1. bookVolume 68 (2019): Issue 1 (March 2019)
Journal Details
License
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English
Open Access

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

Published Online: 28 Mar 2019
Volume & Issue: Volume 68 (2019) - Issue 1 (March 2019)
Page range: 71 - 81
Journal Details
License
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English
Abstract

Few publications report the occurrence of bacteria associated with fungal cells. The presence of bacteria associated with one strain of Pleurotus ostreatus (Fr.) P. Kumm. was described in the literature. We describe the biodiversity of bacteria associated with eight oyster mushroom strains from Japan, Poland, and the USA. The presence of microorganisms associated with all tested P. ostreatus strains was confirmed using fluorescent microscopy. Among 307 sequences, 233 of clones representing 34 genera and 74 sequences were identified as Bacteria. Most of the bacteria associated with the strain PUSAS were related to E. coli and two clones were related to Cupriavidus genus. The biodiversity of clones isolated from fungal strains originating from Japan and Poland ranged from 15 to 32 different bacterial clones. The most often the bacteria related to genus Curvibacter, Pseudomonas, Bacillus, Cupriavidus, Pelomonas, and Propionibacterium were associated with the strains of fungi mentioned above. Laccase-like (LMCO) genes were identified in whole bacterial DNA isolated from the associated bacteria but β-glucosidase and β-xylanase genes were not detected.

Keywords

Introduction

Various types of relationship between two or more organisms are well known among plants and in the animal kingdom. However, little is known about the relationship and interactions between fungi and bacteria. There are three most common types of these relationships. Bacteria can live in the same environment as fungi where both organisms live close to each other but not in direct contact. This kind of relationship is common in various environments like forests, fermented food or animal tissues affected by diseases (Frey-Klett et al. 2011). More complicated type of bacterial-fungal association is mixed biofilms, where bacteria may live on fungal hyphae and are held by the extracellular matrix formed from molecules secreted by both organisms (Donlan and Costerton 2002). This kind of coexistence can be found in medical equipment (Pierce 2005) as well as in some infections (Hogan et al. 2007) or mycorrhizal systems (Sarand et al. 1998). The third type of interactions between these two groups of organisms is endosymbiosis when bacteria live inside fungal cells and do not produce any specific structures. It is the most complex type of relationship and often, in contrast to free-living fungi-associated bacteria it is impossible to cultivate such bacteria outside a fungal host. The presence of unculturable endosymbiotic bacteria was described mostly in cells of arbuscular mycorrhizal fungi belonging to Gigasporaceae family (Bianciotto et al. 1996, 2000, 2003; Bonfante 2003; Cruz et al. 2008). The endosymbiotic bacteria were also observed in the cells of pathogenic fungus Rhizopus microsporus although in this case, authors were able to grow isolated bacteria on microbiological media (Partida-Martinez et al. 2007a; 2007b). Among Basidiomycota such relationship was found in Laccaria bicolor. Similarly to Gigaporaceae endosymbionts, these bacteria were also unculturable (Bertaux et al. 2003). Only one report described bacteria of Burkholderia cepacia complex related with oyster mushroom P. ostreatus. Authors, however, did not establish if these bacteria are endosymbionts or just fungi-related organisms (Yara et al. 2006).

The aim of this work was to identify bacteria associated with eight P. ostreatus strains, and also the description of their biodiversity and assessment of their ability for N2 fixation, cellulose, xylanase, and laccase-like multicopper oxidase activity.

Experimental
Materials and Methods

Fungal strains. Eight strains from different geographical zones (PB63S, PBo6S, PxS, P234, P112 – Poland; PB7’96, PB8 – Japan, PUSAS – the USA) of P. ostreatus were analyzed. All strains were shared by the Department of Fruit, Vegetable and Mushroom Technology at the University of Life Sciences in Lublin. According to our knowledge, the strains analyzed were never cultivated on media containing antibiotics. Before experiments the fungal strains were cultivated for seven days in 28°C on Petri dishes with onion medium (onion extract 1000 ml (150 g of chopped onion boiled in 500 ml distilled H2O, filtered on cotton filter and filled with distilled H2O to 1000 ml, glucose 20 g, peptone 3 g, KH2PO4 1 g, MgSO4 0.5 g, agarose 20 g).

