strains and one Lysinibacillus strain isolated from the environment on STAA medium highlight biotechnological potential

Streptomycin thallous acetate actidione medium is typically used to isolate Brochothrix thermosphacta bacteria from food. Using this medium, three bacterial strains were isolated from the environment. Genomic sequences demonstrated that these bacteria are of the genera Lysinibacillus and Paenibacillus and are of biotechnological interest.

Draft genome of Lysinibacillus fusiformis PwPw_T2 isolated from Ananas comosus revealing acetic acid producing and xenobiotic degrading enzymes

Lysinibacillus fusiformis PwPw_T2 isolated from deteriorating Ananas comosus sample collected from Lagos State, Nigeria putatively possesses genomic features like potential enzymes catalyzing acetic acid production and xenobiotic compounds degradation via various pathways as indicated by its genome sequences. These could make the organism relevant in food waste valorization and micro-biotechnology.

nov., isolated from Iru, fermented African locust beans

A Gram-positive, motile, aerobic, rod-shaped, endospore-forming strain designated IRB4-01T was isolated from fermented African locust beans (Iru) obtained from Bodija market in the city of Ibadan, southwestern Nigeria, during a screening process from food-related sources. IRB4-01T grew at 10-50 °C (optimum, 35-37 °C), pH 6-10 (optimum, pH 7) and in 0-6 % NaCl (optimum, 1-3 %). Phylogenetic analyses based on 16S rRNA and combined short- and long-read genome sequencing revealed that IRB4-01T is closely related to Lysinibacillus cavernae SYSU K30005T and Lysinibacillus boronitolerans 10aT. The cell-wall peptidoglycan type was A4α (Lys-Asp), containing the diagnostic diamino acid lysine. The major polar lipids in strain IRB4-01T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid, while the predominant menaquinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Genomic DNA G+C content was 37.4  mol%, while the digital DNA-DNA hybridization revealed 33.6 and 32.3 % relatedness to L. cavernae SYSU K30005T and L. boronitolerans 10aT, respectively. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome comparisons, strain IRB4-01T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus irui sp. nov. is proposed. The type strain is IRB4-01T (NCIMB 15452T=LMG 32887T). Hybrid genome data are provided on the NCBI database using the Bioproject number PRJNA906010 and accession numbers CP113527 and CP113528. Additionally, a representative 16S rRNA sequence is available with the GenBank accession number OQ566940.

Triple-valve endocarditis due to Lysinibacillus sphaericus infection

Lysinibacillus sphaericus is an environmental organism often considered a contaminant when isolated from patient specimens due to its rare association with human disease. Here we report a case of triple valve endocarditis caused by L. sphaericus infection. To the authors' knowledge, this is the first documented case of endocarditis caused by this bacterium.

Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth

Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 10⁸ CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20-70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain's cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.

Effect of Lysinibacillus isolated from environment on probiotic properties and gut microbiota in mice

Soil microorganisms (SM) are primarily involved in organism degradation, plant nitrogen nutrient immobilization, host microorganisms and oxidation. However, research on the effect of soil-derived Lysinibacillus on the intestinal microbiota spatial disparity of mice is lacking. To test the probiotic properties of Lysinibacillus and the spatial disparity on mice intestinal microorganisms, hemolysis test, molecular phylogenetic analysis, antibiotic sensitivity testing, serum biochemical assays and 16S rRNA profiling were applied. The results showed that Lysinibacillus (LZS1 and LZS2) was resistant to two common antibiotics, Tetracyclines and Rifampin, and sensitive to other antibiotics among the 12 antibiotics tested and negative for hemolysis. In addition, the body weight of group L (treatment of Lysinibacillus, 1.0 × 10⁸ CFU/d for 21days) mice was significantly greater than that of the control group; serum biochemical tests showed that the TG and UREA were significantly lower in group L. The spatial disparity of intestinal microorganisms in mice was significant, treatment of Lysinibacillus (1.0 × 10⁸ CFU/d for 21days) reduced the intestinal microbial diversity and decreased the richness of Proteobacteria, Cyanobacteria and Bacteroidetes in mice. Furthermore, Lysinibacillus treatment enhanced Lactobacillus and Lachnospiraceae richness and significantly reduced 6 bacterial genera in jejunum community, reduced 8 bacterial genera, but increased bacteria at the 4 genera level in cecum microorganisms. In conclusion, this study demonstrated spatial disparity of intestinal microorganisms in mice and probiotic potential of Lysinibacillus isolated from soil.

