Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences

We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy

The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes.

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.

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.

Biofilm forming rhizobacteria affect the physiological and biochemical responses of wheat to drought

Plant growth promoting rhizobacteria (PGPR) can attenuate the adverse effects of water deficit on plant growth. Since drought stress tolerance of bacteria has earlier been associated to biofilm formation, we aimed to investigate the role of bacterial biofilm formation in their PGPR activity upon drought stress. To this end, a biofilm-forming bacterial collection was isolated from the rhizospheres of native arid grassland plants, and characterized by their drought tolerance and evaluated on their plant growth promoting properties. Most bacterial strains formed biofilm in vitro. Most isolates were drought tolerant, produced auxins, showed 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and solubilized mineral phosphate and potassium, but at considerably different levels. Greenhouse experiments with the most promising isolates, B1, B2 and B3, under three levels of water deficit and two wheat varieties led to an increased relative water content and increased harvest index at both moderate and severe water deficit. However, the bacteria did not affect these plant parameters upon regular watering. In addition, decreased hydrogen peroxide levels and increased glutathione S-transferase activity occurred under water deficit. Based on these results, we conclude that by improving root traits and antioxidant defensive system of wheat, arid grassland rhizospheric biofilm forming bacilli may promote plant growth under water scarcity.

Numerous biofilm forming PGPR reside in grass rhizospheres from arid grasslands.

Drought tolerance of wheat is enhanced by bacterial inoculations.

Wheat variety and the level of drought stress modify the plant’s response to the bacteria.

On-line monitoring of industrial interest Bacillus fermentations, using impedance spectroscopy

Impedance spectroscopy is a technique used to characterize electrochemical systems, increasing its applicability as well to monitor cell cultures. During their growth, Bacillus species have different phases which involve the production and consumption of different metabolites, culminating in the cell differentiation process that allows the generation of bacterial spores. In order to use impedance spectroscopy as a tool to monitor industrial interest Bacillus cultures, we conducted batch fermentations of Bacillus species such as B. subtilis, B. amyloliquefaciens, and B. licheniformis coupled with this technique. Each fermentation was characterized by the scanning of 50 frequencies between 0.5 and 5 MHz every 30 min. Pearson's correlation between impedance and phase angle profiles (obtained from each frequency scanned) with the kinetic profiles of each strain allowed the selection of fixed frequencies of 0.5, 1.143, and 1.878 MHz to follow-up of the fermentations of B. subtilis, B. amyloliquefaciens and B. licheniformis, respectively. Dielectric profiles of impedance, phase angle, reactance, and resistance obtained at the fixed frequency showed consistent changes with exponential, transition, and spore release phases.

Evidences for antioxidant response and biosorption potential of Bacillus simplex strain 115 against lead

In this study, we investigated effects of lead on growth response and antioxidant defense protection in a new identified strain isolated from a soil, in the rhizosphere of Sainfoin Hedysarum coronarium L. Different concentrations of lead (0, 0.2, 1.5 and 3 g L^-1) added to Bacillus simplex strain 115 cultures surprisingly did not inhibit its growth. However, a resulting oxidative stress as attested by overproduction of H₂O₂ (+ 6.2 fold) and malondialdehyde (+ 2.3 fold) concomitantly to the enhancement of proteins carbonylation (+ 221%) and lipoxygenase activity (+ 59%) was observed in presence of 3 g L^-1 of lead. Intrinsic antioxidant defenses were revealed by the coupled up-regulation of catalase (+ 416%) and superoxide dismutase (+ 4 fold) activities, with a more important Fe-SOD increase in comparison to the other isoforms. Bioaccumulation assays showed both intracellular and extracellular lead accumulation. Biosorption was confirmed as a particularly lead resistance mechanism for Bacillus simplex strain 115 as the metal sequestration in cell wall accounted for 88.5% to 98.5% of the total endogenous metal accumulation. Potentiality of this new isolated microorganism as a biotechnological tool for agricultural soil lead bioremediation was thus proposed.