Observation of bacteria-like organisms associated with P. ostreatus. Observation of living bacteria-like organisms associated with fungal cells was carried out using a fluorescent microscope and a set of fluorescent dyes (Bianciotto et al. 2000). Total fungal mycelium from one Petri dish of every oyster mushroom strain cultivated for seven days was collected and grounded in a sterile glass mortar in 1 ml of sterile 0.1 M MgSO4. The obtained suspension was stained in a 50-μl volume with the fluorescent dye (Viability/Cytotoxicity Assay Kit for Bacteria, Biotium, USA) according to the manufacturer’s protocol. Observations were made using Nikon Eclipse 90i fluorescent microscope with the Omega XF25 filter. Pictures and videos were taken in the same conditions. The fluorescent kit used in the experiments is composed of two dyes. DMAO migrates through a cell membrane and stains double-stranded DNA of both living and dead bacteria on green or yellow-green color. The second dye, EthD-III migrates through damaged membranes of dead cells only and stains bacterial DNA on red color. This dye is stronger than DMAO and covers its color, thus dead bacteria are visible as red and live bacteria are visible as green or yellow-green organisms.

Isolation of organisms associated with P. ostreatus. Isolation of organisms associated with fungal strains was done from seven-days old fungal culture. The 16 mm diameter roundel was picked and placed mycelium towards to the medium on base and modified solid TSB medium (Sigma-Aldrich, USA), called later in this article as TSAt. The modification consisted of the addition of 1% of Tween 20 to the medium (ApliChem GmbH, Germany) as described by Yara et al. (2006). After 14 days of cultivation in 28°C, 25-mm2 square area of the solid medium with visible microcolonies was picked and placed in 50 ml of liquid TSBt medium (TSB with 1% of Tween 20) in Erlenmeyer flasks. Samples were cultivated for 14 days in 28°C stationary. After cultivation TSAt fragment was removed from samples and samples were centrifuged in 10 000 × g for 10 minutes. The supernatant was poured out and the precipitate was used for further experiments.

DNA isolation. Genomic DNA was extracted from precipitates using Genomic Mini AX Bacteria (A&A Biotechnology, Poland) according to the instructions of the manufacturer. The obtained DNA was purified with PowerClean DNA Clean-Up Kit (MO BIO Laboratories, Inc., USA) in accordance with the manufacturer’s protocol. Purified DNA was stored at −20°C for further experiments.

The identification of the associated organisms was performed using whole DNA isolated from fungal strains. Fresh fungal mycelia were harvested from 25 mm2 square area of the solid medium of 7 days old fungal colonies, then suspended and rubbed in 1 ml of 0.1 M MgSO4 in sterile glass mortars. Suspension in a volume of 100 μl of each fungal strain was used for DNA isolation using PowerSoil DNA Isolation Kit (MO-BIO Laboraories, Inc., USA) according to the manufacturer’s protocol. DNA was purified as described above.

16S rRNA amplification and identification. The confirmation of the bacterial nature of isolated microcolonies was carried out by determining the size of the 16S rRNA gene fragment by PCR. The reaction mixture contained isolated DNA, 2 × PCR RED Master Mix (DNA-GDANSK, Poland) kit, 799f, and 1492r primers, according to a procedure designed to distinguish bacteria and plant mitochondrial the 16S rRNA gene fragment as described by Chelius and Triplett (2001). DNA from Pseudomonas fluorescens PE16 strain was used as bacterial control. DNA isolated from maize cv. Cyrkon (Zea mays L.) was used as plant control. The controls were shared by the Agriculture Microbiology Lab at the Wroclaw University of Environmental and Life Sciences. The electrophoresis of the products obtained was performed (70 min, 100 V) on the agarose gel (0.8%) with 5% ethidium bromide. Bands were visualized in Dark Hood DH 40/50 and analyzed with Gelix-One 1D Software (Biostep GmbH, Germany).

