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

Lysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity

An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to Lysinibacillus fusiformis NRRL NRS-350T (99.7%) and Lysinibacillus sphaericus NRRL B-23268T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15: 0 (52.3%), anteiso-C15: 0 (14.8%), C16:1ω7C alcohol (11.2%), and C16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of Lysinibacillus revealed this strain formed a distinct monophyletic clade with the nearest neighbor being Lysinibacillus fusiformis. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus pinottii sp. nov. is proposed, with type strain PB211T (= NRRL B-65672T, = CCUG 77181T).

Feed nutritional composition affects the intestinal microbiota and digestive enzyme activity of black soldier fly larvae

Introduction

Using black soldier fly larvae (BSFLs) to treat food waste is one of the most promising environmental protection technologies.

Methods

We used high-throughput sequencing to study the effects of different nutritional compositions on the intestinal microbiota and digestive enzymes of BSF.

Results

Compared with standard feed (CK), high-protein feed (CAS), high-fat feed (OIL) and high-starch feed (STA) had different effects on the BSF intestinal microbiota. CAS significantly reduced the bacterial and fungal diversity in the BSF intestinal tract. At the genus level, CAS, OIL and STA decreased the Enterococcus abundance compared with CK, CAS increased the Lysinibacillus abundance, and OIL increased the Klebsiella, Acinetobacter and Bacillus abundances. Diutina, Issatchenkia and Candida were the dominant fungal genera in the BSFL gut. The relative abundance of Diutina in the CAS group was the highest, and that of Issatchenkia and Candida in the OIL group increased, while STA decreased the abundance of Diutina and increased that of Issatchenkia. The digestive enzyme activities differed among the four groups. The α-amylase, pepsin and lipase activities in the CK group were the highest, and those in the CAS group were the lowest or the second lowest. Correlation analysis of environmental factors showed a significant correlation between the intestinal microbiota composition and digestive enzyme activity, especially α-amylase activity, which was highly correlated with bacteria and fungi with high relative abundances. Moreover, the mortality rate of the CAS group was the highest, and that of the OIL group was the lowest.

Discussion

In summary, different nutritional compositions significantly affected the community structure of bacteria and fungi in the BSFL intestinal tract, affected digestive enzyme activity, and ultimately affected larval mortality. The high oil diet gave the best results in terms of growth, survival and intestinal microbiota diversity, although the digestive enzymes activities were not the highest.

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.

Sustainable enhancement of Cr(VI) bioreduction by the isolated Cr(VI)-resistant bacteria

Bioreduction of mobile Cr(VI) to sparingly soluble Cr(III) is an effective strategy for in situ remediations of Cr contaminated sites. The key of this technology is to screen Cr(VI)-resistant bacteria and further explore the sustainable enhancement approaches towards their Cr(VI) reduction performance. In this study, a total of ten Cr(VI)-resistant bacteria were isolated from a Cr(VI) contaminated site. All of them could reduce Cr(VI), and the greatest extent of Cr(VI) reduction (98%) was obtained by the isolated CRB6 strain. The isolated CRB6 was able to reduce structural Fe(III) in Nontronite NAu-2 to structural Fe(II). Compared with the slow bioreduction process, the produced structural Fe(II) can rapidly enhance Cr(VI) reduction. The resist dissolution characteristics of NAu-2 in the redox cycling may provide sustainable enhancement of Cr(VI) reduction. However, no enhancement on Cr(VI) bioreduction by the isolated CRB6 was observed in the presence of NAu-2, which was attributed to the inhibition of Cr(VI) on the electron transfer between the isolated CRB6 and NAu-2. AQDS can accelerate the electron transfer between the isolated CRB6 and NAu-2 as an electron shuttle in the presence of Cr(VI). Therefore, the combination of NAu-2 and AQDS generated a synergistic enhancement on Cr(VI) bioreduction compared with the enhancement obtained by NAu-2 and AQDS individually. Our results highlight that structural Fe(III) and electron shuttle can provide a sustainable enhancement of Cr(VI) reduction by Cr(VI)-reducing bacteria, which has great potential for the effective Cr(VI) in-situ remediation.

