Oceanobacillus (1) and Vibrio (5), were successfully isolated and identified. All 14 bacterial isolates exhibited antibacterial effects. EPB9, identified as Bacillus safensis , consistently showed the strongest inhibition against Escherichia coli , Staphylococcus aureus and Staphylococcus epidermidis , with minimum inhibitory concentrations (MICs) ranging from 0.0625 to 1.0 mg ml-1. In contrast, all 14 isolates showed weak antifungal effects. Both B. safensis (EPB9) and Bacillus australimaris (EPB15) exhibited QSI effects at 100 mg ml-1, showing opaque zones of 3.1±0.9 and 3.8±0.4 mm, respectively. This study is the first to isolate and identify the distinct microbial epiphytic bacterial community of H. durvillei and its potential as an abundant resource for new antibacterial and QSI bioactives.

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder

Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.

Identification and Archive of Mars 2020 Spacecraft Microbial Isolates

To support NASA's Mars 2020 mission, bioassays were performed to ensure the biological cleanliness of the spacecraft, instruments, and hardware assembly areas. Bioassays began in May 2014, as the first components were assembled, and continued until their launch in July 2020. Over this 6-year period, 1811 bioassay sampling sessions were conducted. To understand the nature of microbiological presence on and around the spacecraft, an archive of organisms resulting from the bioassays was assembled. This archive included 4232 microbial specimens preserved as frozen stocks. To date, more than 3489 microbial isolates have been tested by MALDI-TOF mass spectrometry analysis. Identifications were based on high confidence level matches to known microorganisms in the reference spectra database where 39 distinct genera were identified. Gram-positive bacteria were isolated almost exclusively. Most, but not all, were spore-forming genera. The most prevalent genera isolated in order of frequency were Bacillus, Priestia, Paenibacillus, Staphylococcus, Micrococcus, and Streptomyces. Within the largely represented Bacillus-like genera, the five most prevalent species were cereus, licheniformis, horneckiae, subtilis, and safensis.

Microbial and Qualitative Traits of Quinoa and Amaranth Seeds from Experimental Fields in Southern Italy

Quinoa and amaranth are of special interest since they are increasingly used for the development of new bakery products with enhanced nutritional value. The aim of the study was to evaluate the agronomic, microbiological, and nutritional characteristics of quinoa and amaranth seeds grown in Southern Italy. For this reason, quinoa Titicaca and three amaranth accessions (5, 12, and 14) were cultivated in different experimental fields in the Campania Region and analyzed for the cultivation aspects, chemical composition, and microbiological quality of the seeds. All seeds showed a good adaptability to cultivation in the experimental areas of the Mediterranean basin. Quinoa seeds were characterized by their higher protein, fat, and ash content than the amaranth seeds, which were characterized by their higher value in dietary fiber. All seeds, regardless of the geographical area of production, were contaminated with yeasts, moulds, and spore-forming bacteria, mainly Bacillus cereus, B. licheniformis, B. safensis and B. subtilis, as identified by 16S rRNA sequencing analysis. So, the detection of Bacillus spp. must be strongly monitored, as quinoa and amaranth seeds could be used in bread production, where they can cause ropiness, resulting in great economic losses for the industries.

Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture

OBJECTIVES

This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VP_AHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico.

METHODS

Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VP_AHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion Torrent^TM (PGM) and Illumina Miseq^TM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH.

RESULTS

Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively.

CONCLUSIONS

The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.

Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits

Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.

Exploring the Transient Microbe Population on Citrus Butterfly Wings

Microbes carve out dwelling niches in unusual environments. Insects, in general, have been hosts to microbes in different ways. Some insects incorporate microbes as endosymbionts that help with metabolic functions, while some vector pathogenic microbes that cause serious plant and animal diseases, including humans. Microbes isolated from insect sources have been beneficial and a huge information repository. The fascinating and evolutionarily successful insect community has survived mass extinctions as a result of their unique biological traits. Wings have been one of the most important factors contributing to the evolutionary success of insects. In the current study, wings of Papilio polytes, a citrus butterfly, were investigated for the presence of ecologically significant microbes within hours of eclosing under aseptic conditions. Scanning electron microscopy (SEM) revealed the presence of bacteria dwelling in crevices created by a specific arrangement of scales on the butterfly wing. A total of 38 bacterial isolates were obtained from the patched wings of the citrus butterfly, and Bacillus spp. were predominant among them. We probed the occurrence of these microbes to assess their significance to the insect. Many of the isolates displayed antibacterial, antifungal, and biosurfactant properties. Interestingly, one of the isolates displayed entomopathogenic potential toward the notorious agricultural pest mealybug. All the wing isolates were seen to cluster together consistently in a phylogenetic analysis, except for one isolate of Bacillus zhangzhouensis (Papilio polytes isolate [Pp] no. 28), suggesting they are distinct strains. IMPORTANCE This is a first study reporting the presence of culturable microbes on an unusual ecological niche such as butterfly wings. Our findings also establish that microbes inhabit these niches before the butterfly has contact with the environment. The findings in this report have opened up a new area of research which will not only help understand the microbiome of insect wings but might prove beneficial in other specialized studies.

