Introduction

Bacillus cereus sensu lato (sl) is a group of bacteria of medical and agricultural importance. The species of this bacterial group colonize diverse hosts and have different ecological niches. The three most studied species of the group, Bacillus cereus sensu stricto (Bc), Bacillus thuringiensis (Bt), and Bacillus anthracis (Ba), are known for their pathogenic potential. B. cereus is considered an opportunistic pathogen due to food contamination (Ehling-Schulz et al. 2006). B. thuringiensis has been widely used in the biological control of insects due to the production of different toxins, mainly Cry proteins (Schnepf et al. 1998). B. anthracis is considered a pathogenic species to animals, acting even on humans (Pilo and Frey 2011). In these three species, genes encoding virulence and pathogenicity factors are often located in plasmids, including the toxins and capsule components of B. anthracis, Cry proteins in B. thuringiensis, and cereulide synthesis in emetic strains of B. cereus (Schnepf et al. 1998; Ehling-Schulz et al. 2006; Pilo and Frey 2011; Adang et al. 2014).

Several studies classify B. cereus s.l. as a complex phylogenetic group (Tourasse et al. 2011; Okinaka and Keim 2016). Multilocus sequence typing (MLST) data divide the group into seven clusters (I-VII), which show important genetic and host association differences (Guinebretière et al. 2008; Patiño-Navarrete and Sanchis 2017). Strains of B. thuringiensis and B. cereus are located mainly in clusters III and IV (Guinebretière et al. 2008), while strains of B. anthracis are found exclusively in cluster III. Thus, although they may belong to the same phylogenetic group, B. anthracis strains form a distant subcluster from commercially used bioinsecticidal B. thuringiensis strains (Raymond and Federici 2017). However, due to the complexity of the B. cereus group, taxonomic relationships among species remain a subject of debate (Bazinet 2017). Recently, the average nucleotide identity genome species threshold (92.5 ANI) was proposed (Carroll et al. 2020).

Although multiple tools have been used to study taxonomic relationships among B. cereus group species (Guinebretière et al. 2008; Van der Auwera et al. 2013; Liu et al. 2015; Patiño-Navarrete and Sanchis 2017), non-coding RNAs (ncRNAs), which can act as regulatory factors for several genetic and ecological traits (Hör et al. 2018), have never been used. These elements are organized in a database of RNA families (Rfam) according to sequence homology (Kalvari et al. 2018). Furthermore, families of ncRNAs are grouped into classes (sRNA, Leader, Riboswitch, etc.) and functional categories (Gene, Cis-reg, and Intron) through functional and structural similarities (Nieselt and Herbig 2013). Another criterion used for the classification of ncRNAs is related to size, being separated into small non-coding RNA (sRNA), which are frequently found in bacteria (Nobukazu et al. 2013), and Long non-coding RNA (lncRNA) (Amin et al. 2019), which are uncommon elements in bacteria (Harris and Breaker 2018).

In general, ncRNAs can play important roles in controlling cellular processes in bacteria, such as quorum sensing and biofilm formation (Lo 2018), and acting in gene regulation, metabolism, and physiological adaptations (Zur Bruegge et al. 2017; Harris and Breaker 2018; Amin et al. 2019). They also exhibit different modes of action, such as acting on gene expression by base-pairing with the target messenger RNA (mRNA), as in the case of sRNAs (Gripenland et al. 2010; Nitzan et al. 2017; Svenningsen, 2018). Recent studies show that sRNAs can also directly affect mRNA stability without affecting translation by recruiting degradation machinery or interfering with their action (Durand et al. 2017). In the B. cereus group, studies to date have described the occurrence and functional role of some specific ncRNAs, such as Riboswitches and miRNA, for example (Xu et al. 2015; Tang et al. 2016; Sajid et al. 2018; Nie et al. 2019), but have not analyzed the diversity of these elements.

Therefore, this study describes the first comparative genomic analysis of ncRNAs in the B. cereus group aiming to understand the distribution and diversity of these elements in the bacteria of the group, and thus, contributing to their taxonomy/phylogenetic framework discussions. Our results demonstrate that the three main species of the group have a rich profile of ncRNAs, that a great number and diversity of these genetic elements are shared among the three species, and that B. thuringiensis has the highest number of elements, which may help improve the abilities of these species to adapt to various environmental changes.

Materials and methods

The pipeline of tools used in this study is described in Fig. 1.

Fig. 1
figure 1

Pipeline of the tools used in this study

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Genome mining

The B. cereus, B. thuringiensis, and B. anthracis strains with the complete genome sequences available in the Gold "Genomes Online Database" (Mukherjee et al. 2019) (https://gold.jgi.doe.gov/) and the NCBI "National Center for Biotechnology Information" (Johnson et al. 2008) (https://www.ncbi.nlm.nih.gov/genome) databases up to 09/15/2017 were selected for this study. In cases of duplicate genomes with the same nomenclature, both genomes were kept in the analyses due to variations observed in replicon size and the number of plasmids and ncRNAs analyzed in later steps.