Embryo-Like Features in Developing Bacillus subtilis Biofilms

Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Significance of manganese resistant bacillus cereus strain WSE01 as a bioinoculant for promotion of plant growth and manganese accumulation in Myriophyllum verticillatum

Endophytic bacteria are generally helpful for plant growth and protection. Strain WSE01, which was identified as bacillus cereus, was isolated from the stem of Myriophyllum verticillatum and it displayed a high tolerance to Mn (1500 mg/L). The strain was found to be able to produce indole-3-acetic acid (IAA) and siderophores, fix the atmospheric nitrogen and dissolve potassium from insoluble K-bearing minerals. In hydroponic culture experiments, the inoculation of strain WSE01 significantly promoted the growth and increased the leaf enzyme activity in the inoculated plant M. verticillatum. Furthermore, the manganese content was increased by 36.4% in stems and by 54.7% in leaves of the inoculated plant under Mn stress at 400 mg/L, compared to the non-inoculated group. This study suggests that the strain WSE01 has the potential to be used as biocontrol and/or biofertilizing agents for application in macrophyte M. verticillatum and conduces to achieving more effective phytoremediation of metal-contaminated waters.

Evaluation of Bacillus Strains for Plant Growth Promotion and Predictability of Efficacy by In Vitro Physiological Traits

Bacilli are commonly used as plant growth-promoting agents but can be limited in effectiveness to certain crop and soil environments. The objectives of this study were to (1) identify Bacillus strains that can be consistent in promoting the growth of corn, wheat, and soybean and (2) determine whether physiological traits expressed in vitro can be predictive of growth promotion efficacy/consistency and be used for selecting effective strains. Twelve Bacillus strains isolated from wheat rhizospheres were evaluated in greenhouse pot tests with nonsterile soil for their effects on the growth of corn, soybean, and wheat. The strains also were assessed in vitro for multiple physiological traits. All 12 strains increased corn growth significantly compared to the controls. The four most efficacious strains on corn-Bacillus megaterium R181, B. safensis R173, B. simplex R180, and Paenibacillus graminis R200-also increased the growth of soybean and wheat. No set of traits was a predictor of growth promotion efficacy. The number of traits expressed by a strain also was not an indicator of efficacy as strain R200 that was positive for only one trait showed high growth promotion efficacy. Effective strains can be identified through pot tests on multiple crop plants, but in vitro physiological assays are unreliable for strain selection.

Volatiles produced by Bacillus mojavensis RRC101 act as plant growth modulators and are strongly culture-dependent

Volatile organic compounds (VOCs) produced by Plant Growth Promoting Rhizobacteria have recently been investigated due to their role in plant growth promotion and defense. Whereas some bacterial VOCs like 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol produced by strains of Bacillus subtilis and Bacillus amyloliquefaciens promote plant growth, others like hydrogen cyanide and 3-phenylpropionic acid are phytotoxic, inhibiting plant growth. Bacillus mojavensis, a close relative of B. subtilis, is an endophytic bacterium of maize that has been shown to have antagonistic activity against the mycotoxigenic phytopathogen Fusarium verticillioides and growth promotion activity on maize seedlings. To investigate the growth promotion activity of B. mojavensis, Arabidopsis thaliana seedlings were grown on 1/2x Murashige & Skoog (MS) medium in divided Petri dishes while bacteria were grown either on 1/2x MS or nutrient agar (NA) medium, so that only microbial volatiles reached the seedlings. Significant plant growth promotion in Arabidopsis seedlings was observed when 1/2x MS medium was used for bacterial growth. In contrast, phytotoxicity was observed with bacterial growth on NA medium. These results indicate that VOCs produced by B. mojavensis may act as plant growth modulators rather than just promoters. Using Solid Phase Microextraction (SPME) coupled with GC-MS, the plant growth promoting compounds acetoin and 2,3-butanediol were both identified as being produced by B. mojavensis on growth promoting 1/2x MS medium. In contrast, while no phytotoxic VOC was conclusively identified from B. mojavensis on NA medium, detection of relatively high levels of acetone/2-propanone indicates its possible contribution to Arabidopsis phytotoxicity.

