Identification of antibiotic producing B. subtilis and field collected bacterial strains
Initially we tested twelveB. subtilis laboratory strains (B. subtilis subsp. subtilis and subsp. spizizenii, respectively), including well established strains from the German Collection of Microorganisms (DSMZ) on their ability to inhibit the growth of M. luteus. Interestingly, a number of B. subtilis DSM strains: DSM 618, 1087, 6395, 6405, and 8439 showed promising antimicrobial activities with growth inhibition activities comparable to the well-characterized subtilin-producing strain B. subtilis subsp. spizizenii ATCC 6633 (representative examples are given in Fig. 2a). The laboratory strains B. subtilis DSM 3256 and DSM 3258 exhibited semi-large inhibition zones. To get more insight into B. subtilis strains without laboratory history we took random soil samples from various environmental habitats, nutrient-rich farmland and forest (200 m altitude, Hesse, Germany) and alpine environments (2000 m altitude, Vorarlberg, Austria). In a first pasteurization step, we were able to select the spore-forming microorganism out of the natural probes, which were single colony streaked on agar plates (40 single colonies, TY medium). Antibiotic producing strains were identified using M. luteus as a highly sensitive Gram-positive target strain using optimized conditions for the detection of lanthipeptides (Heinzmann et al. 2006) and sactipeptides (Stein et al. 2002). Notably, 20 to 25 percent of the isolated aerobically grown spore-formers inhibited the growth of M. luteus (not shown). Twelve probable antibiotic producing strains were selected: Six strains from the farmland (N), one from the forest (IP), and five strains from alpine environments (HS and HI). The strains with large and clear inhibition zones HS and N5, (Fig. 2a), were later identified as producer of subtilin (Sub+, for a summary see Table 1). In contrast, the strains HI1 and IP exhibited relatively small inhibition zones, both strains were found to be Sub− in further investigations (for a summary see Tab.1).
Phylogenetic analyses of laboratory and field-collected Bacillus strains; genomic organization of SSU rRNA encoding rrn alleles of B. spizizenii and B. subtilis
The 16S rDNA of all spore-forming microorganisms examined (laboratory and field-collected strains) were PCR amplified, sequenced, and their nucleotide sequences were taxonomically classified. B. subtilis strains 168 and ATCC 6051 have a total of ten rrn alleles (Tab. S2, Supplement), each 1552-1554 nucleotides in length; MSA analyzes indicated a few (two to three) nucleotide variations within these individual genomes (Tab. S3, Supplement). It is noteworthy, that B. spizizenii ATCC 6633 has ten identical rrn alleles in both length and nucleotide sequence, whereas for its close relative, the W23 strain, only eight rrn alleles (1552-1554 nucleotides) were found. The B. spizizeni typing strain TU-B-10 contains ten rrn genes, but the genome seems to be organized differently: The organization of the first five rrn alleles is similar to the organization of B. subtilis 168 or B. spizizenii ATCC 663, but the positions of alleles 6-10 indicate extensive genetic re-organization (Tab. S2 Supplement).
Notably, the rrn sequences of the field-collected Bacillus strains HS1 and HS2 (hereinafter referred to as strain HS) and N1, N5, and N6 (referred to as strain N5), as well as the laboratory strains DSM 618 and DSM 6405 were identical to rrn sequences of B. spizizenii ATCC 6633 and W23 (data not shown), suggesting their classification as B.spizizenii (Nakamura et al. 1999; Zeigler et al. 2008; Zeigler 2011). On the other hand, the field-collected strains IP and HI1 (referred to as strain HI) as well as the laboratory strain DSM 3258 are classified as further members of B. subtilis (see Fig. 3a for phylogenetic analyses). As indicated in Fig. 3b, MSA analyses revealed that position 181 of the individual rrn alleles can be used for clear species differentiation between B. subtilis and B. spizizenii. Interestingly, position 600 of the B. spizizenii typing strain TU-B-10 is identical to the B. subtilis sequence, whereas a transition (T/C exchange) was found at this position for the B. spizizenii ATCC 6633 and W23 rrn alleles.