A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations

By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.

Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD

Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynD_PER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynD_PER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynD_PER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynD_PER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.

Qualification of Membrane Filtration for Planetary Protection Flight Implementation

Planetary protection is the practice of preventing forward and backward contamination of solar system bodies. Spacecraft and associated surfaces are sampled to ensure compliance with bioburden requirements. Current planetary protection sampling and processing methodologies consist of extracting microbial cells from wipe or swab samples through a procedure (NASA Standard Assay) that includes sonication, heat shock, and pour-plate steps. The pour-plate steps are laborious and prolonged. Moreover, results can be imprecise because only a fraction of the sample fluid is plated for CFU enumeration (80% for swabs and 25% for wipes). Thus, analysis requires that a pour fraction extrapolation factor be applied to CFU counts to account for bioburden in the remaining sample volume that is not plated. This extrapolation results in large variances for data, decreasing the accuracy of spore bioburden estimation of spacecraft hardware. In this study, we investigated the use of membrane filtration as an alternative method to pour-plate processing. Membrane filtration is an appealing methodology for planetary protection because it can process greater sample volumes and reduces the data variance for bioburden enumeration. A pour fraction extrapolation factor is still applied for both swabs and wipes (92%), however, it is a greater pour fraction than the pour-plate method. Here we present data collected by the Jet Propulsion Laboratory and the Applied Physics Laboratory to experimentally determine the equivalency of membrane filtration to pour-plate methodology for implementation during the NASA Standard Assay. Additionally, we outline the planned procedures for two membrane filtration systems: Pall® Laboratory Manifold system and Milliflex® Plus Vacuum Pump System. Both systems demonstrated equivalence of the membrane filtration method to the pour-plate method.

Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting

Composting, as an effectively bio-oxidative process, has been widely used for converting organic waste to organic fertilizer. However, the low fertilizer efficiency of composting product limited its application in agriculture. To improve the growth-promoting effect of composting product, the present study investigated the bioaugmentation strategy of inoculating indole-3-acetic-acid (IAA)-producing bacteria. Firstly, two IAA-producing bacteria (Bacillus safensis 33C and Rhodococcus rhodochrous YZ) were isolated from composting products with high IAA yields of 39.18 and 16.32 μg mL^-1, respectively. Secondly, the microbial inoculants were prepared with 33C, YZ and a previously isolated IAA-producing strain Corynebacterium stationis 29B. To increase the accumulation of microbial secondary metabolites, microbial inoculants were amended at the secondary fermentation stage of composting. Physicochemical characterization showed that the maturity of composting product was significantly promoted by inoculating microbial inoculants prepared with 33C and 29B (single and combined inoculants). Finally, bioaugmentation with 33C and 29B increased the IAA contents of composting products by 2.9-5.2 times, which benefited the germination and early vegetative growth of plants. In summary, inoculating proper IAA-producing bacteria during secondary fermentation of composting could improve the quality of composting product and expand its application.

Color Catalogue of Life in Ice: Surface Biosignatures on Icy Worlds

With thousands of discovered planets orbiting other stars and new missions that will explore our solar system, the search for life in the universe has entered a new era. However, a reference database to enable our search for life on the surface of icy exoplanets and exomoons by using records from Earth's icy biota is missing. Therefore, we developed a spectra catalogue of life in ice to facilitate the search for extraterrestrial signs of life. We measured the reflection spectra of 80 microorganisms-with a wide range of pigments-isolated from ice and water. We show that carotenoid signatures are wide-ranged and intriguing signs of life. Our measurements allow for the identification of such surface life on icy extraterrestrial environments in preparation for observations with the upcoming ground- and space-based telescopes. Dried samples reveal even higher reflectance, which suggests that signatures of surface biota could be more intense on exoplanets and moons that are drier than Earth or on environments like Titan where potential life-forms may use a different solvent. Our spectra library covers the visible to near-infrared and is available online. It provides a guide for the search for surface life on icy worlds based on biota from Earth's icy environments.