Quality challenges associated with microbial-based cleaning products from the Industry Perspective

Microbial-based cleaning products (MBCPs) continue to gain popularity in the market as environmentally friendly cleaners. The majority of these products contain spores of various Bacillus species. Although the microorganisms used in MBCPs are subject to regulation in Canada under the Canadian Environmental Protection Act, the products themselves are not. Unlike other types of microbial products such as probiotics and biopesticides, the use, manufacture and quality parameters of MBCPs in Canada and other countries are poorly defined and not specifically subject to any required standards. Due to their complexity and nature, these products feature unique quality challenges. We noted the existing MBCPs we analyzed vary vastly in quality; external microbial contaminants, viability of the spores and the biocompatibility of the ingredients are issues that greatly affect product quality. A proper taxonomic identification of the bacterial species used also seems to be a major challenge for a number of manufacturers. A good understanding of the mechanisms governing these quality challenges and the adoption of good practices for the cultivation, harvesting, formulation, and manufacture of these types of products are essential for achieving high-quality performance standards.

Determinación de la actividad antimicrobiana e insecticida de extractos producidos por bacterias aisladas de suelo

Colombia es considerado uno de los países con mayor diversidad biológica, sin embargo, muy poca de esa diversidad ha sido explorada para identificar sustancias biológicamente activas. Los metabolitos secundarios bacterianos pueden presentar actividad frente a patógenos de plantas y animales y representan alternativas biotecnológicas para la industria. El objetivo de este estudio fue evaluar el potencial de diferentes cepas bacterianas aisladas de suelo, para producir sustancias biológicamente activas como antibacterianos, antifúngicos e insecticidas. Un total de 92 extractos metanólicos de metabolitos secundarios bacterianos fueron evaluados. La actividad antibacterial y antifúngica se evaluó mediante el ensayo de difusión en agar frente a diversas bacterias como Bacillus subtilis, Enterococcus faecalis, Escherichia coli y Staphylococcus aureus frente a diferentes hongos Alternaria sp., Colletotrichum sp., Fusarium sp., Pestalotia sp. y Verticillium sp. La actividad insecticida se evaluó determinando el efecto de los extractos sobre la mortalidad de larvas de Aedes aegypti (Diptera) y Spodoptera frugiperda (Lepidoptera). Se determinó que el 50% de los aislamientos bacterianos tuvieron algún tipo de actividad, aunque la mayor actividad biológica se detectó en los extractos producidos por bacterias del género Bacillus, identificados por medio de análisis del ADN ribosomal 16S y por caracterización bioquímica con API® 50 CHB, MicroLogTM y Biolog. Las especies del género Bacillus identificadas han sido caracterizadas como productoras de compuestos antimicrobianos de amplio espectro o de varios compuestos con diferentes actividades. La actividad biológica presentada por los extractos evidencian que los microorganismos terrestres y especialmente, las especies de Bacillus son productores prolíficos de diversas sustancias bioactivas.

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives

Spore-forming bacilli are being explored for the production and preservation of food for many centuries. The inherent ability of production of large number of secretory proteins, enzymes, antimicrobial compounds, vitamins, and carotenoids specifies the importance of bacilli in food chain. Additionally, Bacillus spp. are gaining interest in human health related functional food research coupled with their enhanced tolerance and survivability under hostile environment of gastrointestinal tract. Besides, bacilli are more stable during processing and storage of food and pharmaceutical preparations, making them more suitable candidate for health promoting formulations. Further, Bacillus strains also possess biotherapeutic potential which is connected with their ability to interact with the internal milieu of the host by producing variety of antimicrobial peptides and small extracellular effector molecules. Nonetheless, with proposed scientific evidences, commercial probiotic supplements, and functional foods comprising of Bacillus spp. had not gained much credential in general population, since the debate over probiotic vs pathogen tag of Bacillus in the research and production terrains is confusing consumers. Hence, it’s important to clearly understand the phenotypic and genotypic characteristics of selective beneficial Bacillus spp. and their substantiation with those having GRAS status, to reach a consensus over the same. This review highlights the probiotic candidature of spore forming Bacillus spp. and presents an overview of the proposed health benefits, including application in food and pharmaceutical industry. Moreover, the growing need to evaluate the safety of individual Bacillus strains as well as species on a case by case basis and necessity of more profound analysis for the selection and identification of Bacillus probiotic candidates are also taken into consideration.