BLAST searches revealed, that the field collected Bacillus strains HI2 and HI3 belong to B. macroides and B. licheniformis, respectively. Both species are known for members with a high potential to produce antibiotics. The strain N2 was classified as B. thuringiensis, a class of Bacillus strains some members of which produce the lipopeptide kurstakin (Hathout et al. 2000). No sequence was obtained for strain N3, strain N4 was discarded because no further significant antibiotic activities could be identified under the test conditions used.
SpaS sequence of different B. spizizenii strains, presence of the SpaC protein
For rapid PCR amplification of the subtilin structural gene spaS oligonucleotide primers (SpaS-Seq1 and SpaS_Seq2) complementary to the –35 region of the spaS promoter and the spaS-spaI intergenic region were used. The presence of the spaS gene was verified in the case of B. subtilis strains DSM 618, 1087, 6395, 6405 and 8439, as well as the natural isolates HS and N5 (Fig. 2b; for a summary see Tab.1). Sequences of both the spaS genes and their flanking regions (ribosomal binding site, -10-region) were identical to their counterpart in the ATCC 6633 strain (the GeneBank records for B. subtilis DSM 618, 6405, HS1, and N5 are DQ452514-17, respectively; ATCC 6633: NZ_CP034943.1, and TU-B-10: NC_016047.1). Since the spaS gene was detected within the DNA of all B. spizizenii, we expected also the subtilin maturing proteins in the cultures of these strains. This hypothesis was confirmed by detection of the subtilin cylase SpaC (Fig. 2c) and subtilin dehydratase (SpaB, not shown) within PAGE-separated cell extracts of the W23 strains using SpaC or SpaB specific immunosera, respectively. Most likely, all observed W23-type SpaC proteins are closely related, as EriC of B. subtilis A1/3 with only 85% sequence identity to the SpaC counterpart from the ATCC 6633 strain (Stein et al. 2002a) gave only weak immunoblotting signals. Consistent with these observations is that for the strains which lack spaS (Fig. 2b, strains 168, 3258, HI, and IP), no SpaC protein could be detected in the associated cell extracts either (Fig. 2b); the same applies for SpaB (not shown).
MALDI-TOFMS profiling of B. subtilis culture supernatants
MALDI-TOFMS analyses of butanolic extracts of B. subtilis culture supernatants resulted in well resolved peak clusters (Fig. 4). Prominent cluster between m/z 3280 and 3520 representH+-, Na+- and K+-adducts of the lanthipeptide subtilin and its succinylated species (Chan et al. 1993; Heinzmann et al. 2006) and the sactipeptide subtilosin, respectively (see Tab. 1 for summary). Furthermore, the nonribosomal generated lipoheptapeptide surfactin was identified by MALDI-MS experiments due to characteristic m/z values of its different isoforms. Remarkably, all investigated B. subtilis strains produced surfactin (see Tab. 1 for a summary), notably, with the exception of the laboratory-adapted B. subtilis strain 168, which is known as a surfactin non-producer due to a mutation within the 4’-phosphopantetheine transferase sfp gene which posttranslationally modifies the required surfactin synthetase enzymes (Lambalot et al. 1996). Further MS/MS-fragmentation experiments according to Leenders et al. (1999) unambiguously assign the observed m/z values to the lipoheptapeptide sequence Glu-Leu-Leu-Asp-Val-Leu-Leu which can be clearly assigned to the peptide moiety of surfactin (data not shown). However, the detection of surfactin within the culture supernatants of all investigated B. subtilis strains, and the widespread frequent appearance of the potential to produce surfactin among strains of the genus Bacillus (Peypoux et al. 1999; Kalinovskaya et al. 2002; Torres et al. 2016) restricts the usage of the phenotype “surfactin production” as biomarker for subspecies classification/differentiation (e.g. between B. subtilis and B. spizizenii).
Quantitative determination of subtilin
Subtilin was quantitatively determined in culture supernatants of stationary grown Bacillus cells in Landy medium (Fig. 5a/b). Whereas the production yields of B. subtilis ATCC 6633 (4.9 mg/mL) and the field-collected strainN5 (4.2 mg/mL) were comparable, the strain DSM 618 produces three-fold higher amounts (14.9 mg/mL). The largest subtilin yield was obtained from the laboratory strain B. subtilis DSM 6405 (33 mg/mL) and the field-collected B. subtilis HS (30 mg/mL). Representative chromatograms for these strains are shown in Fig. 5a. A further observation was that the proportion of N-terminally succinylated subtilin also increased with increasing yields of subtilin, especially for the high producer strains 618 and 6405. The production yields of the DSM strains 1087, 6395 and 8439 were similar to the ATCC 6633 strain (data not shown).
