Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
PCR screening of heterotrophic strains isolated from biofilms of Lake Baikal for PKS and NRPS gene fragments_
| Taxonomy | Number of the strains analyzed | Number of the strains with positive PCR signal | ||
|---|---|---|---|---|
| Phylum | Genus | PKS | NRPS | |
| Firmicutes | Bacillus | 42 | 11 | 33 |
| Paenibacillus | 4 | 4 | 4 | |
| Virgibacillus | 1 | 0 | 0 | |
| Staphylococcus | 2 | 0 | 1 | |
| Proteobacteria | Pseudomonas | 45 | 9 | 26 |
| Aeromonas | 29 | 4 | 2 | |
| Serratia | 3 | 2 | 1 | |
| Rhizobium | 1 | 1 | 0 | |
| Brevundimonas | 1 | 0 | 0 | |
| Massilia | 1 | 0 | 0 | |
| Achromobacter | 3 | 0 | 0 | |
| Stenotrophomonas | 3 | 0 | 0 | |
| Devosia | 1 | 1 | 0 | |
| Hydrogenophaga | 1 | 0 | 0 | |
| Yersinia | 1 | 1 | 0 | |
| Sphingomonas | 1 | 0 | 0 | |
| Iodobacter | 1 | 1 | 0 | |
| Roseomonas | 1 | 0 | 0 | |
| Actinobacteria | Rhodococcus | 2 | 0 | 2 |
| Kocuria | 4 | 2 | 1 | |
| Pseudoclavibacter | 3 | 1 | 0 | |
| Plantibacter | 1 | 0 | 0 | |
| Sanguibacter | 1 | 0 | 0 | |
| Pseudarthrobacter | 1 | 0 | 0 | |
| Microbacterium | 4 | 1 | 1 | |
| Salinibacterium | 1 | 0 | 0 | |
| Streptomyces | 1 | 0 | 1 | |
| Micrococcus | 1 | 0 | 0 | |
| Brachybacterium | 1 | 1 | 0 | |
| Clachiihabitans | 1 | 0 | 0 | |
| Microcella | 1 | 0 | 0 | |
| Bacteroidetes | Flavobacterium | 4 | 2 | 1 |
| Total | 167 | 41 | 73 | |
Antagonist activity (Zimens et al_ 2014), and PKS and NRPS genes in the strains isolated from biofilms of Lake Baikal_
| Strain | Antagonist activity | PCR signal to PKS gene | PCR signal to NRPS gene |
|---|---|---|---|
| Paenibacillus sp. 5A | Ec1*, Ec2, Pa, Bs1, Bs2, Ca, Sa, Ef | + | + |
| Paenibacillus sp. 12A | Ec1, Ec2, Pa, Bs1, Bs2, Ca, Sa, Ef | + | + |
| Paenibacillus sp. 7A | Bs1, Bs2, Sa, Ca | + | + |
| Bacillus sp. 2A | Ec1, Bs1, Bs2, Ca | + | + |
| Bacillus sp. 9A | Bs1, Bs2, Ca, Sa, Ef | + | + |
| Bacillus sp. 2B | Ec1, Bs2 | + | + |
Comparative analysis of the sequences of NRPS genes from heterotrophic bacteria_
| Strain | Clone number | Results of BLAST analysis | |
|---|---|---|---|
| Closest homologs | Homology, % | ||
| Paenibacillus spp. 5A and 12A | 5A-4 | WP_029514857 non-ribosomal peptide synthetase [P. polymyxa] | 95 |
| ADJ56349 fengycin A [Bacillus subtilis] | 56 | ||
| 5A-5, 12A-1, 12A-2 | KOS00083 bacitracin synthetase [P. polymyxa] | 97–100 | |
| ABQ96384 fusaricidin synthetase [P. polymyxa] | 96–99 | ||
| 12A-5 | AKH45460 tridecaptin, TrbE [P. polymyxa] | 96 | |
| KOS03006 fusaricidin synthetase [P. polymyxa] | 96 | ||
| 12A-6 | WP_013310169 NRPS/PKS synthase [P. polymyxa] | 96 | |
| KOS01021 bacitracin synthetase [P. polymyxa] | 94 | ||
| AHM66091 bacillorin synthetase b [P. polymyxa SQR-21] | 94 | ||
| AKH45459 tridecaptin B, TrbD [P. polymyxa] | 93 | ||
| KTS81295 fusaricidin synthetase [P. jamilae] | 92 | ||
| 12A-10 | WP_025721680 non-ribosomal peptide synthetase [P. polymyxa] | 99 | |
| ABQ96384 fusaricidin synthetase [P. polymyxa] | 96 | ||
| KOS01669 bacitracin synthetase [P. polymyxa] | 94 | ||
| Bacillus sp. 2B | 2B-1 | WP_080466694 plipastatin synthetase [B. subtilis] | 100 |
| 2B-3 | CAA49816 surfactin synthetase, srfA [B. subtilis] | 99 | |
| Bacillus sp. 2A | 2A-5 | WP_019712401 plipastatin synthetase subunit B [B. subtilis] | 98 |
| ACX47457 fengycin synthetase B [B. subtilis]. | 98 | ||