Green mitigation strategy for cultural heritage: bacterial potential for biocide production

Several biosurfactants with antagonistic activity are produced by a variety of microorganisms. Lipopeptides (LPPs) produced by some Bacillus strains, including surfactin, fengycin and iturin are synthesized nonribosomally by mega-peptide synthetase (NRPS) units and they are particularly relevant as antifungal agents. Characterisation, identification and evaluation of the potentials of several bacterial isolates were undertaken in order to establish the production of active lipopeptides against biodeteriogenic fungi from heritage assets. Analysis of the iturin operon revealed four open reading frames (ORFs) with the structural organisation of the peptide synthetases. Therefore, this work adopted a molecular procedure to access antifungal potential of LPP production by Bacillus strains in order to exploit the bioactive compounds synthesis as a green natural approach to be applied in biodegraded cultural heritage context. The results reveal that the bacterial strains with higher antifungal potential exhibit the same morphological and biochemical characteristics, belonging to the genera Bacillus. On the other hand, the higher iturinic genetic expression, for Bacillus sp. 3 and Bacillus sp. 4, is in accordance with the culture antifungal spectra. Accordingly, the adopted methodology combining antifungal screening and molecular data is represent a valuable tool for quick identification of iturin-producing strains, constituting an effective approach for confirming the selection of lipopeptides producer strains.

A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR

The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified. The RAPD-PCR primer OPO-02 amplified a 0.5kb DNA band specific to B. pumilus 3ZZZ strain and 0.75kb DNA band specific to B. subtilis 3PP. These unique DNA bands may have potential use as SCAR (Sequenced Characterized Amplified Region) molecular markers for identification of arsenic resistant B. pumilus and B. subtilis strains.

Bacterial metabolites from intra- and inter-species influencing thermotolerance: the case of Bacillus cereus and Geobacillus stearothermophilus

Bacterial metabolites with communicative functions could provide protection against stress conditions to members of the same species. Yet, information remains limited about protection provided by metabolites in Bacillus cereus and inter-species. This study investigated the effect of extracellular compounds derived from heat shocked (HS) and non-HS cultures of B. cereus and Geobacillus stearothermophilus on the thermotolerance of non-HS vegetative and sporulating B. cereus. Cultures of B. cereus and G. stearothermophilus were subjected to HS (42 or 65 °C respectively for 30 min) or non-HS treatments. Cells and supernatants were separated, mixed in a combined array, and then exposed to 50 °C for 60 min and viable cells determined. For spores, D values (85 and 95 °C) were evaluated after 120 h. In most cases, supernatants from HS B. cereus cultures added to non-HS B. cereus cells caused their thermotolerance to increase (D ₅₀ 12.2-51.9) when compared to supernatants from non-HS cultures (D ₅₀ 7.4-21.7). While the addition of supernatants from HS and non-HS G. stearothermophilus cultures caused the thermotolerance of non-HS cells from B. cereus to decrease initially (D ₅₀ 3.7-7.1), a subsequent increase was detected in most cases (D ₅₀ 18-97.7). In most cases, supernatants from sporulating G. stearothermophilus added to sporulating cells of B. cereus caused the thermotolerance of B. cereus 4810 spores to decline, whereas that of B. cereus 14579 increased. This study clearly shows that metabolites in supernatants from either the same or different species (such as G. stearothermophilus) influence the thermotolerance of B. cereus.