OF-1 depends on the Ami oligopeptide transporter to kill Streptococcus pneumoniae

Infections caused by antibiotic-resistant Streptococcus pneumoniae are of growing concern for healthcare systems, which need new treatment options. Screening microorganisms in terrestrial environments has proved successful for discovering antibiotics, while production of antimicrobials by marine microorganisms remains underexplored. Here we have screened microorganisms sampled from the Oslo Fjord in Norway for production of molecules that prevent the human pathogen S. pneumoniae from growing. A bacterium belonging to the genus Lysinibacillus was identified. We show that this bacterium produces a molecule that kills a wide range of streptococcal species. Genome mining in BAGEL4 and AntiSmash suggested that it was a new antimicrobial compound, and we therefore named it lysinicin OF. The compound was resistant to heat (100 °C) and polymyxin acylase but susceptible to proteinase K, showing that it is of proteinaceous nature, but most probably not a lipopeptide. S. pneumoniae became resistant to lysinicin OF by obtaining suppressor mutations in the ami locus, which encodes the AmiACDEF oligo peptide transporter. We created ΔamiC and ΔamiEF mutants to show that pneumococci expressing a compromised Ami system were resistant to lysinicin OF. Furthermore, by creating mutants expressing an intact but inactive Ami system (AmiED184A and AmiFD175A) we could conclude that the lysinicin OF activity depended on the active form (ATP-hydrolysing) of the Ami system. Microscopic imaging and fluorescent labelling of DNA showed that S. pneumoniae treated with lysinicin OF had an average reduced cell size with condensed DNA nucleoid, while the integrity of the cell membrane remained intact. The characteristics and possible mode of action of lysinicin OF are discussed.

Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds

We have previously reported the draft genome sequences of 59 endospore-forming Gram-positive bacterial strains isolated from Vietnamese crop plants due to their ability to suppress plant pathogens. Based on their draft genome sequence, eleven of them were assigned to the Brevibacillus and one to the Lysinibacillus genus. Further analysis including full genome sequencing revealed that several of these strains represent novel genomospecies. In vitro and in vivo assays demonstrated their ability to promote plant growth, as well as the strong biocontrol potential of Brevibacilli directed against phytopathogenic bacteria, fungi, and nematodes. Genome mining identified 157 natural product biosynthesis gene clusters (BGCs), including 36 novel BGCs not present in the MIBiG data bank. Our findings indicate that plant-associated Brevibacilli are a rich source of putative antimicrobial compounds and might serve as a valuable starting point for the development of novel biocontrol agents.

Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities

Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.

Lysinibacillus macroides-mediated control of cellulose-producing morphotype of Salmonella

BACKGROUND

Soil-dwelling human pathogens like Salmonella are transmitted by fresh produce such as tomato, spinach, onion and cabbage. With >2600 serovars, it is difficult to classify the good plant colonizers from the non-colonizers. Generally, soil microbiota are classified as autochthonous or zymogenous organisms, based on their ability to survive in soil. However, such information for soil-dwelling human pathogens is not available Thus there is a need to classify these organisms for designing a strategy to prevent their outbreak. Moreover, soil harbours a plethora of microbes, which can be screened for competitive organisms to control such human pathogens.

RESULTS

In this study, we examined whether the morphotype based on the attachment factors (e.g., cellulose and curli fimbri) of Salmonella was important for its colonization of roots. Secondly, we tracked the location of the bacteria in the plant cell. Interestingly, most of the epidermal cells occupied by Salmonella showed propidium iodide-positive nuclei. As an extension of the study, a screening of competitive rhizospheric bacteria was performed. One isolate, identified as Lysinibacillus macroides, was able to inhibit the biofilm of Salmonella and subsequently reduced its colonization on roots.

CONCLUSION

Based on this study, we classified the Rdar (red, dry and rough) morphotypes as good plant colonists. The ability to colonize and subsequent kill the live plant cell throws light on the zymogenous life cycle of soil-dwelling Salmonella. Additionally, Lysinibacillus macroides served as a biocontrol agent by reducing the burden of Salmonella in various vegetables. Such organisms can further be explored to prevent contamination of the food chain. © 2022 Society of Chemical Industry.