The identification of bacteria was performed using a molecular cloning technique. Products of 16S rRNA PCR were purified with PCR SureClean Plus (Bioline LTD., UK) kit. Cloning was carried out with Zero Blunt PCR Cloning Kit (Life Technologies, USA) according to manufacturer’s protocol. The ligation mixture was prepared in 50:1 insert:vector ratio (250 ng of purified product), the ligation step was 30 minutes long. Competent E. coli TOP10 cells (Life Technologies, USA) were transformed with the ligand, spread on LB medium with 50 ppm of kanamycin and inoculated for 24 h in 37°C. Randomly 48 colonies, grown on plates, representing every analyzed fungal strain were picked up and inoculated on LB medium with 50 ppm of kanamycin in 96-well plates. Clones were incubated for 24 h in 37°C and sent to LGC Genomics (Berlin) for plasmids sequencing using the Sanger method with primer M13-29R (5’-CAGGAAACAGCTATGACC-’3). Because of unusual results of PUSAS strain, the clones’ identification procedure was repeated and 96 associated bacteria clones were sent for identification again. Sequences with the length of approximately 700 bp were analyzed using BLAST program in NCBI (USA) database. Sequences of clones identified to species or genus were deposited in NCBI database (Table I). Phylogenetic tree of the identified species or genus was build using the neighbor-joining method with maximum sequence difference set to 0.75. The tree was built in BLAST program and visualized in FigTree 1.4.3 (http://tree.bio.ed.ac.uk).