| 2A-7 | AOA54360 polyketide synthase PksJ [B. subtilis] | 98 | |
| WP_009967299 non-ribosomal peptide synthetase [B. subtilis] | 99 | ||
| 2A-8 | WP_048654751 surfactin synthetase SrfAA [B. subtilis] | 97 | |
| Bacillus sp. 9A | 9A-1 | WP_047474893 non-ribosomal peptide synthetase [B. amyloliquefaciens] | 99 |
| ASB53193 polyketide synthase PksJ [B. velezensis] | 94 | ||
| 9A-4 | AHW81970 bacillomycin [B. subtilis] | 96 | |
| 9A-8 | WP_064777945 surfactin non-ribosomal peptide synthetase SrfAA [B. siamensis] | 98 | |
| 9A-9 | WP_045925809 non-ribosomal peptide synthetase [B. siamensis] | 98 | |
| CCF05308 iturinA synthetase ItuA [B. velezensis CAU B946] | 93 | ||
The strain screening for the presence of enzyme activity_
| Characteristic | Paenibacillus spp. | Bacillus spp. | ||||
|---|---|---|---|---|---|---|
| 5A | 12A | 7A | 2A | 9A | 2B | |
| Phosphatase | – | – | – | + | + | + |
| Catalase | + | + | + | + | + | + |
| Oxidase | – | + | – | – | – | – |
| Gelatinase | – | – | – | + | + | – |
| Caseinase | + | + | + | + | + | + |
| Amylase | + | + | + | + | + | + |
| Lecithinase | + | + | – | + | + | + |
| Lipase | – | – | – | – | – | – |
| Saccharose | + | + | + | – | – | + |
| Glucose | + | + | + | – | – | + |
| Maltose | + | + | + | – | – | – |
| Fructose | + | + | +g* | – | – | + |
| Galactose | +g | +g | + | – | – | – |
| Lactose | + | + | +g | – | – | – |
| Arabinose | + | + | + | – | – | – |
| Raffinose | + | + | + | – | – | – |
| Rhamnose | +g | +g | + | – | – | – |
| Mannose | + | + | + | – | – | + |
| Xylose | + | + | + | – | – | – |
| Sorbitol | + | + | + | – | – | – |
| Inositol | + | + | + | – | – | + |
| Dulcite | +g | +g | + | – | – | – |
| Mannitol | +g | +g | + | – | – | – |
| Proline | – | – | + | + | + | + |
| Leucine | – | – | – | + | + | + |
| Phenylalanine | – | – | – | + | + | + |
| Alanine | – | – | – | + | + | + |
Comparative analysis of the sequences of PKS gene fragments from heterotrophic bacteria_
| Strain name | Clone number | Results of BLAST analysis | |
|---|---|---|---|
| Closest homologs | Homology, % | ||
| Paenibacillus spp. 5A and 12A | 5A-1, 5A-2, 5A-3, 5A-4, 5A-7, 5A-8, 12A-2, 12A-9 | ACN13122 ketosynthase [Streptomyces sp. G2-4] | 99 |
| WP_053325747 polyketide synthase [P. peoriae] | |||
| WP_013310977 polyketide synthase [P. polymyxa] | 98–100 | ||
| 5A-5,12A-1, 12A-5, 12A-6 | ACX31707 ketosynthase [Streptomyces sp. 28HAO] | 99 | |
| WP_013310977 polyketide synthase [P. polymyxa] | 99 | ||
| 5A-6 | WP_013310977 polyketide synthase [P. polymyxa] | 97 | |
| WP_053325747 polyketide synthase [P. peoriae] | 97 | ||
| 12A-7, 12A-10 | WP_053325746 polyketide synthase [P. peoriae] | 97 | |
| WP_023989388 polyketide synthase [P. polymyxa] | 97 | ||
| 12A-8 | WP_053325746 polyketide synthase [P. peoriae] | 96 | |
| WP_023989388 polyketide synthase [P. polymyxa] | 96 | ||
| Paenibacillus sp.7A | 7A-1, 7A-2, 7A-5, 7A-7 7A-3, 7A-4, 7A-6 7A-8 | AIQ67612 erythronolid synthase [P. graminis] | 96-98 |
| WP_042266339 NRPS/PKS-synthase [P. graminis] | 98-99 | ||
| WP_042266418 polyketide synthase [P. graminis] | 99 | ||
| Bacillus spp. 2A and 2B | 2A-1, 2A-3, 2A-4, 2A-6, 2A-7, 2A-8, 2B-3, 2B-4 | ABR19768 polyketide synthase [B. subtilis] | 98-99 |
| 2A-2 | ABR19764 polyketide synthase [Bacillus subtilis] | 98 | |
| ABR19779 polyketide synthase [Actinomycetales bacterium DA20] | 98 | ||