Strain Screening and Particle Formation: a Lysinibacillus boronitolerans for Self-Healing Concrete

Microbial-induced calcite precipitation is a promising technology to solve the problem of cracks in soil concrete. The most intensively investigated microorganisms are urease-producing bacteria. Lysinibacillus that is used as urease-producing bacteria in concrete repair has rarely been reported. In this study, Lysinibacillus boronitolerans with a high urease activity was isolated from soil samples. This strain is salt- and alkali-tolerance, and at pH 13, can grow to ~OD₆₀₀ 2.0 after 24 h. At a salt concentration of 6%, the strain can still grow to ~OD₆₀₀ 1.0 after 24 h. The feasibility of using this strain in self-healing concrete was explored. The data showed that cracks within ~0.6 mm could be repaired naturally with hydration when spores and substrates were added to the concrete in an appropriate proportion. Moreover, the number and morphology of CaCO₃ crystals that were produced by bacteria can be influenced by the concrete environment. An efficiency method to elucidate the process of microbial-induced calcium carbonate crystal formation was established with Particle Track G400. This study provides a template for future studies on the theory of mineralization based on microorganisms. IMPORTANCE The formation of calcium carbonate crystals in concrete by urease-producing bacteria is not understood fully. In this study, a Lysinibacillus boronitolerans strain with a high urease activity was isolated and used to analyze the counts and sizes of the crystals and the relationship with time. The data showed that the number of crystal particles increases exponentially in a short period with sufficient substrate, after which the crystals grow, precipitate or break. In concrete, the rate-limiting steps of calcium carbonate crystal accumulation are spore germination and urease production. These results provided data support for the rational design of urease-producing bacteria in concrete repair.

Exploration of surfactin production by newly isolated Bacillus and Lysinibacillus strains from food related sources

As a lipopeptide (LP), surfactin exhibits properties, such as emulsifying and dispersing ability, which are useful in food industry. Discovery of new LP-producing strains from food sources is an important step towards possible application of surfactin in foods. A total of 211 spore-forming, Gram-positive, and catalase-positive bacterial strains were isolated from fermented African locust beans (iru) and Palm Oil Mill Effluents in a screening process and examined for their ability to produce surfactin. This was achieved by a combination of methods, which included microbiological and molecular classification of strains, along with chemical analysis of surfactin production. Altogether, 29 isolates, positive for oil spreading and emulsification assays, were further identified with 16S rDNA analysis. The strains belonged to nine species including less commonly reported strains of Lysinibacillus, Bacillus flexus, B. tequilensis, and B. aryabhattai. The surfactin production was quantitatively and qualitatively analyzed by high-performance thin-layer chromatography (HPTLC) and liquid chromatography-mass spectrometry (LC-MS). Confirmation of surfactin by MS was achieved in all the 29 strains. Highest surfactin production capability was found in B. subtilis IRB2-A1 with a titer of 1444.1 mg L^-1 .

LF-N1 and Penicillium oxalicum DH-1 Inoculants Corresponds to Composting Performance

The effects of Lysinibacillus sp. LF-N1 and Penicillium oxalicum DH-1 inoculants (LFPO group) on compost succession and the microbial dynamic structure of co-composting wheat straw and cow manure composting were investigated. The inoculants contributed to longer thermophilic stages, higher temperatures (62.8 °C) and lower microbial diversity in the LFPO treatment compared to the control group (CK). Moreover, LFPO inoculation increased the germination index and accelerated organic matter and lignocellulose degradation in the compost. Microbial analysis confirmed that the inoculants effectively altered the microbial communities. The predominant biomarkers for bacteria and fungi in inoculated compost were members of Lysinibacillus and Penicillium, respectively. Functional prediction showed greater lignocellulose degradation and less pathogen accumulation in the LFPO group. The cooccurrence network analysis showed that the network structure in LFPO compost was greatly simplified compared to that in CK. Bacterial cluster A was dominated by Lysinibacillus, and fungal cluster B was represented by Penicillium, which were significantly correlated with temperature and lignocellulose degradation, respectively (p < 0.05). These results demonstrated that the LF-N1 and DH-1 inoculants drove the bacterial and fungal assemblies to induce physicochemical property changes during cocomposting.