In silico identification and classification of ncRNAs

The complete genome sequences were used for ncRNA search and annotation using the cmsearch tool contained in the Infernal program package, "INFERence of RNA ALignment" (Nawrocki et al. 2009) (http://eddylab.org/infernal/) version 1.1.2. Covariance models were extracted from the RNA families database, Rfam (Kalvari et al. 2018) (http://rfam.xfam.org/) version 13.0 (downloaded in 09/2017). In total, 2,686 families and 191 covariance models were used, restricted to families already identified as being in Bacillales, following criteria previously established by Nawrocki (2014). The following criteria or quality filters were employed for investigation: Only sequences that achieved an E-value of 0.01 were used; the tRNA, tmRNA, 5.8S rRNA, and 5S rRNA families (with no regulatory role) were removed from the analysis because they were not the focus of the study; and the lowest-scoring overlaps identified by cmsearch, with the cmsearch_tblout_deoverlap tool version 0.02 (https://github.com/nawrockie/cmsearch_tblout_deoverlap), were removed.

To visualize the distribution of the identified ncRNAs among the genomes, the jVenn tool (Bardou et al. 2014) (http://jvenn.toulouse.inra.fr/app/index.html) was used and edited with the online tool (https://miro.com/). Regarding their occurrence, ncRNA families were classified into three categories: i) common: present in all three species; ii) shared: present in two species and iii) exclusive: present in a single species.

The identified families of ncRNAs were classified into functional/structural categories, classes, and subclasses as described in the Rfam database or literature. The ncrDeep tool was used to identify families whose class information was not described (Chantsalnyam et al. 2020) (http://nsclbio.jbnu.ac.kr/tools/ncRDeep/).

Finally, we separated the ncRNAs according to size, unrelated to the functional/structural categories or classes, thus, we considered as sRNAs the families with up to 500 bp and lncRNAs over 500 bp. For this, we used the Rfam database (Nawrocki et al. 2015).

Statistical analysis

To investigate the relationship between the number of ncRNA families and the size (bp) of chromosomes and plasmids, a normality test (Shapiro–Wilk) and correlation analysis (Spearman's) were performed. The Kruskal–Wallis test was performed to analyze the variance among the three species under study. To analyze the differences between strains in Cluster III and strains in Cluster IV of the MLST, the Mann–Whitney test was performed. These analyses were carried out using SPSS version 25 software.

Multiple locus sequence typing, MLST

The partial sequences of seven housekeeping genes (glpF, gmk, ilvD, pta, pur, pycA, and tpi) from all selected genomes were retrieved via the PubMLST web tool (Jolley et al. 2018) (https://pubmlst.org/), using the MLST strategy described by (Priest et al. 2004) for the B. cereus group. The sequences were concatenated and the resulting sequences from each genome were aligned using the MEGA package version 7.0.26 (Kumar et al. 2016) (https://www.megasoftware.net/). The ClustalW program and neighbor-joining algorithm were used to construct a phylogenetic tree, maintaining the default parameters. Visualization of the phylogenetic tree was performed with the web tool iTOL version 4 (Letunic and Bork 2019) (https://itol.embl.de/).

Genome alignment

The plasmid sequences (Bt YBT-1520 plasmid pBMB293, Bt YWC2-8 plasmid pYWC2-8–1, Bt Bc601 plasmid pBTBC2, Bt IS5056 plasmid pIS56-285, Bt CT-43 plasmid pCT281, Bt HD-29 plasmid pBMB267, Bt HD-1 plasmid pBMB299, and Bt YBT-1518 plasmid pBMB0232) were compared to the Basic Local Alignment Search Tool (Blastn), using the "align two or more sequences" option (https://blast.ncbi.nlm.nih.gov/Blast.cgi).

The program Mauve (Darling et al. 2004) was used within the Geneious Prime® 2020.1.2 toolkit (Restricted) to align the genome of Bt YBT-1518 with the genomes of phylogenetically closed strains (Bt MYBT1846 and Bt 407). The genomic location of Group II introns between the strains was plotted using the ClicoFS tool (http://clicofs.codoncloud.com/).

Evaluation of ncRNA expression

Strains and growth conditions

The expression of ncRNA genes was evaluated in the B. thuringiensis var. thuringiensis 407 Cry- strain (Vilas-Bôas et al. 1998). For DNA extraction, the strain was grown at 30 °C in a liquid Luria–Bertani (LB) medium. For RNA extraction, the strain was grown in LB medium, also at 30 ºC, in triplicate and monitored until it reached O.D600 of around 0.8, corresponding to the end of the logarithmic phase (Gilois et al. 2007).

Selection of ncRNA genes and primer design for validation

We evaluated the expression of some ncRNA genes identified in the researched genomes. We selected genes with low copy numbers (between 1 and 6), with a minimum size of 80 nt, that had been identified in the genome of Bt407 Cry− (the strain used for the gene expression assays), that were present in strains from different clusters of the phylogenetic tree, and that were not found inside genic/ORF regions. The genomic coordinates of these genes in the reference strain (Bt407 Cry−) were identified using the INFERNAL program and used, along with the U-gene program version 1.17.0 (Okonechnikov et al. 2012), to extract the sequences of each element selected for validation. The sequences of the primers and their properties, such as melting temperature and size of the amplified product, are listed in Online Resource Table 3. The primers were synthesized by Invitrogen™.

DNA extraction

DNA samples from the B. thuringiensis 407 Cry- strain were extracted using the Wizard® Genomic DNA Purification kit (Promega), following the protocol for Gram-positive bacteria, with adaptations. Thus, a treatment with 120 µL of lysozyme (10 mg/mL) was added at 37 ºC for 1 h in the step prior to cell lysis. At the end of the extraction procedure, the DNA was rehydrated with 20 µL of DNA Rehydration Solution.