Bacterial Toxins Active against Mosquitoes: Mode of Action and Resistance

Larvicides based on the bacteria Bacillus thuringiensis svar. israelensis (Bti) and Lysinibacillus sphaericus are effective and environmentally safe compounds for the control of dipteran insects of medical importance. They produce crystals that display specific and potent insecticidal activity against larvae. Bti crystals are composed of multiple protoxins: three from the three-domain Cry type family, which bind to different cell receptors in the midgut, and one cytolytic (Cyt1Aa) protoxin that can insert itself into the cell membrane and act as surrogate receptor of the Cry toxins. Together, those toxins display a complex mode of action that shows a low risk of resistance selection. L. sphaericus crystals contain one major binary toxin that display an outstanding persistence in field conditions, which is superior to Bti. However, the action of the Bin toxin based on its interaction with a single receptor is vulnerable for resistance selection in insects. In this review we present the most recent data on the mode of action and synergism of these toxins, resistance issues, and examples of their use worldwide. Data reported in recent years improved our understanding of the mechanism of action of these toxins, showed that their combined use can enhance their activity and counteract resistance, and reinforced their relevance for mosquito control programs in the future years.

Current Insights on the Diverse Structures and Functions in Bacterial Collagen-like Proteins

The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.

Horizontal transfer of large plasmid with type IV secretion system and mosquitocidal genomic island with excision and integration capabilities in Lysinibacillus sphaericus

We identified a ~30-kb genomic island (named GI8) carrying the binary toxin gene operon binA/binB on both the chromosome and large pBsph plasmid in the mosquitocidal Lysinibacillus sphaericus C3-41 strain. We found that GI8 is related to the occurrence of binA/binB within L. sphaericus and displays excision and integration capability by recognizing the attB region, which consists of a 2-nt target site (AT) flanked by an 11-nt imperfect inverted repeat. pBsph and two pBsph-like plasmids (p2362 and p1593) were found to carry a type IV secretion system (T4SS) and displayed transmissibility within a narrow host range specific to L. sphaericus. GI8 can be co-transferred with pBsph as a composite element by integration into its attB site, then excised from pBsph and re-integrated into the chromosomal attB site in the new host. The potential hosts of GI8, regardless of whether they are toxic or non-toxic to mosquito larvae, share good collinearity at the chromosomal level. Data indicated that the appearance of the mosquitocidal L. sphaericus lineage was driven by horizontal transfer of the T4SS-type conjugative plasmid and GI8 with excision and specific integration capability.

Analyses of Livestock-Associated Staphylococcus aureus Pan-Genomes Suggest Virulence Is Not Primary Interest in Evolution of Its Genome

Staphylococcus aureus is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen, S. aureus causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of S. aureus or the host-specific strains' pan-genomes. We report on livestock-associated S. aureus' (LA-SA) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA-SA' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA-SA genomes. We call for comparative microbial and pan-genome research between human and LA-SA that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.

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.

Complete Genome Sequence of Lysinibacillus sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore

Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant

A strain of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from rhizospheric soil of a pepper plant when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain, PB300^T, is closely related to Lysinibacillus macroides DMS 54^T (99.6%) and Lysinibacillus xylanilyticus DSM 23493^T (99.4%). In phenotypic characterisation, the novel strain was found to grow between 15 and 40 °C and tolerate up to 10% (w/v) NaCl. Furthermore, the strain was found to grow in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C_15 : 0 (56.6 %), anteiso-C_15 : 0 (14.6%), C_16 :1ω7C alcohol (9.3%) and C_16 : 0 (7.1%). The cell wall peptidoglycan contains lysine-aspartic acid, as in its close relatives. A draft genome was completed and the DNA G + C content was determined to be 37.5% (mol content). A phylogenomic analysis of the core genome of the new strain and 5 closely related type strains of the genus Lysinibacillus revealed that this strain formed a distinct monophyletic clade with the nearest neighbour being Lysinibacillus boronitolerans. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed relationships for the new strain were below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus capsici sp. nov. is proposed, with type strain PB300^T (= NRRL B-65515^T, = CCUG 72241^T).

vB_LspM-01: a novel myovirus displaying pseudolysogeny in Lysinibacillus sphaericus C3-41

