Table I
Accessing numbers of P. ostreatus clones sequences deposited in NCBI database with most similar strains from NCBI database.
| NCBI accessing number | Parent strain | Number of clones | The most similar strains in NCBI database | |
|---|---|---|---|---|
| Strain name | Accessing number and similarity (%) | |||
| KR779716 | PxS; PBo6S | 2 | Methylobacterium sp. 63 | JF905617 (99) |
| KR779718 | PBo6S | 1 | Corynebacterium ureicelerivorans IMMIB RIV-2301 | CP009215 (99) |
| KR779719 | PBo6S | 1 | Corynebacterium sp. clone YHSS1 | EF658675 (100) |
| KR779720 | PB8 | 1 | Corynebacterium sp. clone OD-12 | KX379256 (100) |
| KR779721 | PxS; PBo6S; PB7’96 | 4 | Weissella cibaria_BM2 | CP027427 (99) |
| MH424523 | P112 | 2 | Weissella confusa SM10 | KU060300 (100) |
| KR779722 | PBo6S; PB63S; P234; PxS | 5 | Paracoccus sp. clone SL36 | HQ264096 (100) |
| MH424529 | PB7’96 | 1 | Paracoccus yeei TWCC 57946 | LC371258 (100) |
| KR779723 | P234 | 1 | Bacillus sp. 1NLA3E | CP005586 (99) |
| KR779725 | PB7’96 | 1 | Bacillus sp. R-66632 | KT185191 (99) |
| KR779726 | P234; PB8; P112; PBo6S | 8 | Bacillus sp. CHORDb1 | MG995009 (100) |
| MH424530 | P112 | 2 | Bacillus sp. clone D | JX505089 (99) |
| MH424531 | PB8 | 1 | Bacillus megaterium Y103 | MH368091 (99) |
| KR779727 | PxS | 1 | Nocardioides_sp. clone EHFS1_S02a | EU071473 (100) |
| KR779728 | PBo6S; PB7’96 | 4 | Nocardioides terrigena DS-17 | NR_044185 (99) |
| KR779729 | PxS | 1 | Citricoccus sp. PL13f_S6 | JF274870 (99) |
| KR779730 | PxS | 1 | Micrococcus sp. EF1B-B144 | KC545358 (99) |
| MH424533 | P234 | 1 | Micrococcus luteus JGTA-S5 | KT805418 (99) |
| MH424534 | PB8 | 1 | Micrococcus sp. cpRA422 | KJ510213 (100) |
| MH424535 | P112 | 1 | Micrococcus sp. strain CAU1456 | MG214549 (99) |
| MH424536 | P234; PxS | 2 | Micrococcus terreus IHBB 9339 | KU921566 (99) |
| KR779731 | PxS; P112; PB7’96; P234; PB8 | 9 | Pelomonas saccharophila ATCC 15946 | NR_115049 (99) |
| KR779732 | P112; P234; PB8 | 5 | Staphylococcus epidermidis_FDAARGOS_161 | CP014132 (99) |
| MH424568 | PxS | 1 | Staphylococcus epidermidis TWSL_19 | KT184899 (100) |
| MH424569 | PxS | 1 | Staphylococcus caprae OZK14 | KT591476 (99) |
| MH424570 | P112 | 1 | Staphylococcus sp. JCE 11 | LT899997 (100) |
| MH424571 | PB8 | 1 | Staphylococcus sp. clone 12L_53 | KP183056 (99) |
| KR779733 | PB8; PBo6S | 2 | Ralstonia solanacearum RSCM | CP025986 (99) |
| MH426745 | PBo6S | 1 | Ralstonia sp. clone DVBSW_M180 | KF755496 (100) |
| KR779734 | PUSAS; PBo6S; P234; PB7’96; P112 | 11 | Cupriavidus metallidurans Ni-2 | CP026544 (100) |
| MH424572 | PBo6S | 1 | Cupriavidus sp. EF11(2012) | JX912460 (99) |
| KR779735 | PxS; P112 | 2 | Propionibacterium granulosum JCM 6498 | NR_113367 (99) |
| MH424575 | P112 | 1 | Propionibacterium sp. clone JPL-2_O14 | FJ957593 (99) |
| KR779736 | PB7’96; P112; PxS; P234; PB63S; Pbo6S | 11 | Propionibacterium sp. clone 12L_77 | KP183061 (99) |