RNA extraction and cDNA synthesis

Total RNA extraction was performed using the lllustra™ RNAspin Mini RNA kit (GE Healthcare illustra™) with adaptations. Initially, centrifuged cell samples were homogenized with 350 μL of lysis buffer, 3.5 µL of β-mercaptoethanol, and glass beads (2 mm) to lyse the cells through vortex agitation. The following steps were performed in accordance with the kit protocol, including a DNAse digestion. RNA was eluted by adding 50 µL of RNAse-free water.

The cDNA was obtained by reverse transcription of total RNA in a 20 µL reaction using the High-Capacity cDNA Reverse Transcription kit (Applied Biosystems™), according to the manufacturer's recommendations. The quality of the RNA and cDNA was analyzed using a Nanodrop 2000 spectrophotometer.

PCR amplification from cDNA

For validation, the obtained cDNA was used to amplify each of the selected ncRNAs. The reactions were carried out in an Applied Biosystems™ A24811 thermal cycler with the QIAGEN TopTaq Master Mix kit following the manufacturer’s specifications and using the primers presented in Online Resource Table 3. PCR products were analyzed on 1% agarose gel electrophoresis, stained with SYBR Safe (Invitrogen™), and visualized in an L-PIX EX photo documentation system (Loccus Biotechnology) with a K9-100L molecular weight marker (1 kb) from Kasvi. Water (negative control) and DNA (positive control) were used as controls of the PCR reactions. In standardization reactions, PCR products were not found when the RT-PCR reactions was run with samples from RNA extraction that were not reversely transcribed (data not shown).

Results

Genomic aspects and in silico identification of ncRNAs

The mining of genomic sequences enabled the selection of 132 complete genomes, with 44 being B. cereus, 40 being B. thuringiensis, and 48 being B. anthracis. Chromosome size varied slightly among species, with B. anthracis having the lowest chromosome variation (from 5.20 to 5.25 Mb) and B. thuringiensis having the highest variation (from 5.21 to 6.00 Mb). The GC content of the chromosomal sequences was about 35%, and no differences were observed among the three species (Online Resource Table 4).

Figure 2A graphically presents the chromosomal size (Mb) and number of chromosomal ncRNAs of each strain studied; they are represented by spots. The data from the three species enabled us to identify three distinct clusters. The first one, positioned around 5.20 Mb, was composed by three strains of B. cereus and all strains of B. anthracis, indicating that this last species showed little variation in chromosome size and number of ncRNAs identified. The second cluster, positioned between 5.20 and 5.60 Mb, was composed of most B. cereus strains grouped with some B. thuringiensis strains, which demonstrates that these species showed more variation in number of ncRNAs and chromosome size as compared to B. anthracis. The third cluster, composed exclusively of B. thuringiensis strains, positioned between 5.60 and 6.00 Mb, demonstrates that some strains of this species showed greater chromosome size than the other evaluated strains. Four strains were not included in the clusters because they presented divergent chromosome sizes. One example is strain Bt YBT-1518, which had the largest chromosome among all studied (6.00 Mb) and the highest number of ncRNAs identified (332).

Fig. 2
figure 2

Scatter plots representing the correlation between replicon size and the number of ncRNAs identified in the three species. Each spot corresponds to a replicon of a B. cereus s.l. strain. The red lines represent the Coefficients of Determination R2. A Chromosomes–the blue circle represents the chromosome clustering of the B. anthracis strains with some strains of B. cereus. The red circle represents the chromosome cluster of the B. cereus and B. thuringiensis strains. The green circle represents the chromosome cluster of the B. thuringiensis strains. B Plasmids–the black circle represents a cluster of plasmids with high numbers of identified ncRNAs

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Distribution analysis between chromosome size and the number of ncRNAs was calculated by the Shapiro–Wilk normality test, which showed that the data did not show a normal distribution (W = 0.778, p value < 0.05, and W = 0.543, p value < 0.05, respectively). Spearman's test indicated a high positive correlation (Rho = 0.811, p value < 0.01 and Linear R2 = 0.524) between number of ncRNAs and size (in bp) of chromosomes. This reveals that as the size of a chromosome increases, the number of identified ncRNAs increases as well.

The number of identified chromosomal ncRNAs varied among strains (Table 1). The Kruskal–Wallis test demonstrated that the number of ncRNAs differed significantly (p < 0.001) among the three species. Thus, the results of this study demonstrated that B. anthracis strains showed the smallest average chromosome size and the smallest average of ncRNAs. Similarly, B. thuringiensis strains presented both the largest average chromosome size and the highest average of chromosomal ncRNAs (Table 1), which may be due to the existence of B. thuringiensis strains with chromosome enlargement (Fig. 2A).

Table 1 Genetic data and presence of chromosomal and plasmid ncRNA in B. cereus, B. thuringiensis and B. anthracis
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Analysis of the plasmid content of the 132 selected genomes identified 386 plasmids. Plasmids were not found in all strains of the three species, but were greater among B. thuringiensis strains, which also showed the highest average of plasmids per strain (Table 1). The average genome increase caused by the presence of plasmids was also higher among B. thuringiensis strains (12%), reaching 24% in Bt MC28 and Bt IS5056 strains (Online Resource Table 4). Among B. cereus strains, the presence of the plasmids led to an average increase of 6% in genome size, with a maximum of 14% in Bc 03BB108 and Bc C1L; in B. anthracis, the average increase was 5%, with a maximum of 6% in Ba 14RA5914 (Online Resource Table 4). The GC content among plasmids of the three species was similar: B. cereus plasmids averaged 33.21%, B. thuringiensis 33.28%, and B. anthracis 32.77%, as expected for species with a common ancestral origin (Nishida 2012).