Lysinibacillus sphaericus has great application potential not only in the biocontrol of mosquitoes but also in the bioremediation of toxic metals. Phages contribute to the genetic diversity and niche adaptation of bacteria, playing essential roles in their life cycle, but may also cause economic damage for industrially important bacteria through phage contamination during fermentation. In this study, the L. sphaericus phage vB_LspM-01, which belongs to the Myoviridae family, was isolated and characterized. Results showed that vB_LspM-01 could specifically infect most tested L. sphaericus isolates but was not active against isolates belonging to other species. Furthermore, phage-born endolysin exhibited a broader antimicrobial spectrum than the host range of the phage. The vB_LspM-01 genome had no obvious similarity with that of its host, and ca. 22.6% of putative ORFs could not get a match with the public databases. Phylogenic analysis based on the putative terminase large subunit showed high similarity with the phages identified with pac-type headful packaging. The vB_LspM-01 encoding genes were only detected in a tiny percentage of L. sphaericus C3-41 individual cells in the wild population, whereas they showed much higher frequency in the resistant population grown within the plaques; however, the phage genes could not be stably inherited during host cell division. Additionally, the vB_LspM-01 encoding genes were only detected in the host population during the logarithmic growth phase. The mitomycin C induction helped the propagation and lysogeny-lysis switch of vB_LspM-01. The study demonstrated that vB_LspM-01 can be present in a pseudolysogenic state in L. sphaericus C3-41 populations.

A toxin-antitoxin system is essential for the stability of mosquitocidal plasmid pBsph of Lysinibacillus sphaericus

Lysinibacillus sphaericus C3-41 carries a large low-copy-number plasmid pBsph, which encodes binary toxin proteins. Our previous study found that the transcriptional activator TubX plays an important role in the newly identified type Ⅲ TubRZC replication/partition system in pBsph, and that a vector consisting of tubRZC and tubX is not as stable as pBsph, indicating the presence of other maintenance module(s). In this study, we identified that orf9 and orf10 are necessary for the stability of pBsph by a series of deletion and complementation experiments. Bioinformatics analysis showed that ORF9 contains a PIN domain of VapBC toxin-antitoxin (TA) system, whereas ORF10 share no significant sequence similarity to any of the characterized antitoxins in the database. Further studies revealed that orf9 and orf10 are transcribed as an operon. The overexpression of ORF9 repressed the growth of both Escherichia coli and L. sphaericus, which can be alleviated by overexpression of ORF10. The deletion of orf10 individually or orf9-10 together resulted a decrease on plasmid stability which was restored by the complementation of corresponding gene(s), suggesting that ORF10 plays an important role in plasmid stability. In addition, it was found the plasmid stability is related with the transcription level of tubRZ, and overexpression of TubRZ could neutralize the negative effect on plasmid stability caused by the deletion of orf9-orf10. Moreover, the recombinant vector containing tubRZC, tubX and orf9-10 was more stable than the ones containing only tubRZC and either tubX or orf9-10. The data indicate that the plasmid maintenance system on pBsph includes orf9-orf10 TA system.

Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization

Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens.In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities. Our analyses found high variation in genome size and gene content among the eight Pseudomonas genomes analyzed (strains UM270, Pf0-1, A506, F113, SBW25, PICF-7, UK4 and UW4). A core genome of 3,039 coding DNA sequences (CDSs) was determined, with 599 CDSs present only in the UM270 genome. From these unique UM270 genes, a set of 192 CDSs was found to be involved in signaling, rhizosphere colonization and competence, highlighted as important traits to achieve an effective biocontrol and plant growth promotion.

A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials

The toxic lineage (TL) of Lysinibacillus sphaericus has been extensively studied because of its potential biotechnological applications in biocontrol of mosquitoes and bioremediation of toxic metals. We previously proposed that L. sphaericus TL should be considered as a novel species based on a comparative genomic analysis. In the current work, we constructed the first manually curated metabolic reconstruction for this species on the basis of the available genomes. We elucidated the central metabolism of the proposed species and, beyond confirming the reported experimental evidence with genomic a support, we found insights to propose novel applications and traits to be considered in further studies. The strains belonging to this lineage exhibit a broad repertory of genes encoding insecticidal factors, some of them remain uncharacterized. These strains exhibit other unexploited biotechnological important traits, such as lactonases (quorum quenching), toxic metal resistance, and potential for aromatic compound degradation. In summary, this study provides a guideline for further research aimed to implement this organism in biocontrol and bioremediation. Similarly, we highlighted the unanswered questions to be responded in order to gain a deeper understanding of the L. sphaericus TL biology.