| KR779737 | PxS; PB8; P234; P112 | 5 | Pseudomonas sp. 09C 129 | CP025261 (100) |
| KR779738 | PB7’96 | 1 | Pseudomonas _uorescens 2F9 | KT695813 (100) |
| MH424593 | PB7’96 | 2 | Pseudomonas__uorescens_PF85 | MF838663 (100) |
| MH424580 | PB8; PB63S | 2 | Pseudomonas simiae strain 4G1010 | KY939757 (100) |
| MH424594 | P112 | 1 | Pseudomonas _uorescens L228 | CP015639 (100) |
| MH424599 | PB7’96 | 1 | Pseudomonas lurida MYb11 | CP023272 (100) |
| KR779740 | P112; PB63S; PB7’96 | 4 | Acidovorax sp. clone M_KL_81_14 | KP967499 (100) |
| MH427201 | PB63S; PBo6S | 3 | Acidovorax sp. clone CSC28 | JN541150 (100) |
| KR779742 | PUSAS | 11 | Escherichia coli DA33137 | CP029579 (100) |
| MH427368 | PUSAS | 21 | Escherichia coli 2012C-4502 | CP027440 (100) |
| KR779743 | PUSAS | 31 | Escherichia coli 2015C-3125 | CP027763 (100) |
| MH427381 | PUSAS | 1 | Escherichia coli 2013C-3342 | CP027766 (100) |
| KR779745 | PxS | 1 | Lactobacillus sakei PR11 | KX139193 (99) |
| MH427585 | PxS | 1 | Lactobacillus sakei DS4 | CP025839 (99) |
| MH427654 | PB8 | 1 | Lactobacillus sakei FAM18311 | CP020459 (99) |
| KR779746 | PxS | 1 | Legionella sp. L-29 | AB856218 (98) |
| KR779747 | PxS | 1 | Finegoldia magna JCM 1766 | NR_113383 (99) |
| KR779748 | PxS | 1 | Sporosarcina psychrophila DSM 6497 | CP014616 (100) |
| KR779749 | PBo6S | 1 | Streptococcus pneumoniae 11A | CP018838 (99) |
| KR779750 | PB8 | 1 | Kocuria rhizophila 3330 | KP345929 (100) |
| KR779751 | PB8 | 1 | Lactococcus garvieae MJF010 | MH057260 (100) |
| KR779752 | P234 | 1 | Del_ia lacustris SH2 | MH014970 (100) |
| KR779753 | P234 | 1 | Pectobacterium carotovorum subsp. brasiliense BC1 | CP009769 (100) |
| KR779754 | P234 | 1 | Oryzihumus leptocrescens S32011-b | AB649006 (100) |
| KR779755 | P234 | 1 | Tumebacillus sp. 7B-408 | KF441681 (99) |
| KR779756 | P112 | 1 | Achromobacter mucicolens OZK37 | KT716268 (100) |
| KR779757 | PB7’96 | 1 | Herbaspirillum sp. WW2 | KU495919 (100) |
| MH427999 | P234; PBo6S; PB8; PB63S; PxS; PB7’96; P112 | 35 | Curvibacter sp. clone Z2_KL_466-12 | KP967473 (100) |
| MH428000 | PB63S, PB7’96; P112 | 3 | Curvibacter sp. clone CX 18.4 | KX260804 (99) |
| MH428038 | P234 | 1 | Acidobacteria clone SEW_08_293 | HQ598999 (99) |
| MH428102 | PB7’96 | 1 | Acidobacteria clone SEW_08_084 | HQ598816 (99) |
| MH428220 | P112 | 1 | Paenibacillus typhae xj7 | NR_109462 (99) |
| MH428377 | P112 | 1 | Paenibacillus marchantiophytorum R55 | NR_148618 (99) |
| MH428379 | P234 | 1 | Acinetobacter sp. SWBY1 | CP026616 (99) |
| MH428572 | P234 | 1 | Acinetobacter towneri MTCC11368T | KM070563 (99) |
| MH428659 | PBo6S | 1 | Streptomyces rishiriensis JCM 4686 | LC002811 (99) |
| MH428674 | PBo6S | 1 | Streptomyces sp. 111013air4 | KP262513 (99) |
| MH428833 | PB7’96 | 1 | Sphingomonas sp. CAU-S5 | MF113252 (99) |
Fig. 1.