Among the B. anthracis strains, ncRNAs were identified in all plasmids, while in the other two species, ncRNAs were identified in 58% and 61% of the plasmids of B. cereus and B. thuringiensis, respectively (Table 1). The Kruskal–Wallis test showed no significant difference in the number of ncRNAs identified in the plasmids of the three species (p = 0.107).

The Shapiro–Wilk test for all 386 plasmids evaluated in this study demonstrated that the size in bp and the number of ncRNAs did not follow a normal distribution (W = 0.798, p value < 0.05, and W = 0.639, p value < 0.05, respectively), while Spearman's test demonstrated a moderate and significant correlation between plasmid size and the number of ncRNAs (Rho = 0.625, p value < 0.01). Figure 2B illustrates that many plasmids follow the trend of the straight line, while others are located distantly, indicating a moderate linear relationship between the variables.

In addition, some plasmids (black circle) showed a high number of ncRNAs compared to other plasmids of the same size (from 150 to 350 kb). Blastn alignment demonstrated that these plasmids are similar to each other because they showed identity values between 87.07 and 100.00 and coverage ranging from 58 to 99% (Online Resource Table 5), except for plasmid pBMB0232 from the B. thuringiensis strain YBT-1518, which obtained the lowest coverage among the strains (0% to 2%). Analysis of these plasmids identified only Group II Introns, indicating that the presence of this genetic element precedes the dispersal and diversification events of these plasmids among B. thuringiensis strains.

Figure 2B highlights two other plasmids from B. thuringiensis strains, which showed the highest amounts of ncRNAs identified in a single plasmid. The plasmid pBMB0233 with 240.661 kb, from strain YBT-1518, has 24 ncRNAs, as well as plasmid pYC1 with 761.374 kb, from strain YC-10, has 33 ncRNAs. Furthermore, the bottom of Fig. 2B reveals some large B. cereus plasmids that have no ncRNAs or only one ncRNA—for example, the unique plasmid from B. cereus strain FM1 with 402.61 kb and plasmid pRML01 from Bc strain HN001 with 435.42 kb. Sequence alignment of these plasmids by Blastn showed low identity and coverage values (data not shown), indicating that these plasmids did not have the same genetic origin.

Identification and occurrence of ncRNA families

One of the objectives of this study was to verify the occurrence of ncRNA families in B. cereus s.l. We identified 65 families of ncRNAs among the three species, which were assigned as described in the Rfam database. B. thuringiensis is the species with the highest number of families, a total of 64, while B. cereus presented 55 families and B. anthracis presented 43 families (the least) of ncRNAs (Online Resource Fig. 6, Table 1). Through the Kruskal–Wallis test, we identified that the difference in the number of families between species was significant for the chromosomes (p < 0.001), while there was no difference for the plasmids (p = 0.051) (Table 1).

Most of the families (43 of 64) were classified as common (Online Resource Fig. 6). In addition, B. cereus and B. thuringiensis strains shared 11 families. However, B. anthracis strains did not share ncRNA families with the other two species separately (Online Resource Fig. 6 and Online Resource Table 6). In addition, 10 families exclusive to B. thuringiensis strains, and one family exclusive to B. cereus strains, were identified (Online Resource Fig. 6 and Online Resource Table 6). Together, these data indicate that ncRNA acquisition occurred both at the common ancestor of the three species (ncRNA families classified as common) and after separation from B. anthracis (ncRNA families shared between B. cereus and B. thuringiensis). Moreover, after the separation between the latter two species, B. thuringiensis strains continued to acquire ncRNAs at a higher frequency than B. cereus strains, as they had a higher number of unique families.

Among the common families, most are located on chromosomes such as the SurA, BtsR1, and RsaE families, which are related to sporulation (Silvaggi et al. 2006; Irnov et al. 2010), defense and pathogenicity (Peng et al. 2018), oxidative stress (Durand et al. 2017; Marincola et al. 2019), and virulence (Geissmann et al. 2009; Guillet et al. 2013). The chromosomal copy number per strain was highly variable among the families (Table 2 and Online Resource Table 6), but the copy number of each family was similar among the three species. In plasmids, the occurrence of the ncRNA families was always a single copy or a low copy number (Table 2). A few families located both on chromosomes and on plasmids were also identified (T-box, BsrC, crcB, cspA, Intron_gpI, RsaE, SAM, SurA, ykok, Intron_gpII, group-II-D1D4-5, yidF, and L21_leader) (Online Resource Table 6). A large proportion of these families are present on the chromosomes of most strains, whereas on plasmids they were found in few strains, except for the group-II-D1D4-5 and Intron_gpII families, which were identified in high copy number on a larger number of B. thuringiensis plasmids.

Table 2 Distribution of ncRNA families identified in B. cereus s.l
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Of the 11 families shared by B. cereus and B. thuringiensis, six were found exclusively on chromosomes (5_ureB_sRNA, Histone, rli38, rsaJ, sau-5971, and group-II-D1D4-4). Three were found exclusively on plasmids (Bacillus-plasmid, CRISPR-DR43, and rliF) and two were found on both chromosomes and plasmids (epsC and rli40) (Online Resource Table 6). In addition, all families of ncRNAs classified as shared were found in a single copy or a low copy number on chromosomes and plasmids (Table 2).