| 2B-1 | WP_032721576 polyketide synthase [B. subtilis] | 97 | |
| AGA23985 NRPS/PKS-synthase [B. subtilis subsp. subtilis BSP1] | 97 | ||
| 2B-2 | ABR19775 polyketide synthase [B. subtilis] | 98 | |
| 2B-5 | WP_043940121 polyketide synthase [Bacillus sp. YP1] | 98 | |
| WP_009967299 polyketide synthase [B. subtilis] | 98 | ||
| 2B-6, 2B-8 | ACG70843 polyketide synthase [Bacillus sp. WPhG3] | 99 | |
| 2B-7 | ABR19767 polyketide synthase [B. subtilis] | 98 | |
| Bacillus sp. 9A | 9A-1 | AIO09652 ketosynthase [Bacillus sp. LX-110] | 99 |
| 9A-3, 9A-5 | ACG70841 polyketide synthase [Bacillus sp. WPySW2] | 98 | |
| AGL92430 polyketide synthase [B. amyloliquefaciens] | 99 | ||
| 9A-10 | WP_016936042 polyketide synthase [B. siamensis] | 99 | |
| WP_047474891 polyketide synthase [B. amyloliquefaciens] | 99 | ||
Comparative analysis of the sequences of PKS genes from heterotrophic bacteria_
| Strain | Clone number | Results of BLAST analysis | |
|---|---|---|---|
| Homologs with identified protein | Homology, % | ||
| Paenibacillus 5A and 12A | 5A-1, 5A-2, 5A-3, 5A-4, 5A-7, 5A-8, 12A-2, 12A-9 | EJD67453 difficidin synthase, (DfnD) [Bacillus sp. 916] | 71 |
| EIF13796 difficidin synthase, (DfnG) [Bacillus sp. 5B6] | 71 | ||
| 5A-5, 12A-1, 12A-5, 12A-6 | BAP05593 calyculin synthase, (CalE), uncultured [Entotheonella sp.] | 71 | |
| ADN68476 sorangicin synthase, (SorA) [Sorangium cellulosum So ce12] | 71 | ||
| 5A-6 | WP_004619353 erythronolid synthase, [Clostridium papyrosolvens DSM 2782] | 75 | |
| EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6] | 73 | ||
| 12A-7, 12A-10 | ADD82940 batumin synthase, (Bat2) [P. fluorescens BCCM_ID9359] | 70 | |
| ABK51300 bryostatin synthase, (BryC) [Endobugula sertula] | 69 | ||
| 12A-8 | EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6] | 72 | |
| ADN68477 sorangicin synthase, (SorB) [Sorangium cellulosum So ce12] | 72 | ||
| Paenibacillus sp.7A | 7A-1, 7A-2, 7A-5, 7A-7 | AIQ67612 erythronolid synthase, [P. graminis DSM 15220] | 97 |
| 7A-3, 7A-4, 7A-6 | CUB31962 plipastatin synthase, [B. amyloliquefaciens] | 53 | |
| WP004618786 erythronolid synthase, [Clostridium papyrosolvens DSM 2782] | 50 | ||
| 7A-8 | WP_013663185 erythronolid synthase, [Marinomonas mediterranea MMB-1] | 43 | |
| ADB12491 epothilone synthase, (EpoD) [Sorangium cellulosum KYC3013] | 43 | ||
| Bacillus spp. 2A and 2В | 2A-1, 2A-3, 2A-4, 2A-6, 2A-7, 2A-8, 2В-3, 2В-4 | EJD66458 bacillaene synthase, (BaeN) [Bacillus sp. 916] | 85 |
| 2A-2 | BAP05593 calyculin synthase, (CalE), [Entotheonella sp.] | 71 | |
| EJD67453 difficidin synthase, (DfnD) [Bacillus sp. 916] | 70 | ||
| 2B-1 | EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6] | 85 | |
| 2B-2 | EIF13280 bacillaene synthase, (BaeM) [Bacillus sp. 5B6] | 84 | |
| 2B-5 | EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6] | 71 | |
| 2B-6, 2B-8 | EJD66458 bacillaene synthase, (BaeN) [Bacillus sp. 916]. | 87 | |
| 2B-7 | EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6]. | 86 | |
| AFZ90784 bacillaene synthase, (BaeL) [B. methylotrophicus AS43.3] | 86 | ||
| Bacillus sp. 9A | 9A-1 | WP_049628737 difficidin synthase, [Bacillus sp. JFL15] | 98 |
| 9A-3, 9A-5 | EJD66458 bacillaene synthase, (BaeN) [Bacillus sp. 916] | 94 | |
| 9A-10 | EIF13279 bacillaene synthase, (BaeL) [Bacillus sp. 5B6] | 97 | |