Influence of Bacillus safensis and Bacillus pumilus on the electrochemical behavior of 2024-T3 aluminum alloy

In this work, electrochemical techniques were employed to evaluate the contribution to the corrosion and corrosion inhibition of 2024-T3 aluminum alloy by two Gram-positive bacteria. In addition, polarized impedance was used to determine the microbial effect on the cathodic and anodic reactions. These microorganisms were collected from a tropical environment due to the favorable bacterial growth of this kind of climate. The alloy was exposed to the sterile medium and inoculated for up to 12 days evaluating the microbiological and electrochemical behavior. The results by linear scanning voltammetry showed that the B. safensis and B. pumilus caused a dual effect of increase and decrease currents, and through electrochemical impedance spectroscopy, showed in some cases, inductive loop, which could be associated with local corrosion and another case, an increasing impedance could be related to protection. In addition, a morphological characterization was performed by scanning electron microscopy before and after exposure, showing an increase in copper precipitation in the vicinity of the intermetallic phases by bacteria, attributed to local corrosion, but, in general, a significant effect of damages was not observed.

Probiotic Bacillus safensis NPUST1 Administration Improves Growth Performance, Gut Microbiota, and Innate Immunity against Streptococcus iniae in Nile tilapia (Oreochromis niloticus)

Probiotics are considered ecofriendly alternatives to antibiotics as immunostimulants against pathogen infections in aquaculture. In the present study, protease-, amylase-, cellulase-, and xylanase-producing Bacillus safensis NPUST1 were isolated from the gut of Nile tilapia, and the beneficial effects of B. safensis NPUST1 on growth, innate immunity, disease resistance and gut microbiota in Nile tilapia were evaluated by feeding tilapia a basal diet or basal diet containing 105 and 106-107 CFU/g for 8 weeks. The results showed that the weight gain, feed efficiency and specific growth rate were significantly increased in tilapia fed a diet containing 106 CFU/g and 107 CFU/g B. safensis NPUST1. Intestinal digestive enzymes, including protease, amylase and lipase, and hepatic mRNA expression of glucose metabolism and growth-related genes, such as GK, G6Pase, GHR and IGF-1, were also significantly increased in the 106 CFU/g and 107 CFU/g B. safensis NPUST1 treated groups. Immune parameters such as phagocytic activity, respiratory burst and superoxide dismutase activity in head kidney leukocytes, serum lysozyme, and the mRNA expression of IL-1β, IL-8, TNF-α and lysozyme genes were significantly induced in the head kidney and spleen of 106 CFU/g and 107 CFU/g B. safensis NPUST1 treated fish. The cumulative survival rate was significantly increased in fish fed a diet containing 106 CFU/g and 107 CFU/g B. safensis NPUST1 after challenge with Streptococcus iniae. Dietary supplementation with B. safensis NPUST1 improves the gut microbiota of Nile tilapia, which increases the abundance of potential probiotics and reduces the abundance of pathogenic pathogens. The present study is the first to report the use of B. safensis as a potential probiotic in aquaculture, and a diet containing 106 CFU/g B. safensis NPUST1 is adequate for providing beneficial effects on growth performance and health status in tilapia.

A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides

Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.

Gut Microbiota Modulation as a Potential Target for the Treatment of Lung Infections

The gastrointestinal and respiratory systems are colonized by a complex ecosystem of microorganisms called the microbiota. These microorganisms co-evolved over millions of years with the host, creating a symbiotic relationship that is fundamental for promoting host homeostasis by producing bioactive metabolites and antimicrobial molecules, and regulating the immune and inflammatory responses. Imbalance in the abundance, diversity, and function of the gut microbiota (known as dysbiosis) have been shown to increase host susceptibility to infections in the lungs, suggesting crosstalk between these organs. This crosstalk is now referred to as the gut-lung axis. Hence, the use of probiotics, prebiotics, and synbiotics for modulation of gut microbiota has been studied based on their effectiveness in reducing the duration and severity of respiratory tract infections, mainly owing to their effects on preventing pathogen colonization and modulating the immune system. This review discusses the role and responses of probiotics, prebiotics, and synbiotics in the gut-lung axis in the face of lung infections.

Draft Genome Sequences of Heat Shock-Tolerant Microbes Isolated from a Spacecraft Assembly Facility

Heat shock-tolerant microorganisms belonging to the orders Bacillales and Micrococcales were isolated from the Spacecraft Assembly Facility at the Jet Propulsion Laboratory, and 63 draft genome sequences were assembled and identified. Further analyses of these genomes can provide insight into methods for preventing forward contamination.

Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches

Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Background

Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.

Results

Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K⁺ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair.

Conclusion

Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.

Full-Genome Sequence of Bacillus safensis Strain IDN1, Isolated from Commercially Available Natto in Indonesia

We isolated a strain of Bacillus safensis, which we called IDN1, from natto sold in Indonesia. In order to gain insights into its genomic structure and understand its biology, we used the Oxford Nanopore MinION platform followed by PCR to verify the ends and determine its full circular genome sequence.