Of the families identified exclusively in a single species, the one exclusive to B. cereus (tsr25) was detected only on the chromosome of a single strain, sequenced twice, Bc E33L (CP000001.1 and CP009968.1). Meanwhile, from the 10 families exclusive to B. thuringiensis (Online Resource Table 6), five were identified only on chromosomes (ncr1175, PyrG_leader, rliI, RNAI, and ykkC- ykkD), two were identified only on plasmids (group-II-D1D4-2 and mir-10), and three were present on chromosomes and plasmids (group-II-D1D4-1, group-II-D1D4-3, and group-II-D1D4-6) (Online Resource Table 6). Most of these exclusive families also showed a limited ability to spread in the group, occurring in few phylogenetically related strains and in a single copy, except for group-II-D1D4-1, group-II-D1D4-2, group-II-D1D4-3, and group-II-D1D4-6, which occurred in a higher percentage of strains and in more copies than the other exclusive families (Table 2 and Online Resource Table 6).

In this study, we separated the ncRNAs according to size, unrelated to the functional/structural categories or classes, thus, we considered as sRNAs the families with up to 500 bp and lncRNAs over 500 bp. Thus, 63 families were classified as sRNAs and their copy numbers varied from 0 to 48 among strains (Table 2). Two families (SSU_rRNA_bacteria and LSU_rRNA_bacteria) were classified as lncRNA and identified with 10–16 copies per strain. Therefore, most of the identified families belong to the sRNA class, as previously described in other bacterial groups (Mars et al. 2016; Wolf et al. 2018), also confirming the low occurrence of lncRNAs for the B. cereus group.

Functional/structural categories and classes of ncRNAs

Through the Rfam database and literature (Li et al. 2016; Fiannaca et al. 2017; Harris and Breaker 2018; Amin et al. 2019; Lee et al. 2019; Drecktrah et al. 2020; Geissler et al. 2021), all identified families were distributed into three functional/structural categories, nine classes, and three subclasses (Fig. 3 and Table 2). Each functional/structural category was investigated for relative abundance. Thus, the functional/structural category with the highest abundance in B. cereus s.l. was Cis-reg with 67.78%, followed by Gene with 25.28% and Intron with the lowest abundance of 6.94% (Fig. 3). Among the classes, Riboswitch, Leader, rRNA, sRNA, and Group II introns accounted for between 37.83% and 5.85% of the ncRNA molecules, while the classes with the lower abundance were Group I introns, ribozyme, miRNA, and CRISPR, reaching up to 1.09% each (Fig. 3).

Fig. 3
figure 3

Functional/structural categories and classes of ncRNAs identified in chromosomes and plasmids of B. cereus, B. thuringiensis, and B. anthracis. *Boxes with dotted borders represent the number of families of each class

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The occurrence of ncRNA classes varied between chromosomes and plasmids. Thus, the Leader, Riboswitch, and sRNA were identified mainly on chromosomes, whereas the Group II introns class was identified on both chromosomes and plasmids (Table 2). In addition, the number of families identified in B. cereus s.l. for each class was investigated. The sRNA presented 23 families that can regulate the expression of target genes at the post-transcriptional level (Sajid et al. 2018; Sridhar and Gayathri 2019). The Riboswitch presented 21 families; this class contains ncRNAs capable of controlling gene expression at the transcriptional and translational levels (Hör et al. 2018) and, then, to respond to environmental changes. With seven families, the Leader class is composed of ncRNA families that regulate translation (Irnov et al. 2010) and interact with metabolism-related proteins (Xia et al. 2012). The Group II introns contained seven families; these elements are ribozymes that act as mobile genetic elements, predominantly as retroelements (Harris and Breaker 2018; Toro et al. 2018; Fayad et al. 2019).

Among the classes found to have a lower incidence, ribozyme and rRNA were composed of two families, whose function is to catalyze reactions, such as RNA splicing, RNA cleavage, and protein synthesis (Moore and Steitz 2002; Lehmann and Schmidt 2003; Skilandat and Sigel 2013). The CRISPR, miRNA, and Group I introns are represented by a single family (Fig. 3, Table 2). CRISPR can provide defense mechanisms against viruses and may be inactivated in some strains (Grissa et al. 2007; Zheng et al. 2020), miRNA has already been described as acting in insect resistance to B. thuringiensis (Xu et al. 2015), while Group I introns have the same function as elements of the Group II introns (Harris and Breaker 2018).

Group II introns

Since the class of Group II introns (Group-II-D1D4 and Intron_gpII) correspond to 77% of the ncRNAs identified in B. thuringiensis plasmids and to 72% and 62% in B. cereus and B. anthracis plasmids, respectively, it was further analyzed in both chromosomes and plasmids. The sum of these elements found on the chromosomes of all B. thuringiensis strains was 487 copies, 103 copies on all B. cereus strains, and no copies on the chromosomes of B. anthracis. The Kruskal–Wallis test for the number of Group II introns in the chromosomes showed a significant difference between B. cereus, B. anthracis and B. thuringiensis species (p < 0.001). This result highlights the great number of these elements in B. thuringiensis strains, especially on the strain Bt YBT-1518 that showed about one-third (32.6%) of the Group II introns from this species. Hence, a total of 159 copies of Group II introns were identified on the chromosome of the Bt YBT-1518 (Fig. 4) and when this strain was compared to the three species, the difference was statistically significant (p < 0.001).