Microscopic picture of analyzed oyster mushroom cells treated with fluorescent dyes under the fluorescent microscope. Strains: a) P234, b) PBo6S, c) PB8, d) P112, e) PB63S, f) PUSAS, g) PB7’96, h) PxS. Bacteria-like organisms, marked with white arrows, are visible as small green or yellow-green rods against fungal cells.
Fig. 2.
Bacteria-like organisms microcolonies growing deeply in TSAt medium after 10 days long cultivation. Strains: a) P234, b) PBo6S, c) PB8, d) P112, e) PB63S, f) PUSAS, g) PB7’96, h) PxS.
Fig. 3.
Agarose gel electrophoresis showing products of PCR with 799f and 1942r primers of analyzed oyster mushroom, maize cv. Cyrkon (Zea mays L.) (line C) and bacterial strain Pseudomonas fluorescens PE16 (line PE16) DNA. The product of 700 bp is characteristic for bacterial 16S rRNA, the product of 1100 bp is characteristic for plant mitochondrial DNA. M – marker; B – blind control.
Table II
Number and identification of clones obtained from analyzed P. ostreatus strains.
| Genus | Similarity based on 700 bp sequence of the 16S rRNA gene | Number of clones | Origin P. ostreatus strains | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| The most closely related strain in NCBI | NCBI accession number(% of similarity) | USA | Japan | Poland | |||||||
| PUSAS | PB8 | PB7’96 | PBo6S | P234 | PxS | PB63S | P112 | ||||
| Escherichia | E. coli DA33137 | CP029579 (100) | 64 | 11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| E. coli 2012C-4502 | CP027440 (100) | 21 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| E. coli 2015C-3125 | CP027763 (100) | 31 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| E. coli 2013C-3342 | CP027766 (100) | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Curvibacter | Curvibacter sp. clone Z2_KL_466-12 | KP967473 (100) | 38 | 0 | 6 | 8 | 4 | 6 | 4 | 2 | 5 |
| Curvibacter sp. clone CX 18.4 | KX260804 (99) | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | ||
| Propionibacterium | Propionibacterium sp. clone 12L_77 | KP183061 (100) | 14 | 0 | 0 | 1 | 1 | 2 | 2 | 2 | 3 |
| P. granulosum JCM 6498 | 113367 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | ||
| Propionibacterium sp. clone JPL-2_O14 | FJ957593 (99) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| Bacillus | Bacillus sp. CHORDb1 | MG995009 (100) | 13 | 0 | 2 | 0 | 1 | 2 | 0 | 0 | 3 |
| Bacillus sp. clone D | JX505089 (99) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | ||
| Bacillus sp. 1NLA3E | CP005586 (99) | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | ||
| Bacillus sp. R-66632 | KT185191 (99) | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ||
| Bacillus megaterium Y103 | MH368091 (99) | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Cupriavidus | C. metallidurans Ni-2 | CP026544 (100) | 12 | 2 | 2 | 1 | 3 | 2 | 0 | 0 | 2 |
| Cupriavidus sp. EF11(2012) | JX912460 (99) | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ||
| Pseudomonas | Pseudomonas sp. 09C 129 | CP025261 (100) | 12 | 0 | 2 | 0 | 0 | 1 | 1 | 0 | 1 |
| P. fuorescens PF85 | MF838663 (100) | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | ||
| P. simiae 4G1010 | KY939757 (100) | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | ||
| P. fuorescens L228 | CP015639 (100) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| P. fuorescens 2F9 | KT695813 (100) | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ||
| P. lurida MYb11 | CP023272 (100) | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ||
| Staphylococcus | S. epidermidis FDAARGOS_161 | CP014132 (99) | 9 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 2 |
| S. epidermidis TWSL_19 | KT184899 (100) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| S. caprae OZK14 | KT591476 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| Staphylococcus sp. JCE 11 | LT899997 (100) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| Staphylococcus sp. clone 12L_53 | KP183056 (100) | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Pelomonas | P. saccharophila ATCC 15946 | NR_115049 (99) | 9 | 0 | 2 | 1 | 0 | 2 | 3 | 0 | 1 |
| Acidovorax | Acidovorax sp. clone M_KL_81_14 | KP967499 (100) | 4 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 2 |
| Acidovorax sp. clone CSC28 | JN541150 (100) | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | |
| Weissella | W. cibaria BM2 | CP027427 (99) | 6 | 0 | 0 | 1 | 2 | 0 | 1 | 0 | 0 |
| W. confusa SM10 | KU060300 (100) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | ||