We isolated a strain of Bacillus safensis, which we called IDN1, from natto sold in Indonesia. In order to gain insights into its genomic structure and understand its biology, we used the Oxford Nanopore MinION platform followed by PCR to verify the ends and determine its full circular genome sequence.

Markers to Rapidly Distinguish Bacillus paralicheniformis From the Very Close Relative, Bacillus licheniformis

As close relatives, Bacillus paralicheniformis is often wrongly identified as Bacillus licheniformis. In this study, two genetic markers are presented based on fenC and fenD from the fengycin operon of B. paralicheniformis to rapidly distinguish it from B. licheniformis. The fengycin operon is one of the few present in B. paralicheniformis but absent in B. lichenformis up to date. Using these markers, two presumptive B. paralicheniformis isolates each were recovered from a set of isolates previously identified as B. licheniformis by Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) or identified only to genus level as Bacillus by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as B. paralicheniformis having the closest similarity with B. paralicheniformis ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.

Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility

A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12T was anteiso C15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C20 : 4 ω6,9,12,16c) was present in strain B12T and Kineococcus glutinatus YIM 75677T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12T. Multi-locus sequence and whole genome sequence analyses confirmed that B12T clades with other Kineococcus species. Average nucleotide identity of strain B12T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12T in order Kineosporiales, confirming that strain B12T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12T (=FJII-L1-CM-PAB2T; NRRL B-65556T, DSM 110506T).

Survey and Evaluation of Spacecraft-Associated Aluminum-Degrading Microbes and Their Rapid Identification Methods

Aluminum corrosion has become a major obstacle in spacecraft construction given that aluminum is used extensively throughout the construction process. Despite its many attributes in strength and durability, aluminum is susceptible to corrosion, in particular, corrosion due to microbial contamination. Scientists have encountered a number of problems with microbial aluminum corrosion within spacecraft components. Here, we summarize recent findings with regard to the phenomenon of microbiologically influenced corrosion (MIC) on space stations in the context of microbial strains isolated from the Mir space station (Mir) and the International Space Station (ISS). Given that strains found on spacecraft are of terrestrial origin, an understanding of the contribution of Al-corrosive microbes to corrosion and related risks to space travel and astronaut health is essential for implementation of prevention strategies. Accordingly, an efficient rapid identification method of microbes with the capability to degrade aluminum is proposed. In particular, onboard implementation of a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is addressed. The use of a MALDI-TOF MS on board spacecraft will be crucial to future successes in space travel given that traditional methods of identifying corrosive species are far more time-consuming. Identification of microbes by way of a MALDI-TOF MS may also aid in the study of microbial corrosion and be a valuable asset for MIC prevention.

Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader

Huge quantities of keratinaceous waste are a substantial and almost totally unexploited protein resource which could be upgraded for use as high value-added products by efficient keratinolytic enzymes. In this study, we found that Bacillus sp. 8A6 can efficiently degrade chicken feather after 24 h growth. According to phylogenetic analysis, the strain (formerly identified as Bacillus pumilus 8A6) belongs to the B. pumilus species clade but it is more closely related to B. safensis. Hotpep predicted 233 putative proteases from Bacillus sp. 8A6 genome. Proteomic analysis of culture broths from Bacillus sp. 8A6 cultured on chicken feathers or on a mixture of bristles and hooves showed high abundance of proteins with functions related to peptidase activity. Five proteases (one from family M12, one from family S01A, two from family S08A and one from family T3) and four oligopeptide and dipeptide binding proteins were highly expressed when Bacillus sp. 8A6 was grown in keratin media compared to LB medium. This study is the first to report that bacterial proteases in families M12, S01A and T3 are involved in keratin degradation together with proteases from family S08.

Screening, identification and application of soil bacteria with nematicidal activity against root-knot nematode (Meloidogyne incognita) on tomato

BACKGROUND

Root-knot nematodes (Meloidogyne spp.) are soilborne pathogens that can cause great damage to and economic loss of crops globally. Owing to the high toxicity of chemicals toward humans and the environment, the use of biocontrol bacteria, a promising method for controlling root-knot nematodes, has gained attention.

RESULTS

To screen novel bacterial strains for their ability to control root-knot nematodes, 106 bacterial strains were isolated from soil. Eight of the obtained isolates exhibited satisfactory nematicidal activity against Meloidogyne incognita at 2-fold dilutions (approximately 3 × 10¹²  CFU mL^-1 ) after 12 h of exposure. Based on their physiological, biochemical and molecular (16S rRNA and gyrB gene sequences) characteristics, the eight strains were identified as Bacillus halotolerans, B. kochii, B. oceanisediminis, B. pumilus, B. toyonensis, B. cereus, Pseudomonas aeruginosa and B. pseudomycoides. In greenhouse and field experiments, the eight isolates suppressed M. incognita up to 69.96% compared to the control. Additionally, the yield of tomato increased 1.4-26.1% over that of the control.