Inducible boron resistance via active efflux in Lysinibacillus and Enterococcus isolates from boron-contaminated agricultural soil

Phylogenetically diverse bacteria tolerate high boron concentrations while others require it for metabolic purposes despite the metalloid being toxic beyond a threshold. Boron resistance and plant growth promoting attributes of two bacterial strains, Lysinibacillus sp. OL1 and a novel Enterococcus sp. OL5, isolated from boron-fertilizer-amended cauliflower fields were investigated in this study. OL1 and OL5 grew efficiently in the presence of 210-230 mM boron, and resistance was found to be inducible by small amounts of the element: 5 to 50 mM boron pre-exposure progressively shortened the lag phase of growth in the presence of 200 mM boron. Intracellular boron accumulation was also found to be regulated by the level of pre-exposure: no induction or induction by small amounts led to higher levels of intracellular accumulation, whereas induction by high concentrations led to lower accumulation. These data, in the context of the strains' overall resistance towards 200 mM boron, indicated that induction by higher boron concentrations turned potential efflux mechanisms on, while resistance was eventually achieved by continuous cellular entry and exit of the ions. Involvement of solute efflux in boron resistance was corroborated by the genome content of the isolates (genes encoding proteins of the ATP-binding cassette, major facilitator, small multidrug resistance, multi antimicrobial extrusion, and resistance-nodulation-cell division, family/superfamily). Bacteria such as OL1 and OL5, which resist boron via influx-efflux, potentially lower boron bioavailability, and therefore toxicity, for the soil microbiota at large. These bacteria, by virtue of their plant-growth-promoting attributes, can also be used as biofertilizers.

Lysinibacillus xylanilyticus Strain GIC41 as a Potential Plant Biostimulant

To identify Lysinibacillus strains with the potential to function as plant biostimulants, we screened 10 previously isolated Lysinibacillus strains from the rhizosphere and soil for their plant growth-promoting (PGP) effects. In vitro tests showed that all strains produced indole-3-acetic acid. In primary screening, the PGP effects of these strains were assessed on spinach seedlings grown on Jiffy-7 pellets; strains GIC31, GIC41, and GIC51 markedly promoted shoot growth. In secondary screening, the PGP efficacies of these three strains were examined using spinach seedlings grown in pots under controlled conditions. Only GIC41 exerted consistent and significant PGP effects; therefore, it was selected for subsequent experiments. The results of 6-week glasshouse experiments revealed that GIC41 markedly increased shoot dry weight by ca. 12–49% over that of the control. The impact of fertilization levels on the PGP efficacy of GIC41 was investigated using pot experiments. The application of a specific level of fertilizer was required for the induction of sufficient PGP effects by this strain. The phylogenetic ana­lysis based on the 16S rDNA sequence identified GIC41 as L. xylanilyticus. Collectively, these results show the potential of strain GIC41 to function as a plant biostimulant.

strain YL and elastic properties of its biogenic CaCO3 towards biocement application

BACKGROUND

Biocement, calcifying bacteria-incorporated cement, offers an environmentally-friendly way to increase the cement lifespan. This work aimed to investigate the potential use of Lysinibacillus sp. strain YL towards biocement application in both theoretical and experimental ways.

METHODS AND RESULTS

Strain YL was grown using calcium acetate (Ca(C₂ H₃ O₂ )₂ ), calcium chloride (CaCl₂ ) and calcium nitrate (Ca(NO₃ )₂ ). Maximum bacterial growth of ~0.09 hr-1 and the highest amount of CaCO₃ precipitation of ~8.0 g/L were obtained when using Ca(C₂ H₃ O₂ )₂ . The SEM and XRD results confirmed that biogenic CaCO₃ were calcites. The bulk, Young's and shear moduli of biogenic CaCO₃ calculated via the VRH approximation were ~1.5-2.3 times larger than those of ordinary Portland cement. The Poisson's ratio was 0.382 and negative in some directions, suggesting its ductility and auxetic behaviors. The new model was developed to explain the growth kinetic of strain YL in the presence of Ca(C₂ H₃ O₂ )₂ , whose concentration was optimized for biocement experiments. Strain YL could increase the compressive strength of cement up to ~50% higher than that of the uninoculated cement.

CONCLUSION

Strain YL is a promising candidate for biocement applications. This work represents the trials of experiments and models allowing quantitatively comparison with large-scale production in the future.

Effect of zinc-resistant Lysinibacillus species inoculation on growth, physiological properties, and zinc uptake in maize (Zea mays L.)