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

NCBI accessing numberParent strainNumber of clonesThe most similar strains in NCBI database
Strain nameAccessing number and similarity (%)
KR779716PxS; PBo6S2Methylobacterium sp. 63JF905617 (99)
KR779718PBo6S1Corynebacterium ureicelerivorans IMMIB RIV-2301CP009215 (99)
KR779719PBo6S1Corynebacterium sp. clone YHSS1EF658675 (100)
KR779720PB81Corynebacterium sp. clone OD-12KX379256 (100)
KR779721PxS; PBo6S; PB7’964Weissella cibaria_BM2CP027427 (99)
MH424523P1122Weissella confusa SM10KU060300 (100)
KR779722PBo6S; PB63S; P234; PxS5Paracoccus sp. clone SL36HQ264096 (100)
MH424529PB7’961Paracoccus yeei TWCC 57946LC371258 (100)
KR779723P2341Bacillus sp. 1NLA3ECP005586 (99)
KR779725PB7’961Bacillus sp. R-66632KT185191 (99)
KR779726P234; PB8; P112; PBo6S8Bacillus sp. CHORDb1MG995009 (100)
MH424530P1122Bacillus sp. clone DJX505089 (99)
MH424531PB81Bacillus megaterium Y103MH368091 (99)
KR779727PxS1Nocardioides_sp. clone EHFS1_S02aEU071473 (100)
KR779728PBo6S; PB7’964Nocardioides terrigena DS-17NR_044185 (99)
KR779729PxS1Citricoccus sp. PL13f_S6JF274870 (99)
KR779730PxS1Micrococcus sp. EF1B-B144KC545358 (99)
MH424533P2341Micrococcus luteus JGTA-S5KT805418 (99)
MH424534PB81Micrococcus sp. cpRA422KJ510213 (100)
MH424535P1121Micrococcus sp. strain CAU1456MG214549 (99)
MH424536P234; PxS2Micrococcus terreus IHBB 9339KU921566 (99)
KR779731PxS; P112; PB7’96; P234; PB89Pelomonas saccharophila ATCC 15946NR_115049 (99)
KR779732P112; P234; PB85Staphylococcus epidermidis_FDAARGOS_161CP014132 (99)
MH424568PxS1Staphylococcus epidermidis TWSL_19KT184899 (100)
MH424569PxS1Staphylococcus caprae OZK14KT591476 (99)
MH424570P1121Staphylococcus sp. JCE 11LT899997 (100)
MH424571PB81Staphylococcus sp. clone 12L_53KP183056 (99)
KR779733PB8; PBo6S2Ralstonia solanacearum RSCMCP025986 (99)
MH426745PBo6S1Ralstonia sp. clone DVBSW_M180KF755496 (100)
KR779734PUSAS; PBo6S; P234; PB7’96; P11211Cupriavidus metallidurans Ni-2CP026544 (100)
MH424572PBo6S1Cupriavidus sp. EF11(2012)JX912460 (99)
KR779735PxS; P1122Propionibacterium granulosum JCM 6498NR_113367 (99)
MH424575P1121Propionibacterium sp. clone JPL-2_O14FJ957593 (99)
KR779736PB7’96; P112; PxS; P234; PB63S; Pbo6S11Propionibacterium sp. clone 12L_77KP183061 (99)
KR779737PxS; PB8; P234; P1125Pseudomonas sp. 09C 129CP025261 (100)
KR779738PB7’961Pseudomonas _uorescens 2F9KT695813 (100)
MH424593PB7’962Pseudomonas__uorescens_PF85MF838663 (100)
MH424580PB8; PB63S2Pseudomonas simiae strain 4G1010KY939757 (100)
MH424594P1121Pseudomonas _uorescens L228CP015639 (100)
MH424599PB7’961Pseudomonas lurida MYb11CP023272 (100)
KR779740P112; PB63S; PB7’964Acidovorax sp. clone M_KL_81_14KP967499 (100)
MH427201PB63S; PBo6S3Acidovorax sp. clone CSC28JN541150 (100)
KR779742PUSAS11Escherichia coli DA33137CP029579 (100)
MH427368PUSAS21Escherichia coli 2012C-4502CP027440 (100)
KR779743PUSAS31Escherichia coli 2015C-3125CP027763 (100)
MH427381PUSAS1Escherichia coli 2013C-3342CP027766 (100)
KR779745PxS1Lactobacillus sakei PR11KX139193 (99)
MH427585PxS1Lactobacillus sakei DS4CP025839 (99)
MH427654PB81Lactobacillus sakei FAM18311CP020459 (99)
KR779746PxS1Legionella sp. L-29AB856218 (98)
KR779747PxS1Finegoldia magna JCM 1766NR_113383 (99)
KR779748PxS1Sporosarcina psychrophila DSM 6497CP014616 (100)
KR779749PBo6S1Streptococcus pneumoniae 11ACP018838 (99)
KR779750PB81Kocuria rhizophila 3330KP345929 (100)
KR779751PB81Lactococcus garvieae MJF010MH057260 (100)
KR779752P2341Del_ia lacustris SH2MH014970 (100)
KR779753P2341Pectobacterium carotovorum subsp. brasiliense BC1CP009769 (100)
KR779754P2341Oryzihumus leptocrescens S32011-bAB649006 (100)
KR779755P2341Tumebacillus sp. 7B-408KF441681 (99)
KR779756P1121Achromobacter mucicolens OZK37KT716268 (100)
KR779757PB7’961Herbaspirillum sp. WW2KU495919 (100)
MH427999P234; PBo6S; PB8; PB63S; PxS; PB7’96; P11235Curvibacter sp. clone Z2_KL_466-12KP967473 (100)
MH428000PB63S, PB7’96; P1123Curvibacter sp. clone CX 18.4KX260804 (99)
MH428038P2341Acidobacteria clone SEW_08_293HQ598999 (99)
MH428102PB7’961Acidobacteria clone SEW_08_084HQ598816 (99)
MH428220P1121Paenibacillus typhae xj7NR_109462 (99)
MH428377P1121Paenibacillus marchantiophytorum R55NR_148618 (99)
MH428379P2341Acinetobacter sp. SWBY1CP026616 (99)
MH428572P2341Acinetobacter towneri MTCC11368TKM070563 (99)
MH428659PBo6S1Streptomyces rishiriensis JCM 4686LC002811 (99)
MH428674PBo6S1Streptomyces sp. 111013air4KP262513 (99)
MH428833PB7’961Sphingomonas sp. CAU-S5MF113252 (99)

NifH gene identification. The identification of NifH gene was performed by PCR with PolF and PolR primers according to the procedure described by Poly et al. (2001). The reaction mixture contained the tested DNA, 5 × Hot FIREPol Blend Master Mix buffer, and the primers mentioned above. Agarose gel electrophoresis of products was performed (agarose 2%, ethidium bromide 5%, electrophoresis time of 60 min, voltage 100 V). Products were visualized as described above. As a control, Azospirillum barsieliense 35Bb strain was used (Król and Perzynski 2005).

β-glucosidase gene identification. The identification of β-glucosidase gene was performed by PCR with bgluF and bgluR2 primers according to the procedure described by Canizares et al. (2011). The reaction mixture contained the isolated DNA, 5 × Hot FIRE-Pol Blend Master Mix buffer, and the primers mentioned above. Products visualization was performed as described above.