Production of Bacillus amyloliquefaciens OG and its metabolites in renewable media: valorisation for biodiesel production and p-xylene decontamination

Biosurfactants are important in many areas; however, costs impede large-scale production. This work aimed to develop a global sustainable strategy for the production of biosurfactants by a novel strain of Bacillus amyloliquefaciens. Initially, Bacillus sp. strain 0G was renamed B. amyloliquefaciens subsp. plantarum (syn. Bacillus velezensis) after analysis of the gyrA and gyrB DNA sequences. Growth in modified Landy's medium produced 3 main recoverable metabolites: surfactin, fengycin, and acetoin, which promote plant growth. Cultivation was studied in the presence of renewable carbon (as glycerol) and nitrogen (as arginine) sources. While diverse kinetics of acetoin production were observed in different media, similar yields (6-8 g·L^-1) were obtained after 72 h of growth. Glycerol increased surfactin-specific production, while arginine increased the yields of surfactin and fengycin and increased biomass significantly. The specific production of fengycin increased ∼10 times, possibly due to a connecting pathway involving arginine and ornithine. Adding value to crude extracts and biomass, both were shown to be useful, respectively, for the removal of p-xylene from contaminated water and for biodiesel production, yielding ∼70 mg·g^-1 cells and glycerol, which could be recycled in novel media. This is the first study considering circular bioeconomy to lower the production costs of biosurfactants by valorisation of both microbial cells and their primary and secondary metabolites.

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize

Heavy metals (HMs) are one of the major ecological problem related to human activities. Phytoremediation is a promising "green technology" for soil and water reclamation, and it can be improved by means of the use of chelants. In the past particular attention was paid on the effects of HMs and/or chelants on plant health, but much less on their effects on rhizosphere communities. To shed light on the interaction among plant-HM-chelant-rhizobacterial community a pot experiment was set up. Maize plants were grown on uncontaminated, multi-metal (copper and zinc) contaminated and chelants artificially amended soils. A high concentration of HMs was detected in the different maize organs; chelants improved the accumulation capacity of the maize plants. The rhizosphere bacterial community isolated from control plants showed the largest biodiversity in terms of bacterial genera. However, the addition of HMs reduced the number of taxa to three: Bacillus, Lysinibacillus and Pseudomonas. The effects of HM treatment were counteracted by the addition of chelants in terms of the genetic biodiversity. Furthermore, several bacterial strains particularly resistant to HMs and chelants were isolated and selected. Our study suggests that the combined use of resistant bacteria and chelants could improve the phytoremediation capacity of maize.

Bacillus mojavensis RRC101 Lipopeptides Provoke Physiological and Metabolic Changes During Antagonism Against Fusarium verticilliodes

The mycotoxigenic pathogen Fusarium verticillioides threatens the quality and utility of maize across industrial and agricultural purposes. Chemical control is complicated by the intimate endophytic lifestyle of the pathogen with its host. Bacillus mojavensis RRC101, a maize-endophytic bacterium, has been observed to reduce F. verticillioides disease severity and fumonisin accumulation when coinoculated to maize. Genome sequencing and annotation identified a number of biocontrol-relevant pathways in RRC101. Biochemical assays confirmed the presence and activity of surfactin- and fengycin-type lipopeptides, with fengycins responsible for antifungal activity against F. verticillioides. This antagonism manifests as inhibition of filamentous growth, with microscopy revealing hyphal distortions, vacuolization, and lysis. F. verticillioides secondary metabolism also responds to antagonism, with lipopeptide challenge inducing greater fumonisin production and, in the case of fengycins, eliciting pigment accumulation at sites of inhibition. Together, these data suggest that antibiotic and toxin production are components of a complex biochemical interaction among maize endophytes, one pathogenic and one beneficial.

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe

Background

We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were reported. Therefore, to characterize its biological and medical significance, we sought to determine and analyze the complete genome sequence of Bacillus sp. NRRL B-14911.

Results

Based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) genes, sequence analysis of the 16S-23S rDNA intergenic transcribed spacers, phenotypic microarray, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we propose that this organism belongs to the species Bacillus infantis, previously shown to be associated with sepsis in a newborn child. Analysis of the complete genome of Bacillus sp. NRRL B-14911 revealed several virulence factors including adhesins, invasins, colonization factors, siderophores and transporters. Likewise, the bacterial genome encodes a wide range of methyl transferases, transporters, enzymatic and biochemical pathways, and insertion sequence elements that are distinct from other closely related bacilli.