Soil contamination by heavy metals is one of the major abiotic stresses that cause retarded plant growth and low productivity. Among the heavy metals, excessive accumulations of zinc (Zn) cause toxicity to plants. The toxicity caused by Zn could be managed by application of Zn-tolerant plant growth-promoting (PGP) bacteria. In this study, five Zn-tolerant bacteria (100-400 mg^-1 Zn resistant) were selected and identified as Lysinibacillus spp. based on 16S rRNA gene sequencing. The PGP properties of the Lysinibacillus spp. showed the production of indole acetic acid (60.0-84.0 μg/ml) and siderophore, as well as solubilization of potassium. Furthermore, the isolates were evaluated under greenhouse condition with 2 g kg^-1 Zn stress and without Zn stress along with control on Zea mays. The results showed that Lysinibacillus spp. coated seeds enhanced plant growth attributes and biomass yield in both conditions compared with control plants. The enhancement of root growth ranged from 49.2 to 148.6% and shoot length from 83.3 to 111.7% under Zn-stressed soils. Also, the inoculated seedlings substantially enhanced chlorophyll a and b, proline, total phenol, and ascorbic acid. The uptake of Zn by maize root ranged from 31.5 to 210.0% compared with control plants. Therefore, this study suggested that the tested Zn-tolerant Lysinibacillus spp. may be used for cultivation of Z. mays in Zn-contaminated agricultural lands.

Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus

Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.

nov., isolated from cave soil

A Gram-stain-positive, motile, rod-shaped and endospore-forming strain, SYSU K30002^T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. SYSU K30002^T grew at 28-40 °C (optimum, 37 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-4 % (w/v) NaCl (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4α (Lys-Asp). The cell-wall sugars of SYSU K30002^T were ribose, galactose and mannose, and MK-7 was the menaquinone. The major fatty acids were iso-C_15 : 0, C_16 : 1 ω7c alcohol and iso-C_16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The G+C content of the genomic DNA was 36.1 mol%. The average nucleotide identity values between SYSU K30002^T and its closest relatives were below the cut-off level (95-96 %) for species delineation. Based on phenotypic, chemotaxonomic and genome comparisons, strain SYSU K30002^T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillusantri sp. nov. is proposed. The type strain is SYSU K30002^T (=KCTC 33955^T=CGMCC 1.13504^T).

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

HiCrome Bacillus agar for presumptive identification of Bacillus and related species isolated from honey samples

This study aimed to evaluate the performance of Hicrome Bacillus™ agar for isolation and rapid identification of the aerobic spore-forming bacteria most frequently found in honey samples. A collection of 197 bacterial isolates of Bacillus, Brevibacillus, Lysinibacillus, Paenibacillus, and Rummeliibacillus belonging to different species that have been reported in honey were screened for their abilities to grow and for their colony colors and medium appearance in HiCrome Bacillus agar. Also, 21 strains from culture collections were used for comparison and quality controls. A flowchart utilizing a combination of colony and media characteristics in the chromogenic medium and a set of simple biochemical and morphological tests were elaborated for quick presumptive identification. A procedure for direct isolation from honey samples was developed. In conclusion, HiCrome Bacillus agar in combination with simple microbiological tests was highly useful for rapid and reliable identification of most Bacillus, Brevibacillus, Lysinibacillus and Paenibacillus species commonly found in honey samples facilitating isolation from polymicrobial honey.

Feasibility of using RFLP of PCR-amplified 16S rRNA gene(s) for rapid differentiation of isolates of aerobic spore-forming bacteria from honey

This study aimed to assess the feasibility of using RFLP of PCR-amplified 16S rRNA gene (s) by using universal primers 27f/1492r and a combination of three restriction enzymes, AluI, CfoI, and TaqI, for a low-cost, rapid screen for a primarily differentiation of isolates of the complex of aerobic spore-forming bacteria commonly found in honey samples. The described method produced unique and distinguishable patterns to differentiate among 80 isolates belonging to 26 different species of Bacillus, Brevibacillus, Lysinibacillus, Rummeliibacillus, and Paenibacillus reported in honey and other apiarian sources.

Data associated with the characterization and presumptive identification of Bacillus and related species isolated from honey samples by using HiCrome Bacillus agar

The dataset described in this paper provides information on the morphological features of 24 different species of the genera Bacillus, Paenibacillus, Brevibacillus, Lysinibacillus, and Rummeliibacilluswhen growing in HiCrome Bacillus agar. The species studied are common contaminants of honey. In support to the recent publication entitled “HiCrome Bacillus agar for presumptive identification of Bacillus and related species isolated from honey samples” (2), a collection of 197 bacterial isolates belonging to 24 different species of aerobic spore-forming bacteria have been screened for their colony appearance and color and any substrate color change of HiCrome Bacillus agar at 24 and 48 h of incubation. Two simple flowcharts utilizing a combination of colony and media characteristics in the chromogenic medium and a set of simple biochemical and morphological tests were developed for quick presumptive identification.

