Biodiversity of Bacteria Associated with Eight  (Fr.) P. Kumm. Strains from Poland, Japan and the USA

MARIUSZ ADAMSKI; STANISLAW J. PIETR

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Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA

MARIUSZ ADAMSKI

STANISLAW J. PIETR

| 28 mar 2019

Polish Journal of Microbiology

Volumen 68 (2019): Edición 1 (March 2019)

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Article Category: original-paper

Publicado en línea: 28 mar 2019

Páginas: 71 - 81

DOI: https://doi.org/10.21307/pjm-2019-009

Palabras clave
biodiversity, associated bacteria, fluorescent microscopy, 16S rRNA PCR

© 2019 Mariusz Adamski and Stanisław J. Pietr et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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.

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.

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.

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.

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.

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
NCBI accessing number	Parent strain	Number of clones	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)

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
	The most closely related strain in NCBI	NCBI accession number(% of similarity)		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	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	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	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
Weissella	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
Paracoccus	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	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	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	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
Paenibacillus	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
Acinetobacter	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	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

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Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA

Article Category: original-paper

Publicado en línea: 28 mar 2019

Páginas: 71 - 81

DOI: https://doi.org/10.21307/pjm-2019-009

Palabras clave
biodiversity, associated bacteria, fluorescent microscopy, 16S rRNA PCR

© 2019 Mariusz Adamski and Stanisław J. Pietr et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

Accessing numbers of P. ostreatus clones sequences deposited in NCBI database with most similar strains from NCBI database.

Number and identification of clones obtained from analyzed P. ostreatus strains.

Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA

Article Category: original-paper

Publicado en línea: 28 mar 2019

Páginas: 71 - 81

DOI: https://doi.org/10.21307/pjm-2019-009

Palabras clavebiodiversity, associated bacteria, fluorescent microscopy, 16S rRNA PCR

© 2019 Mariusz Adamski and Stanisław J. Pietr et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

Accessing numbers of P. ostreatus clones sequences deposited in NCBI database with most similar strains from NCBI database.

Number and identification of clones obtained from analyzed P. ostreatus strains.

Palabras clave
biodiversity, associated bacteria, fluorescent microscopy, 16S rRNA PCR