CONCLUSION

The strains of B. halotolerans DDWA, B. kochii DDWB, B. oceanisediminis DDWC and B. pseudomycoides JNC have potential to control M. incognita, which has not been previously reported. © 2020 Society of Chemical Industry.

Whole-Genome Sequences of an Abortive Bacillus safensis Strain Isolated from a Mare's Uterus

This is a report of two Bacillus safensis genomes sequenced from separate cultures isolated from the uterus of a 16-year-old Westphalian mare that aborted a dead fetus. This strain represents the first case of a B. safensis-associated equine abortion and the first case of infection caused by this bacterium.

Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia

The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 μm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 μm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.

Bacillus glennii sp. nov. and Bacillus saganii sp. nov., isolated from the vehicle assembly building at Kennedy Space Center where the Viking spacecraft were assembled

Two Gram-stain-positive, motile, endospore-forming, aerobic strains, designated V44-8^T and V47-23a^T, were isolated from environmental air sampling at the vehicle assembly building at Cape Canaveral, Florida, where the Viking spacecraft were assembled. Growth was observed at pH 7-9 (optimum, pH 9) for strain V44-8^T, and pH 5-10 (pH 9) for strain V47-23a^T. Both strains displayed growth in 0-5 % NaCl with an optimum at 1 % for strain V44-8^T; 0 % for strain V47-23a^T. Strains V44-8^T and V47-23a^T grew optimally at 32 °C, (15-32 °C) and 25 °C (20-45 °C), respectively. The cell wall of both strains contained meso-diaminopimelic acid as the diagnostic diamino acid. Both strains contained phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. The predominant cellular fatty acids were anteiso-C_15 : 0, iso-C_14 : 0 and iso-C_15 : 0. Strain V47.23a^T shared its highest 16S rRNA sequence similarity with Bacillus cavernae DSM-105484^T at 96.9%, and V44.8^T with Bacillus zeae DSM-103964^T at 96.6 %. Based on their phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analyses, the isolates were identified as being a members of the genus Bacillus that forms a separate clade when compared to close relatives. Average nucleotide identity and average amino acid identity values between strains V44-8^T and DSM-103964^T were 72.1% and 67.5 %; V47-23a^T and DSM-105484^T were 62.4% and 69.1%, respectively. Based on the phenotypic, genomic and biochemical data, strains V44-8^T and V47-23a^T represent two novel species in the genus Bacillus for which the names Bacillus glennii sp. nov. [type strain, V44-8^T (=ATCC BAA-2860^T =DSM 105192^T)], and Bacillus saganii sp. nov. [V47-23a^T (=ATCC BAA-2861^T=DSM 105190^T)] are proposed.

Bacillus safensis JG-B5T affects the fate of selenium by extracellular production of colloidally less stable selenium nanoparticles

Understanding the impact of microorganisms on the mobility of selenium (Se) is important for predicting the fate of toxic Se in the environment and improving wastewater treatment technologies. The bacteria strain Bacillus safensis JG-B5T, isolated from soil in a uranium mining waste pile, can influence the Se speciation in the environment and engineered systems. However, the mechanism and conditions of this process remain unknown. This study found that the B. safensis JG-B5T is an obligate aerobic microorganism with an ability to reduce 70% of 2.5 mM selenite to produce red spherical biogenic elemental selenium nanoparticles (BioSeNPs). Only extracellular production of BioSeNPs was observed using transmission electron microscopy. The two-chamber reactor experiments, genome analysis and corona proteins identified on BioSeNPs suggested that the selenite reduction process was primarily mediated through membrane-associated proteins, like succinate dehydrogenase. Extracellular presence and low colloidal stability of BioSeNPs as indicated by ζ-potential measurements, render B. safensis JG-B5T an attractive candidate in wastewater treatment as it provides easy way of recovering Se while maintaining low Se discharge. As this microorganism decreases Se mobility, it will affect Se bioavailability in the environment and decreases its toxicity.