In Vitro Selection and Identification of Potential Probiotics Isolated from the Gastrointestinal Tract of Nile Tilapia, Oreochromis niloticus

Fish gut bacteria can be used as probiotics for aquaculture. The aim of this study is to screen and identify beneficial probiotic bacteria from the gut of Nile tilapia, Oreochromis niloticus. Nine out of one hundred thirty-five isolates were non-pathogenic through intraperitoneal injection and had antibacterial activities with at least a strain from the five isolated fish pathogens, Aeromonas sobria, Aeromonas hydrophila, Pseudomonas aeruginosa, Pseudomonas putida, and Staphylococcus aureus. Further tests showed that such isolates can survive in the presence of high bile concentration (10%) and at different acidic pH values. A strains (14HT) was sensitive to all selected antibiotics, two strains were (9HT and 11HT) resistant to streptomycin and three strains (9HT, 11HT and 38HT) had resistance to two antibiotics. Four isolates (11HT, 33HT, 38HT and 41HT) had an amylase and a protease activities and one strain (47HT) showed only amylase activity. Based on 16S rRNA gene analysis, the isolated strains were identified as follows: Lactococcus lactis (8HT, 9HT, 11HT and 33HT); Enterococcus faecalis (14HT), Lysinibacillus sp. (38HT) and Citrobacter freundii (39HT, 41HT and 47HT).

Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions

Surface layers (S-layers) are components of the cell walls throughout the Bacteria and the Archaea that provide protection for microorganisms against diverse environmental stresses, including metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in an archaeon for which the S-layer represents the only cell wall component. Here, we test the hypothesis originally proposed in cyanobacteria that a “shedding” mechanism exists for replacing S-layers that have become mineral-encrusted, using Lysinibacillus sp. TchIII 20n38, metallotolerant gram-positive bacterium, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, depending on physiological state of the cells and metal exposure times, leading to the encrustation of the S-layer and changes in the cell morphology as observed by scanning electron microscopy. Using Nanoscale Secondary Ion Mass Spectrometry, we show that mineral-encrusted S-layers are shed by the bacterial cells after a period of latency (2 days under the conditions tested) in a heterogeneous fashion likely reflecting natural variations in metal stress resistance. The emerging cells regenerate new S-layers as part of their cell wall structure. Given the wide diversity of S-layer bearing prokaryotes, S-layer shedding may represent an important mechanism for microbial survival in metal-contaminated environments.

Exploring the Potentials of Lysinibacillus sphaericus ZA9 for Plant Growth Promotion and Biocontrol Activities against Phytopathogenic Fungi

There is an ongoing hunt for biologically active compounds that can combat phytopathogenic fungi and improve plant growth without causing any hazards to the environment. Consequently the present study aims at deciphering the plant growth promotion and antifungal capability of Lysinibacillus sphaericus ZA9. The bacterium was previously isolated and identified in our laboratory from maize rhizosphere using 16S rRNA gene sequencing. The test bacterium L. sphaericus ZA9 was found to produce high quantity of IAA (697 μg/ mL); siderophores (195.79 μg/ mL), HCN and hydrolytic enzyme as compared to the reference strain Bacillus sphaericus Z2-7. The bacterium was also capable of solubilizing silicates (Si), phosphates (P), and potassium (K). The bacterium enhanced the seedling vigor and germination of seeds pretreated with it and promoted the shoot length of both cucumber and tomato seeds in greenhouse experiment. L. sphaericus ZA9 and its cell free culture supernatant showed varied antagonistic behavior against Alternaria alternata, Curvularia lunata, Aspergillus sp., Sclerotinia sp., Bipolaris spicifera, Trichophyton sp. Fermentation broth culture of L. sphaericus ZA9 was then used to isolate antifungal metabolites by silica column chromatography. Identification and determination of antifungal compounds was carried out by Thin-layer chromatography (TLC) followed by NMR spectroscopy. Two compounds were isolated and identified as 2-pentyl-4-quinolinecarboxylic acid (C₁₅H₁₇NO₂) which is a quinoline alkaloid and 1- methylcyclohexene which is a cycloalkene. Compound 1; 2-Penthyl-4-quinolinecarboxylic acid was found to be highly antagonistic against most of the fungi tested as compared to the bacterium itself. Its activity was comparable to that of fungicide Benlate, while compound 2; 1- methylcyclohexene did not show any antifungal activity.