Conclusions

The complete genome sequence of Bacillus sp. NRRL B-14911 provided in this study may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence. Additionally, this bacterium may serve as a useful tool to establish a disease model that permits systematic analysis of autoimmune events in various susceptible rodent strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2900-2) contains supplementary material, which is available to authorized users.

Antagonist effects of Bacillus spp. strains against Fusarium graminearum for protection of durum wheat (Triticum turgidum L. subsp. durum)

Bacillus species are attractive due to their potential use in the biological control of fungal diseases. Bacillus amyloliquefaciens strain BLB369, Bacillus subtilis strain BLB277, and Paenibacillus polymyxa strain BLB267 were isolated and identified using biochemical and molecular (16S rDNA, gyrA, and rpoB) approaches. They could produce, respectively, (iturin and surfactin), (surfactin and fengycin), and (fusaricidin and polymyxin) exhibiting broad spectrum against several phytopathogenic fungi. In vivo examination of wheat seed germination, plant height, phenolic compounds, chlorophyll, and carotenoid contents proved the efficiency of the bacterial cells and the secreted antagonist activities to protect Tunisian durum wheat (Triticum turgidum L. subsp. durum) cultivar Om Rabiia against F. graminearum fungus. Application of single bacterial culture medium, particularly that of B. amyloliquefaciens, showed better protection than combinations of various culture media. The tertiary combination of B. amyloliquefaciens, B. subtilis, and P. polymyxa bacterial cells led to the highest protection rate which could be due to strains synergistic or complementary effects. Hence, combination of compatible biocontrol agents could be a strategic approach to control plant diseases.

16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S–23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S–23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2–57.9 mol%. Five distinct ITS types were identified: ITS^none (without tRNA genes), ITS^Ala(TGC), ITS^{Ala(TGC)+Ile(GAT)}, ITS^{Ile(GAT)+Ala(TGC)}, and ITS ^{Ile(GAT)+Pseudo}. All of the identified tRNA^Ala(TGC) molecules consisted of 73 bases, and all of the tRNA^Ile(GAT) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S–23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.

Gene expression and molecular characterization of a chaperone protein HtpG from Bacillus licheniformis

Heat shock protein 90 (Hsp90/HtpG) is a highly abundant and ubiquitous ATP-dependent molecular chaperone consisting of three flexibly linked regions, an N-terminal nucleotide-binding domain, middle domain, and a C-terminal domain. Here the putative htpG gene of Bacillus licheniformis was cloned and heterologously expressed in Escherichia coli M15 cells. Native-gel electrophoresis, size exclusion chromatography, and cross-linking analysis revealed that the recombinant protein probably exists as a mixture of monomer, dimer and other oligomers in solution. The optimal conditions for the ATPase activity of B. licheniformis HtpG (BlHtpG) were 45°C and pH 7.0 in the presence of 0.5mM Mg(2+) ions. The molecular architecture of this protein was stable at higher temperatures with a transition point (Tm) of 45°C at neutral pH, whereas the Tm value was reduced to 40.8°C at pH 10.5. Acrylamide quenching experiment further indicated that the dynamic quenching constant (Ksv) of BlHtpG became larger at higher pH values. BlHtpG also experienced a significant change in the protein conformation upon the addition of ATP and organic solvents. Collectively, our experiment data may provide insights into the molecular properties of BlHtpG and identify the alteration of protein structure to forfeit the ATPase activity at alkaline conditions.

The Prevalence and Control of Bacillus and Related Spore-Forming Bacteria in the Dairy Industry

Milk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry.

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations .

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes

Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches.

Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus

BACKGROUND

Lysinibacillus sphaericus (formerly named Bacillus sphaericus) is incapable of polysaccharide utilization and some isolates produce active insecticidal proteins against mosquito larvae. Its taxonomic status was changed to the genus Lysinibacillus in 2007 with some other organisms previously regarded as members of Bacillus. However, this classification is mainly based on physiology and phenotype and there is limited genomic information to support it.