Fig. 4
figure 4

Quantity of class Group II introns on the chromosomes and plasmids. Compared to the quantity identified in the B. thuringiensis strain YBT-1518

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Among the plasmids, 503 copies of Group II introns were identified in B. thuringiensis strains, while 121 copies were identified in B. cereus, and 93 copies were identified in B. anthracis (Fig. 4). The Kruskal–Wallis test for the number of Group II introns in the plasmids also showed a difference between the three species—B. cereus, B. thuringiensis, and B. anthracis (p < 0.001). However, we observed that B. cereus and B. thuringiensis exhibit no significant difference regarding the copy number of Group II introns (p = 0.495), while the pairwise analysis showed that B. anthracis is different from the other two species (Ba-Bc p = 0.011; Ba-Bt p < 0.001). Similarly, to the chromosomes, the plasmids of the strain Bt YBT-1518 showed a remarkable number of Group II introns, corresponding to 10% of the elements found in all B. thuringiensis plasmids. Therefore, Bt YBT-1518 showed 42 copies in four plasmids (three copies in plasmid pBMB0229, three copies in pBMB0230, 13 copies in pBMB0232, and 23 copies in pBMB0233). In addition, when Bt YBT-1518 was compared to B. cereus, B. thuringiensis, and B. anthracis, the Kruskal–Wallis test demonstrated a statistically significant difference (p = 0.004), indicating that the distribution of these elements in this strain is significantly different from the distribution in the plasmids of the three species.

From the first analysis, concerning the correlation among the replicons and the number of copies of ncRNAs, the strain Bt YBT1518 has already shown a divergent profile of ncRNAs content, with the highest number of chromosomal ncRNAs identified among all the evaluated strains and with a higher number of ncRNAs in the plasmids than other strains. Given the results for Group II introns, we observe that these elements are responsible for the higher number of ncRNAs in this strain. Due to this atypical profile, the statistical analyses between the species were also performed excluding Bt YBT1518. However, the result of the analysis of variance did not change, so we retained Bt YBT1518 in the overall comparative analyses.

Therefore, the genomic context of these elements was analyzed by aligning the chromosomal sequence of Bt strain YBT-1518 with the chromosomal sequences of Bt strain MYBT1846 and Bt 407 (Online Resource Fig. 7 A), which are closely related phylogenetically. Thus, on the chromosome of Bt strain MYBT1846, four copies of the Group II class introns were identified, whereas in Bt strain 407, six copies were identified (Online Resource Fig. 7 A). Elements belonging to the class Group II introns were detected both in highly conserved regions and in regions with low conservation among the three genomes (Online Resource Fig. 7 A). This result indicates that the acquisition and spread of these elements in strain Bt YBT-1518 took place after the evolutionary divergence of the three strains. This statement is also true for plasmid analysis, as these elements were observed in the plasmids of Bt strains MYBT1846 and Bt 407, although in smaller quantities (Online Resource Fig. 7 B), as compared to the occurrence in the plasmids of Bt strain YBT-1518.

Correlation between ncRNAs and phylogeny

Due to the complex taxonomic and phylogenetic relationships among B. cereus, B. thuringiensis, and B. anthracis, an MLST tree containing all strains of this study was constructed and classified into clusters according to Guinebretière et al. (2008). Moreover, we include data about the occurrence of ncRNAs in chromosomes and plasmids, aiming to obtain a profile of the distribution of ncRNAs in correlation with the phylogenetic and ecological classification of these strains.

Analyzing the phylogenetic tree (Additional file 1), one can see that B. cereus and B. thuringiensis strains are distributed all over the clusters, while B. anthracis strains form a highly clonal subcluster that remains separate from the other species, as described previously (Rasko et al. 2005; Tourasse et al. 2011; Bazinet 2017). Cluster IV contains B. thuringiensis strains, widely used as a bioinsecticide, and environmental strains of B. cereus. On the other hand, pathogenic B. cereus strains and B. anthracis strains, in addition to some B. thuringiensis strains, are part of cluster III.

Concerning ncRNA, the families common to the three species were present in most of the strains in all clusters and represent the majority of ncRNA families. Meanwhile, most of the ncRNA families shared between B. cereus and B. thuringiensis showed a limited ability to spread, being shared mainly by a few phylogenetically related strains (Additional file 1), except for Histone3, epsC, and rli40 families, which were found in a large number of strains in both clusters (Online Resource Table 6). The exclusive families also had a limited ability to spread in the group, as they were not identified in more than one strain and presented a single copy in the genomes in which they were found, except for the families group-II-D1D4-1, group-II-D1D4-2, group-II-D1D4-3, and group-II-D1D4-6, which are found in many strains and have a higher copy number. Analyzing this information was essential to selecting ncRNAs for use in the PCR expression validation step.

The comparative analysis of ncRNA abundance on chromosomes revealed differences between MLST cluster III and cluster IV. The Mann–Whitney test showed that the distribution of the number of families (p = 0.000) and the number of ncRNAs (p = 0.000) was different between the two clusters. However, in the analysis of ncRNA abundance in plasmids, the Mann–Whitney test showed no difference between clusters III and IV for either the number of families (p = 0.890) or the number of ncRNAs (p = 0.644).