The LspC3-41I restriction-modification system is the major determinant for genetic manipulations of Lysinibacillus sphaericus C3-41

Background

Lysinibacillus sphaericus has been widely used in integrated mosquito control program and it is one of the minority bacterial species unable to metabolize carbohydrates. In consideration of the high genetic conservation at genomic level and difficulty of genetic horizontal transfer, it is hypothesized that effective restriction-modification (R-M) systems existed in mosquitocidal L. sphaericus.

Results

In this study, six type II R-M systems including LspC3–41I were predicted in L. sphaericus C3–41 genome. It was found that the cell free extracts (CFE) from this strain shown similar restriction and methylation activity on exogenous Bacillus/Escherichia coli shuttle vector pBU4 as the HaeIII, which is an isoschizomer of BspRI. The Bsph_0498 (encoding the predicted LspC3–41IR) knockout mutant Δ0498 and the complement strain RC0498 were constructed. It was found that the unmethylated pBU4 can be digested by the CFE of C3–41 and RC0498, but not by that of Δ0498. Furthermore, the exogenous plasmid pBU4 can be transformed at very high efficacy into Δ0498, low efficacy into RC0498, but no transformation into C3–41, indicating that LspC3–41I might be a major determinant for the genetic restriction barrier of strain C3–41. Besides, lspC3–41IR and lspC3–41IM genes are detected in other two strains besides C3–41 of the tested 16 L. sphaericus strains, which all belonging to serotype H5 and MLST sequence type (ST) 1. Furthermore, the three strains are not horizontal transferred, and this restriction could be overcome by in vitro methylation either by the host CFE or by commercial methytransferase M. HaeIII. The results provide an insight to further study the genetic restriction, modification and evolution of mosquitocidal L. sphaericus, also a theoretical basis and a method for the genetic manipulations of L. sphaericus.

Conclusions

LspC3–41I is identified as the major determinant for the restriction barrier of L. sphaericus C3–41. Only three strains of the tested 16 L. sphaericus strains, which all belonging to serotype H5 and ST1 by MLST scheme, contain LspC3–41I system. Two different methods can be used to overcome the restriction barrier of the three isolates to get transformants efficiently: 1) to methylate plasmid DNA prior to the electroporation; and 2) to delete the major restriction endonuclease encoding gene lspC3–41IR.

Staphylococcus sciuri bacteriophages double-convert for staphylokinase and phospholipase, mediate interspecies plasmid transduction, and package mecA gene

Staphylococcus sciuri is a bacterial pathogen associated with infections in animals and humans, and represents a reservoir for the mecA gene encoding methicillin-resistance in staphylococci. No S. sciuri siphophages were known. Here the identification and characterization of two temperate S. sciuri phages from the Siphoviridae family designated ϕ575 and ϕ879 are presented. The phages have icosahedral heads and flexible noncontractile tails that end with a tail spike. The genomes of the phages are 42,160 and 41,448 bp long and encode 58 and 55 ORFs, respectively, arranged in functional modules. Their head-tail morphogenesis modules are similar to those of Staphylococcus aureus ϕ13-like serogroup F phages, suggesting their common evolutionary origin. The genome of phage ϕ575 harbours genes for staphylokinase and phospholipase that might enhance the virulence of the bacterial hosts. In addition both of the phages package a homologue of the mecA gene, which is a requirement for its lateral transfer. Phage ϕ879 transduces tetracycline and aminoglycoside pSTS7-like resistance plasmids from its host to other S. sciuri strains and to S. aureus. Furthermore, both of the phages efficiently adsorb to numerous staphylococcal species, indicating that they may contribute to interspecies horizontal gene transfer.

Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species

Background

Early in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.

Results

The genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.

Conclusions

The current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3056-9) contains supplementary material, which is available to authorized users.