Antifungal activity of endophytic Bacillus safensis B21 and its potential application as a biopesticide to control rice blast

Endophytic bacteria are potential biocontrol agents for the control of fungal diseases. Here, an endophyte strain, B21, was isolated from Osmanthus fragrans Lour. fruits and identified as Bacillus safensis by analysis of its 16S rDNA gene sequence and its biochemical and physiological characteristics. The culture filtrate showed antifungal activity against Magnaporthe oryzae, which causes rice blast disease, and the IC₅₀ of the methanol extract was 15.56 μg/mL, which was significantly lower than that of carbendazim (25.16 μg/mL). The antifungal activity of the methanol extract was stable at a wide range of pH values (1-9) and temperatures (40-100 °C). Two antifungal compounds were isolated by organic extraction, silica gel column chromatography and high-performance liquid chromatography (HPLC). Based on electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance spectrometry (NMR) analyses, the structures of the antifungal compounds were identified as iturin A2 and iturin A6. Additionally, the hyphae treated with iturin (iturin A2 or iturin A6) could be stained with the fluorescent dye propidium iodide (PI), indicating that these two compounds inhibited the growth of hyphae by changing the hyphal membrane permeability. In field experiments, spray treatment with fermentation broth resulted in a lower disease index than treatment with carbendazim, as did the culture filtrate. The results suggest that strain B21 and its bioactive compounds have the potential to be developed into a biopesticide for the biocontrol of rice blast.

Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics

BACKGROUND

Culturomics can ascertain traces of microorganisms to be cultivated using different strategies and identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry or 16S rDNA sequencing. However, to cater to all requirements of microorganisms and isolate as many species as possible, multiple culture conditions must be used, imposing a heavy workload. In addition, the fast-growing bacteria (e.g., Escherichia) surpass the slow-growing bacteria in culture by occupying space and using up nutrients. Besides, some bacteria (e.g., Pseudomonas) suppress others by secreting antibacterial metabolites, making it difficult to isolate bacteria with lower competence. Applying inhibitors to restrain fast-growing bacteria is one method to cultivate more bacterial species from human feces.

RESULTS

We applied CHIR-090, an LpxC enzyme inhibitor that has antibacterial activity against most Gram-negative bacteria, to culturomics of human fresh feces. The antibacterial activity of CHIR-090 was first assessed on five Gram-negative species of bacteria (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Bacteroides vulgatus), all of which are commonly isolated from the human gut. Then, we assessed suitable concentrations of the inhibitor. Finally, CHIR-090 was applied in blood culture bottles for bacterial cultivation. In total, 102 species from five samples were identified. Of these, we found one new species, two species not reported previously in the human gut, and 11 species not previously isolated from humans.

CONCLUSIONS

CHIR-090 can suppress E. coli, P. aeruginosa, K. pneumoniae, Pro. vulgaris, but not B. vulgatus. Compared with the non-inhibitor group, CHIR-090 increased bacteria isolation by 23.50%, including four species not reported in humans and one new species. Application of LpxC enzyme inhibitor in culturomics increased the number of species isolated from the human gut.

Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile

Genome analysis of Bacillus safensis RP10, a strain from the soil of Atacama Desert in northern Chile, reflects a bacterium adapted to live in soil containing high levels of heavy metals, high salt conditions, and low carbon and energy sources.

Microscopic Characterization of Biological and Inert Particles Associated with Spacecraft Assembly Cleanroom

NASA cleanrooms are certified by particle counts and are humidity-controlled, temperature-regulated, and oligotrophic in nature for assembling spacecraft subsystems. Microorganisms, which are not part of the cleanroom certification metrics, should not be overlooked when assessing the cleanliness of the facility since they can enter through soil or air, shed from humans, adapt to the oligotrophic conditions, and subsequently could contaminate spacecraft. These biogenic particles need to be identified to extend our knowledge of biological contamination for future NASA mission use. This study collected particles from the cleanroom and estimated the distribution of fallout microbial cell and inert dust particles using microscopy and molecular techniques. Aluminum coupon-based polycarbonate filter assemblies were deployed in the spacecraft assembly cleanroom facility to collect fallout particles. Epifluorescence and electron microscopy showed that particles varied in size and structure, and displayed live/dead biological and inert particle signatures from sources that include spores and fungal hyphae. Additionally, correlative epifluorescence and field emission scanning electron microscopy, combined with energy-dispersive X-ray analysis (for elemental compositions) methods, differentiated whether microbes adhering to particles were live/dead cells or inert particles. This visualization approach allowed for the classification of microorganisms as being standalone (free-living) or associated with a particle, as well as its characteristic size. Furthermore, time-course microscopy was used to determine the microbial cell growth and confirm the biological/molecular identification. Routine investigation of cleanroom biological and inert fallout particles will help to determine the biological load of spacecraft components and will also have direct relevance to the pharmaceutical and medical industries. One of the main objectives for NASA’s current and future missions is to prevent forward and back contamination of exploring planets. The goal of this study is to determine the association of microorganisms with the inert, natural cleanroom fallout particles and to ascertain whether microorganisms prefer to adhere to a particle size. A novel microscopy technique was developed, and by utilizing various molecular techniques, particles and associated microbial phylogeny were characterized. An accurate assessment of the microbes associated with cleanroom particles is necessary to protect the health of the people who occupy the room for long duration for aeronautical, medical, and pharmaceutical industries.