GC-Content of the subtilin gene cluster spa
Our results show that for all B. spizizenii strains characterized so far, the Sub+ phenotype is a characteristic feature. The analysis of the base compositions of a given genome is a common strategy to investigate gene history (Garcia-Vallvé et al. 2000; Popa et al. 2001). Remarkably, in all analyzed
B. spizizenii genomes the average GC-content of the subtilin gene cluster with 36 % is significantly lower (about 8 %) than the GG content of about 44 % of respective GC-content average of the respective B. spizizenii host genome (Fig. 6 and Tab S3, supporting information). This observation is a strong hint that B. spizizenii acquired the subtilin gene cluster most likely from another organism by a recent horizontal gene transfer event as is hypothesized for a number of lanthipeptide producers (Zhang et al. 2012).
Nakamura et al. (1999) proposed the classification of Bacillus subtilis strains into two classes: The 168-type strains into (1) B subtilis subsp. subtilis, and W23-type strains into (2) B. subtilis subsp. spizizenii. Classical chemotaxonomy differentiates between both classes by the composition of their cell wall teichoic acids: Whereas 168-type strains are endowed with the essential major teichoic acids poly(glycerol phosphate) and the non-essential minor teichoic acids poly(glucopyranosyl N-acetylgalactosamine 1-phosphate), the W-23-type mainly consists of poly(ribitol phosphate) (Lazarevic et al. 2002). Very recently, B. subtilis subsp. spizizenii was promoted to species status on the basis of comparative genomics and secondary metabolite (mycosubtilin and bacillaene) production (Dunlap et al. 2020). The experiments presented in this study have revealed that all B. spizizenii strains from both laboratory (ATCC 6633, DSM 618, 1087, 6395, 6405, and 8439) as well as natural origin (HS and N5) produced identical mixtures of antibiotics including the lanthipeptide subtilin, the sactipeptide subtilosin, as well as nonribosomally biosynthesized lipopeptides from the surfactin class (Tab. 1). However, the lanthipeptide subtilin cannot be used as a characteristic for closely related species differentiation since the production of subtilin and subtilin-related structures has also been found in B. subtilis A1/3 (Stein et al. 2002a), and other Bacillus strains (Bacillus sp., Velho et al. 2013, (B. mojavensis, Reva et al. 2020; B. vallismortis, Kim et al. 2018; B. intestinalis, Xu et al. 2015).
Our finding that different strains produce different amounts of subtilin - the yield of the HS strain was 7-fold superior to the original subtilin producer B. subtilis ATCC 6633 (Heinzmann et al. 2006), imply differential efficiencies in subtilin production. The examined B. spizizenii strains may have developed different genetic elements for the regulation of the extremely complex system of subtilin biosynthesis, such as repressor (AbrB) or activator (Sigma factor H) elements or variations in the promoter regions (-35 region) (Stein et al. 2002b and 2003; Kleerebezem 2004; Kleerebezem et al. 2004; Spieß et al. 2015). Furthermore, also the subsequent steps in subtilin biosynthesis for example post-translational dehydration of serine (threonine), addition of neighboring cysteines (Kiesau et al. 1997; Helfrich et al. 2007), and final processing (Stein and Entian 2002; Corvey et al. 2003) might exhibit differential efficiency in the investigated strains.
Recently, it was shown that succinylation of subtilin is a consequence of high glucose concentrations in the culture medium, for example the Landy medium (Bochmann et al. 2015). We found especially for the strains with very high production rates of subtilin - HS and DSM 6405, that the proportion of succinylated subtilin species were significantly increased compared to the unsuccinylated species (data not shown). Since N-terminal succinylated subtilin shows less antimicrobial activity, this could also be a necessary self-protection mechanism of B. subtilis cells against the antibacterial effect of their own product (Heinzmann et al. 2006; Geiger et al. 2019). The B. spizizenii strain TU-B-10 turned out to be an extraordinary exception, here the production of a subtilin isoform EtnS (entianin) was identified, which differs from subtilin in three conservative amino acid exchanges: L6V, A15L, and L24I (Fuchs et al. 2011).