RESULTS

In this study, four genomes of L. sphaericus were sequenced and compared with those of 24 representative strains belonging to Lysinibacillus and Bacillus. The results show that Lysinibacillus strains are phylogenetically related based on the genome sequences and composition of core genes. Comparison of gene function indicates the major difference between Lysinibacillus and the two Bacillus species is related to metabolism and cell wall/membrane biogenesis. Although L. sphaericus mosquitocidal isolates are highly conserved, other Lysinibacillus strains display a large heterogeneity. It was observed that mosquitocidal toxin genes in L. sphaericus were in close proximity to genome islands (GIs) and mobile genetic elements (MGEs). Furthermore, different copies and varying genomic location of the GIs containing binA/binB was observed amongst the different isolates. In addition, a plasmid highly similar to pBsph, but lacking the GI containing binA/binB, was found in L. sphaericus SSII-1.

CONCLUSIONS

Our results confirm the taxonomy of the new genus Lysinibacillus at the genome level and suggest a new species for mosquito-toxic L. sphaericus. Based on our findings, we hypothesize that (1) Lysinibacillus strains evolved from a common ancestor and the mosquitocidal L. sphaericus toxin genes were acquired by horizontal gene transfer (HGT), and (2) capture and loss of plasmids occurs in the population, which plays an important role in the transmission of binA/binB.

Biodegradation of carbofuran in soils within Nzoia River Basin, Kenya

Carbofuran (2,3-dihydro-2,2-dimethylbenzofuran-7-yl methylcarbamate) has been used within the Nzoia River Basin (NRB), especially in Bunyala Rice Irrigation Schemes, in Kenya for the control of pests. In this study, the capacity of native bacteria to degrade carbofuran in soils from NRB was investigated. A gram positive, rod-shaped bacteria capable of degrading carbofuran was isolated through liquid cultures with carbofuran as the only carbon and nitrogen source. The isolate degraded 98% of 100-μg mL(-1) carbofuran within 10 days with the formation of carbofuran phenol as the only detectable metabolite. The degradation of carbofuran was followed by measuring its residues in liquid cultures using high performance liquid chromatography (HPLC). Physical and morphological characteristics as well as molecular characterization confirmed the bacterial isolate to be a member of Bacillus species. The results indicate that this strain of Bacillus sp. could be considered as Bacillus cereus or Bacillus thuringiensis with a bootstrap value of 100% similar to the 16S rRNA gene sequences. The biodegradation capability of the native strains in this study indicates that they have great potential for application in bioremediation of carbofuran-contaminated soil sites.

Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923

Bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize nicotinic acid. We report here the availability of a draft genome for B. niacini, which we will use to understand the evolution of its namesake phenotype, which appears to be unique among the species in its phylogenetic neighborhood.

Bacillus mesonae sp. nov., isolated from the root of Mesona chinensis

A Gram-stain-positive, short rod-shaped and motile, mildly halotolerant, endospore-forming bacterium, FJAT-13985T, was isolated from the internal tissues of Mesona chinensis root. Strain FJAT-13985T grew at 20–45 °C (optimum 30 °C) and pH 5.7–9.0 (optimum pH 7.0) and in the presence of 0–2 % (w/v) NaCl [optimum 1 % (w/v)]. The strain was catalase-positive and oxidase-negative. The cell wall of strain FJAT-13985T contained meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (97.4 %). The major fatty acids of the strain were anteiso-C15 : 0 (23.3 %) and iso-C15 : 0 (40.8 %). The DNA G+C content was 41.64 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FJAT-13985T is a member of the genus Bacillus and is most closely related to Bacillus drentensis DSM 15600T (98.4 %), Bacillus vireti DSM 15602T (98.2 %) and Bacillus novalis DSM 15603T (98.3 %). DNA–DNA hybridization indicated that relatedness between strain FJAT-13985T and its closest relative, B. drentensis DSM 15600T, was 36.63 %. The phenotypic, chemotaxonomic and genotypic properties clearly indicate that strain FJAT-13985T represents a novel species of the genus Bacillus , for which the name Bacillus mesonae sp. nov. is proposed. The type strain is FJAT-13985T ( = DSM 25968T = CGMCC1.12238T).