Effects of potential probiotic Bacillus velezensis K2 on growth, immunity and resistance to Vibrio harveyi infection of hybrid grouper (Epinephelus lanceolatus♂ × E. fuscoguttatus♀)

Nowadays, there is no suitable treatment for vibriosis in groupers. So an eco-efficient and environmentally friendly treatment is necessary for the grouper industry. Probiotic-feeding has been a promising strategy to control the bacterial pathogens in aquaculture. A new Bacillus velezensis strain named K2 was isolated from the intestinal tract of healthy grouper, and exhibited wide antimicrobial spectrum of against fish pathogens, including Vibrio harveyi, Vibrio alginolyticus, Aeromonas hydrophila, Aeromonas veronii, Aeromonas caviae, Enterococcus casseliflavus and Lactococcus garvieae. Moreover, results of the safety of B. velezensis K2 showed that intraperitoneal injection of K2 in healthy grouper did not cause any pathological abnormality or death, indicating this bacteria could be considered as a candidate probiotic in aquaculture. Groupers were fed with the diets containing 1 × 10⁷ cfu/g of B. velezensis K2 for 4 weeks. Various immune parameters were examined at 1, 2, 3, and 4 weeks of post-feeding. Results showed that diets supplemented with K2 significantly increased serum acid phosphatase (ACP) activity (P < 0.05). Results of the mRNA expression of immune-related genes in the head kidney of hybrid grouper showed that the expression of lysozyme gene was significantly upregulated after 1 and 2 weeks of feeding (P < 0.05). A significant up-regulation of the expression of piscidin, IgM and MyD88 were detected at day 21, whereas the TLR3 and TLR5 showed lower expression compared to the controls during 21 days, and a significant decrease of TLR3 gene was found at day 28 (P < 0.05). After challenge with V. harveyi, the survival rate of fish administrated with the strain K2 for 28 days was signifiacantly higher than the controls without this strain (P < 0.05). These results collectively suggest that B. velezensis K2 is a potential probiotic species to improve health status and disease resistance and can be developed as a probiotic agent in grouper industry.

Biodegradation of methyl and butylparaben by bacterial strains isolated from amended and non-amended agricultural soil. Identification, behavior and enzyme activities of microorganisms

The aim of the present study was to investigate the kinetics of methylparaben (MPB) and butylparaben (BPB) removal, two emerging pollutants with possible endocrine disrupting effects, from agricultural soil with and without amendment with compost from sewage sludge used as biostimulant. Compound removal is explained by a first-order kinetic model with half-life times of 6.5/6.7 days and 11.4/8.2 days, in presence/absence of compost, for MPB and BPB respectively. % R² for the fitted model were higher than 96% in all cases. Additionally, isolation of bacteria capable to grow using MPB or BPB as carbon source was also carry out. Laboratory tests demonstrated the ability of these bacteria to biodegrade MPB and BPB from culture media in more than 95% in some cases. These strains showed high ability to biodegrade the compounds. Ten isolates, most of them related to Gram positive bacteria of the genus Bacillus, were identified by 16S rRNA gene sequencing. The study of the enzymatic activities of the isolates revealed both esterase (C4) and esterase-lipase activities.

Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know?

To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.

Insights Into the Cultivable Microbial Ecology of "Manna" Ash Products Extracted From Fraxinus angustifolia (Oleaceae) Trees in Sicily, Italy

Microbial communities characterizing a specific food matrix, generally, strongly contribute to both its composition, and properties for food applications. To our knowledge, this is the first study to investigate the cultivable microbial ecology of Sicilian “Manna” ash products in order to acquire new information on the hygienic quality, shelf-life and potential application of this traditional food. To this purpose, several manna samples belonging to different commercial categories were collected and subjected to the analysis of bacteria, yeasts, and filamentous fungi. Furthermore, an investigation of the sugar content and physicochemical parameters was performed. The results of our study followed the trend generally reported for other sugary foods. Conversely, as regards microbiological analyses, in the present study, the presence of microorganisms at high levels confirmed their survival in stressing conditions characterizing this food matrix in a viable and cultivable form. Most species were osmophilic, endophytic bacteria, antagonistic of fungi pathogen of plants. Yeasts were the most abundant microbial populations and a total of six species were identified: Candida aaseri, Candida lactis-condensi, Citeromyces matritensis, Lachancea thermotolerans, Saccharomyces cerevisiae, and Zygosaccharomyces bailii. Filamentous fungi included five genera, which were considered common contaminants of honey and of other foods due to their xerophilic characteristics. Interestingly, our results suggest that the strains of L. thermotolerans isolated in this study might be evaluated for their potential to act as starters either singly or in multi-combination for food applications.