Validation

For the in vitro validation, nine families were selected based on phylogenetic distribution, the abundance of each family in the tree species, and the number of copies in the genomes. These families belong to the three functional and structural categories (Genes, Cis-Reg, and Intron). The description of the families, as well as the primers used, are presented in Online Resource Table 3. All ncRNAs were amplified from the cDNA of B. thuringiensis var. thuringiensis 407 Cry- from the end of the exponential phase with the size corresponding to the amplicon (Fig. 5, Online Resource Table 3). This demonstrates their presence in the RNA samples of the tested strain and confirms their expression.

Fig. 5
figure 5

Validation of the ncRNAs families (Bacteria_large_SRP, BsrF, epsC, Intron_gpI, ncr1575, pan, PyrR, RNaseP_bact_b and RsaE) by RT-PCR. The ncRNAs were checked on agarose gel for presence in DNA and cDNA of the Bt 407 Cry- strain, in a culture with O.D.600 around 0.8. The molecular weight markers are indicated on the left of the image and correspond to the size in bp, and the amplicon on the right

Full size image

Discussion

Bacteria of the Bacillus cereus group colonize several ecological niches and infect different hosts. The phylogeny of this group is complex, with polyphyletic clades and paraphyletic species (Guinebretière et al. 2008; Tourasse et al. 2011; Liu et al. 2015; Bazinet 2017; Raymond and Federici 2017). Recently, a new taxonomic nomenclature, based on an average nucleotide identity genome species threshold (92.5 ANI) was proposed (Carroll et al. 2020). Although ncRNAs have several important physiological roles (Nitzan et al. 2017; Harris and Breaker 2018; Svenningsen, 2018), the role of these genetic elements in this bacterial group is based on studies of specific interest (Xu et al. 2015; Lu et al. 2018; Nie et al. 2019). Thus, in this study, we describe the prevalence, diversity, and genomic localization of ncRNAs in a high number of B. cereus, B. thuringiensis, and B. anthracis strains, and validate the expression of some ncRNAs in Bt strain 407.

The in silico strategy allowed us to identify ncRNA sequences in the chromosomes of all strains studied, with variation in the average number of chromosomal ncRNAs among the three species. The evaluation of the set of selected strains demonstrates that B. anthracis strains showed no variation in chromosome size besides presenting the smallest chromosomes within the group—a result in agreement with the clonality of this species (Rasko et al. 2005; Kolstø et al. 2009). B. cereus strains, in contrast, showed variation in chromosome size, with a gain in genetic material, although this variation was greater among B. thuringiensis strains, as the latter species presented the strains with the largest chromosomes detected, as already observed in other studies (Cardoso et al. 2019; Fayad et al. 2019). Thus, in B. thuringiensis, some strains showed more important genetic material gain than the other strains evaluated in this study. The results regarding the number of ncRNAs in the chromosomes of B. thuringiensis strains reflect these differences in the chromosomal profile of the species due to the positive correlation between replicon size and number of ncRNAs. In addition, the chromosome of B. thuringiensis showed the highest number of families and the highest absolute number of ncRNAs, followed by B. cereus and, finally, B. anthracis.

Strains of B. anthracis exhibit low genetic diversity and are believed to have diverged from an ancestral B. cereus through the acquisition of two large plasmids (pXO1 and pXO2) that contain genes encoding for characteristic virulence factors (Pilo and Frey 2011; Moayeri et al. 2015). Thus, the plasmid content is very similar among their strains (Online Resource Table 6) ( et al. 2000; Helgason; Rasko et al. 2005;). Furthermore, the use of the in silico strategy to search for ncRNAs in plasmids demonstrated that among B. anthracis strains, all analyzed plasmids had ncRNA (Table 1), with minimal variation with respect to the number or variety of families identified. This result, again, agrees with the fact that this species is highly clonal. However, among B. cereus and B. thuringiensis strains, plasmid content is highly variable. Thus, the results of this study demonstrated that the B. thuringiensis species shows a higher percentage of plasmid-bearing strains, as well as a higher number of plasmids per strain; as a consequence, the presence of these plasmids allows for a greater average increase in genome size (Zhong et al. 2011; Patiño-Navarrete and Sanchis 2017; Fayad et al. 2019). In contrast to what was seen for B. anthracis, the presence of ncRNA is not a common feature of all B. cereus and B. thuringiensis plasmids, which can be explained by the wide plasmid network in these species, especially in B. thuringiensis. However, the frequency of plasmids carrying ncRNAs is higher in B. cereus and B. thuringiensis, and the presence of plasmid ncRNAs (in absolute numbers) is higher in B. thuringiensis. This large and diverse plasmid network may have been responsible for the lack of statistical difference in the number of ncRNA among the three species in the analysis of variance.‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬

Concerning the results of ncRNA families in plasmids, we observed a large number of Group II introns on the plasmids of all three species, especially in B. thuringiensis. This class of ncRNAs consists of elements characterized as ribozymes that act as mobile genetic elements (Harris and Breaker 2018; Toro et al. 2018; Fayad et al. 2019). Therefore, the abundance of these elements in B. cereus group strains reinforces the role of horizontal genetic transfer (HGT) in genome plasticity, evolution, and the acquisition of novel ncRNAs, as already observed for Streptococcus agalactiae (Wolf et al. 2018).