| Micrococcus | M. luteus JGTA-S5 | KT805418 (100) | 6 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Micrococcus sp. cpRA422 | KJ510213 (100) | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Micrococcus sp. EF1B-B144 | KC545358 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| Micrococcus sp. strain CAU1456 | MG214549 (99) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| M. terreus IHBB 9339 | KU921566 (99) | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | ||
| Paracoccus | Paracoccus sp. clone SL36 | HQ264096 (100) | 6 | 0 | 0 | 0 | 1 | 1 | 2 | 1 | 0 |
| P. yeei TWCC 57946 | LC371258 (100) | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ||
| Nocardioides | N. terrigena DS-17 | NR_044185 (99) | 5 | 0 | 0 | 2 | 2 | 0 | 0 | 0 | 0 |
| Nocardioides sp. clone EHFS1_S02a | EU071473 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| Ralstonia | R. solanacearum RSCM | CP02598 (99) | 3 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| Ralstonia sp. clone DVBSW_M180 | KF755496 (100) | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ||
| Corynebacterium | C. ureicelerivorans IMMIB RIV-2301 | CP009215 (99) | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| Corynebacterium sp. clone YHSS1 | EF658675 (100) | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ||
| Corynebacterium sp. clone OD-12 | KX379256 (100) | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Lactobacillus | L. sakei FAM18311 | CP020459 (99) | 3 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| L. sakei PR11 | KX139193 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| L. sakei DS4 | CP025839 (99) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | ||
| Acidobacteria | Acidobacteria clone SEW_08_293 | HQ598999 (99) | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Acidobacteria clone SEW_08_084 | HQ598816 (99) | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ||
| Paenibacillus | P. typhae xj7 | NR_109462 (99) | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| P. marchantiophytorum R55 | NR_148618 (99) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| Acinetobacter | Acinetobacter sp. SWBY1 | CP026616 (99) | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| A. towneri MTCC11368T | KM070563 (99) | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | ||
| Streptomyces | S. rishiriensis JCM 4686 | LC002811 (99) | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| Streptomyces sp. 111013air4 | KP262513 (99) | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ||
| Legionella | Legionella sp. L-29 | AB856218 (98) | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Finegoldia | F. magna JCM 1766 | NR_113383 (99) | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Sporosarcina | S. psychrophila DSM 6497 | CP014616 (100) | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Streptococcus | S. pneumoniae 11A | CPO18838 (99) | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| Kocuria | K. rhizophila 3330 | KP345929 (100) | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Lactococcus | L. garvieae MJFO10 | MH057260 (100) | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Delfia | D. lacustris SH2 | MHO 14970 (100) | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Pectobacterium | P. carotovorum subsp. brasiliense BC1 | CP009769 (100) | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Oryzihumus | O. leptocrescens S32011-b | AB649006 (100) | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Tumebacillus | Tumebacillus sp. 7B-408 | KF441681 (99) | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Achromobacter | A. mucicolens OZK37 | KT716268 (100) | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Herbaspirillum | Herbaspirillum sp. WW2 | KU495919 (100) | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Citricoccus | Citricoccus sp. PL13f_S6 | JF274870 (99) | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Sphingomonas | Sphingomonas sp. CAU-S5 | MF113252 (99) | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Number of diferent clones | X | X | X | 5 | 15 | 16 | 17 | 18 | 17 | 8 | 17 |
| Number of genus | X | X | 32 | 2 | 9 | 13 | 13 | 15 | 13 | 5 | 12 |
| Number of unidentified clones of Bacteria | X | X | 74 | 0 | 6 | 10 | 14 | 10 | 15 | 7 | 12 |
Fig. 4.
Phylogenetic tree of identified bacteria associated with P. ostreatus strains representatives and most similar to them sequences from NCBI database. As an outgroup sequence Thermosipho sp. MV1063 (AJ419874) was used. The scale bar represents the number of changes per nucleotide position. Accession numbers are given at the end of each sequence.
Fig. 5.
Agarose gel electrophoresis showing products of PCR with Cu1AF and Cu2R primers and analyzed oyster mushroom DNA. Visible 140 bp band represents amplified LMCO genes. M – marker; B – blind control.