Rhizoremediation of cadmium-contaminated soil associated with hydroxamate siderophores isolated from Cd-resistant plant growth-promoting Dietzia maris and Lysinibacillus strains

In search of multitrait plant growth-promoting (PGP) inoculants, we introduced two cadmium-resistant bacterial strains, C4 (PG), C5 (WB), and their consortium C6 (PG × WB) isolated from metal-contaminated industrial waste-fed canal near West Bengal. The test isolates were biochemically characterized and screened in vitro for siderophore production. The infrared spectra revealed the hydroxamate nature of the siderophore produced. Further in green house, siderophore-based seed inoculation with selected PGP isolates exhibited stimulatory effects on seed germination (up to 85.4%), chlorophyll index (22.9 spad unit), shoot and root length (70% and 62.7%), tiller numbers (38.82%), spikelet numbers (52.2%), straw yield (62.2%), grain yield (76.1%), total dry matter of root and shoot (55.56% and 64.4%, respectively), and grain yields (76.1%) of tested wheat cultivars. The 16S rRNA sequencing identified strain PG and WB as Dietzia maris and Lysinibacillus sp. strains. Furthermore, inoculation of C6 (consortium) in both cultivar UP-2565 and KS-227 showed maximum Cd sorption capacity in roots (38.3% and 67.1%) and shoots (68.4% and 67.5%), respectively. Both the strains and their consortium showed a great potential to increase the growth and yield of wheat cultivars, which can also be utilized for rhizoremediation process.

Identification of chondroitin-like molecules from biofilm isolates Exiguobacterium indicum A11 and Lysinibacillus sp. C13

AIMS

The study aims to investigate whether the bacteria from biofilms can produce chondroitin-like molecules (CLMs).

METHODS AND RESULTS

Chondroitin belongs to the class of glycosaminoglycans. Forty bacteria from biofilms were isolated and screened for the production of glycosaminoglycans. Two isolates A11 and C13 produced 43 and 26 mg l(-1) of chondroitinase AC II degradable glycosaminoglycans, respectively, suggesting the possibility of production of CLMs by them. These isolates were identified using 16S rDNA sequencing technique and fatty acid methyl ester analysis. These were recognized as Exiguobacterium indicum A11 (NCIM 5531) and Lysinibacillus sp. C13 (NCIM 5532) respectively. These strains were also characterized using polar lipid content and biochemical tests. The identity of the glycosaminoglycans produced was further confirmed using agarose gel electrophoresis, fourier transform infrared spectroscopy and proton nuclear magnetic resonance spectroscopy.

CONCLUSIONS

Prokaryotic biofilms were found to be a good source of bacteria synthesizing CLMs. Two wild strains producing significant amount of the same were identified and characterized.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study exploring natural biofilms for the production of the therapeutic molecule, chondroitin/glycosaminoglycan. These isolates may be prospective new alternatives to recombinant strains that are reported for the production of chondroitin/glycoaminoglycan at an industrial scale. The production by these wild strains could be commercially attractive if the production is higher and/or can be improved further by strain improvement/process engineering. Further, these are new additions to the scientific literature on glycosaminoglycan-producing micro-organisms.

Protease characteristics of bacteriocin producing Lysinibacilli, isolated from fruits and vegetable waste

This study describes the physical stability and optimization of nutrient components for an extracellular protease produced by Bacillus strains isolated from fruits and vegetable waste, Lucknow, India. The isolated proteases could hydrolyze various native proteinaceous substrates such as bovine serum albumin, casein, skim milk, but not the gelatin. The strain JX416854 and isolate 10 yielded maximum protease (831; 703 U/ml) under optimized conditions: Nutrient, Casein broth; pH 7.0; shaking condition 37°C for 36 h. Crude protease exhibited activity over a wide range of pH (6.0-10.0) and found to be stable at (10-70°C), pH stable at 7- 9.0. The significant protease activity was observed with divalent cations Ca2+ and Mg2+ and EDTA. Further, significant blood destaining properties and stabilities with detergents were also observed. Thus, the significant potency and stability of these enzymes indicated their industrial importance and could be an alternative protease for various industrial applications.