Characterization and Initial Application of Endophytic Bacillus safensis Strain ZY16 for Improving Phytoremediation of Oil-Contaminated Saline Soils

Hydrocarbon-degrading and plant-growth-promoting bacterial endophytes have proven useful for facilitating the phytoremediation of petroleum-contaminated soils with high salinity. In this study, we identified Bacillus safensis strain ZY16 as an endophytic bacterium that can degrade hydrocarbons, produce biosurfactants, tolerate salt, and promote plant growth. The strain was isolated from the root of Chloris virgata Sw., a halotolerant plant collected from the Yellow River Delta. ZY16 survived in Luria-Bertani (LB) broth with 0–16% (w/v) sodium chloride (NaCl) and grew well in LB broth supplemented with 0–8% NaCl, indicating its high salt tolerance. The endophytic strain ZY16 effectively degraded C₁₂–C₃₂n-alkanes of diesel oil effectively, as well as common polycyclic aromatic hydrocarbons under hypersaline conditions. For example, in mineral salts (MS) liquid medium supplemented with 6% NaCl, ZY16 degraded n-undecane, n-hexadecane, n-octacosane, naphthalene, phenanthrene, and pyrene, with degradation percentages of 94.5, 98.2, 64.8, 72.1, 59.4, and 27.6%, respectively. In addition, ZY16 produced biosurfactant, as confirmed by the oil spreading technique, surface tension detection, and emulsification of para-xylene and paraffin. The biosurfactant production ability of ZY16 under hypersaline conditions was also determined. Moreover, ZY16 showed plant-growth-promoting attributes, such as siderophore and indole-3-acetic acid production, as well as phosphate solubilization. To assess the enhanced phytoremediation of saline soils polluted by hydrocarbons and the plant-growth-promotion ability of ZY16, a pot trial with and without inoculation of the endophyte was designed and performed. Inoculated and non-inoculated plantlets of C. virgata Sw. were grown in oil-polluted saline soil, with oil and salt contents of 10462 mg/kg and 0.51%, respectively. After 120 days of growth, significant enhancement of both the aerial and underground biomass of ZY16-inoculated plants was observed. The soil total petroleum hydrocarbon degradation percentage (a metric of phytoremediation) after incubation with ZY16 was 63.2%, representing an elevation of 25.7% over phytoremediation without ZY16 inoculation. Our study should promote the application of endophytic B. safensis ZY16 in phytoremediation by extending our understanding of the mutualistic interactions between endophytes and their host plants.

The Spectrum of Interactions between Cryptococcus neoformans and Bacteria

Cryptococcus neoformans is a major fungal pathogen that infects immunocompromised people and causes life-threatening meningoencephalitis. C. neoformans does not occur in isolation either in the environment or in the human host, but is surrounded by other microorganisms. Bacteria are ubiquitously distributed in nature, including soil, and make up the dominant part of the human microbiota. Pioneering studies in the 1950s demonstrated antifungal activity of environmental bacteria against C. neoformans. However, the mechanisms and implications of these interactions remain largely unknown. Recently, interest in polymicrobial interaction studies has been reignited by the development of improved sequencing methodologies, and by the realization that such interactions may have a huge impact on ecology and human health. In this review, we summarize our current understanding of the interaction of bacteria with C. neoformans.

Comparative Study of the Colonization of Chromolaena and Tobacco Plants by Bacteria safensis CS4 using Different Methods of Inoculation

BACKGROUND AND OBJECTIVES

This study entails the effectiveness of colonization of bacterial endophytes following inoculation of the cells in plants.

METHODOLOGY

Different methods of inoculation including seed immersion, root immersion and foliar spray were studied on Chromolaena odorata and Nicotiana tabacum for 10, 20 and 30 days. This was to ascertain the colonization ability of the endophytic strain amongst the two set of plants. The foliar parts of the plants were assessed post inoculation for the presence of the bacteria strain, followed by the growth parameters in the plant. Significant differences at p<0.05 of colonization were established by the different inoculation methods.

RESULTS

Foliar spray demonstrated the highest colonization in both Chromolaena and tobacco plants followed by root immersion. Leaf inoculation in tobacco plant demonstrated a positive colonization which is not significant. However, seed inoculation provided colonization in Chromolaena plant at 10, 20 and 30 days post inoculation at a frequency lower than that of tobacco. With root immersion in Chromolaena, there was colonization at 10 days post inoculation, no colonization at 20 days post inoculation, but colonization re-appeared at 30 days (PI). Growth index measured demonstrated a positive relationship between the inoculation of the endophyte and the growth parameters which included stem length and germination rate.

CONCLUSION

This study, therefore, showed that the bacteria strain B. safensis CS4 can effectively be horizontally transferred into tobacco and Chromolaena plants using different methods. Foliar spraying demonstrated the optimal colonization of the strain in the plant leaves.