Of all the strains with Group II introns analyzed in this study, B. thuringiensis strain YBT-1518 deserves special attention. Our results showed that this strain has a different profile of ncRNAs as compared to all other evaluated strains due to the significant increase in the number of copies of Group II introns. However, the sum of the size of these elements (16.774 kb) were not the main responsible for the increase in the genome size of this strain (chromosome of 6.00 Mb). Furthermore, the presence of these transposable elements in a high copy number did not cause the loss of toxicity, which is active against nematode larvae (Zheng et al. 2016). This toxicity results mainly from the activity of the product of three genes, i.e., one located on the chromosome (cry5Ba2) and two located on the plasmid pBMB0228, app6Aa1 (formerly cry6Aa2) and xpp55Aa1 (formerly cry55Aa1) (Wang et al. 2014; Crickmore et al. 2020).

Regarding the number of ncRNAs that this study identified, we demonstrated the wide prevalence of ncRNAs in the three species studied, especially in B. thuringiensis, which presented a higher number of ncRNA copies and families than the other species. The results presented here, along with previous results from the research group, demonstrate that B. thuringiensis has accumulated different metabolic regulators, both on the chromosome, as in the case of ncRNAs (as demonstrated here), and on plasmids, as can be observed for ncRNAs and Rap-Phr quorum sensing systems (Cardoso et al. 2019). Rap-phr systems regulate essential processes such as sporulation in bacteria of the B. cereus group (Fazion et al. 2018; Cardoso et al. 2019) and were identified in all studied strains, being found in a higher abundance in plasmids of B. thuringiensis than of the other species of the group. Moreover, the accumulation of these systems in B. thuringiensis plasmids may favor a fine regulation of bacterial metabolism to environmental variations (Cardoso et al. 2020). These data are in agreement with the already described plasticity of the B. thuringiensis genome (Gillis et al. 2018), enabling this bacterium to better adapt to the environment, possibly due to its complex ecological niche (Argôlo-Filho and Loguercio 2014; Mishra et al. 2017).

Few studies have conducted broad genomic analysis of ncRNAs in different bacterial strains or groups. However, it is not possible to perform an absolute numerical comparison between these studies and our results because, in addition to interspecific differences, this variation can be attributed to variations in bioinformatics tools that predict and identify ncRNAs. For example, in the annotation study performed by (Geissler et al. 2021), using the Rfam tool, the authors identified 230 ncRNAs in Bacillus subtilis strain 168; however, the number of ncRNAs annotated in this strain changed with other tools: RefSeq = 212; BsubCyc = 183; Dar et al. Riboswitches = 82, and Nicolas et al. Predictions = 153 (Geissler et al. 2021).

However, the results of the comparative analysis of ncRNAs in other bacterial groups highlight the importance of these genetic elements for the adaptation of bacteria to the environment. Thus, Wolf et al. (2018), in a previous work developed by our research group, verified a great variation of ncRNAs in S. agalactiae strains, which were distributed in three clusters, corresponding to different hosts (Cluster 0: fish; Cluster 1: mammals; and Cluster 2: fish and mammals). In addition, they observed a correlation between the number of RNA families and the origin (cluster) of the strains, demonstrating that ncRNAs may be involved with the bacterial-host interaction in pathogenic species.

Other studies have observed that sRNAs can be conserved between related species. Chen et al. (2011) observed, in the genus Clostridium, that many sRNAs are conserved among physiologically related species, mainly for pathogenic species as compared to solvogenic and cellulolytic species. They even showed a correlation between the number of sRNAs and genome size for pathogenic species, hypothesizing that the amount of sRNAs is related to the organism’s physiology (Chen et al. 2011). Similar results were observed in the study by Wurtzel (2012), which compared the transcriptome of Listeria monocytogenes and Listeria innocua, revealing both species-specific and conserved sRNAs. Several of these elements were conserved at the genomic level, but were expressed in only one of the species. This suggests that there is a difference between pathogenic and non-pathogenic species, which indicates that regulation by ncRNAs may be an evolutionary strategy allowing species to rapidly adapt to environmental changes (Wurtzel et al. 2012). The aspects that these different studies observed can be assumed to pertain to the B. cereus group, whose diversity (number of copies and families) may contribute to the establishment of such diverse ecological niches observed among species and strains even if no species-specific ncRNAs have been identified.

Besides the in silico analysis of ncRNAs within the B. cereus s.l., we evaluated the expression of nine families of ncRNAs by RT-PCR; all of them were validated. These results are essential because they confirm the occurrence of these elements previously identified by computational methods. Also, besides being present in the genome, they are transcribed, which leads to a better understanding of these elements in this group of bacteria.

By analyzing the composition, distribution, and number of ncRNAs in B. anthracis, B. cereus, and B. thuringiensis strains, it was possible to obtain an overview of the diversity of these RNAs in this bacterial group. First, we can highlight the wider analysis of ncRNA families in bacteria that had not been classified so far. Furthermore, our results contribute to the discussion of the phylogenetic question of the B. cereus group, as they confirm previous studies indicating that: a) the three species are closely related (high number of common ncRNA families); b) B. anthracis is a clonal species (conserved profile of families and number of ncRNAs) and easily differentiated from B. cereus and B. thuringiensis; and c) B. thuringiensis has the genome with greater plasticity (with more chromosomal ncRNAs and unique families) and B. cereus is in the intermediate position between the two other species. Finally, the acquisition and maintenance of genetic elements that present regulatory profiles in the genomes of B. cereus strains, especially those identified as B. thuringiensis, may lead to advantages regarding their ability to adapt, multiply, and disseminate in different environments. Further studies should address the expression of these genetic elements in different conditions.