β-xylanase gene identification. For the identification of the β-xylanase gene, PCR was performed with XynF and XynR primers according to the procedure described by Khandeparker et al. (2011). The reaction mixture contained the isolated DNA, 5 × Hot FIRE-Pol Blend Master Mix buffer and the primers mentioned above. Products visualization was performed as described above.

LMCO genes identification. The identification of LMCO (laccase-like multicopper oxidase) genes was performed by PCR with Cu1AFand Cu2R primers according to the procedure described by Kellner et al. (2008). The reaction mixture contained the isolated DNA, 5 × Hot FIREPol Blend Master Mix buffer and the primers mentioned above. Products visualization was performed as described above.

Results

A number of small bacteria-like organisms were observed inside and outside of cells of all analyzed oyster mushroom strains. They were visible as small green or yellow-green rods. The microscopic image is shown in Fig. 1. The bacteria-like organisms were marked with white arrows. Several of the cells observed were motile inside of fungal hyphae what is presented in materials published online (PxS – https://youtu.be/G93Rm0tHIgg; P234 – https://youtu.be/pxApJvCshQ0; PB7’96 – https://youtu.be/JZdGXSyDdG4; PB63S – https://youtu.be/A4U4MtUeIiU). After 10 days of cultivation, a lot of small objects were observed growing deeply in the medium around and outside fungal mycelia of all inoculates (Fig. 2). Such growth was not observed on TSA medium without addition of Tween 20. Tween 20 is used usually as a surfactant to disperse cells in solutions. Some of the bacteria also use Tween 20 as a source of fatty acids. No objects were observed in control samples that were not inoculated with fungi. Similar results were described previously by Yara et al. (2006). Blocks of media containing objects were used for cells isolation. After 14 days of stationary cultivation in the liquid TSBt medium, a white precipitate was observed on flasks bottom for all oyster mushrooms strains analyzed. After centrifugation, this precipitate was used for DNA amplification protocol.

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.

As a result of PCR performed with DNA obtained from precipitant and 799f and 1492r primers, a 700 bp product was obtained (Fig. 3). Product that size is characteristic only for bacterial DNA as it is a part of the bacterial 16S rRNA gene. For comparison, the reaction with maize DNA provided two bands: one of 1100 bp which is characteristic for plant mitochondrial DNA and second of size about 700 bp, characteristic for bacteria. The reason for this phenomenon is that maize cultivar used in experiment carry endophytic bacteria in its tissues (Pisarska and Pietr 2015).

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.

The total number of 307 sequences was obtained as a result of the sequencing of plasmid clones. The detailed number of identified clones with the most similar strains from NCBI database is presented in Table II. The species or genus was determined for 233 of them and for the remaining 74 sequences we were not able to identify higher taxonomic level than domena of Bacteria. All clones were identified only for PUSAS strain originated from the USA. Among other seven fungal strains, the unidentified clones occurred in the range from 7 to 15. Among tested strains of fungi, the lower biodiversity of bacteria was found for the strain PUSAS, which contained 64 clones closely related to E. coli and only two clones related to Cupriavidus genus. The only one genus, which occurred in all fungal strains analyzed but PUSAS, was Curvibacter and it was represented by 38 clones. Propionibacterium genus was found in six of eight fungal strains analyzed. It was not present only in PUSAS and PB8 strains. The total number of identified Propionibacterium strains was 14. Another genus found in six of P. ostreatus strains was Cupriavidus. It occurred in a total number of 13 clones in all fungal strains except PxS and PB63S. Bacteria belonging to genus Pseudomonas were also identified in a number of 12 clones from six fungal strains (except PUSAS and PBo6S). Genus Pelomonas was identified as nine clones from five fungal strains: P234, PB7’96, PB8, PxS, and P112. Bacteria from genus Paracoccus in a number of six were found in almost all of P. ostreatus strains from Poland (except P112). The remaining clones identified were as follows: Bacillus – 13 clones (in P234, PBo6S, PB8, P112), Staphylococcus – nine clones (in P234, PB8, PxS, P112), Acidovorax – seven clones (in PB7’96, PBo6S, PB63S, P112), Weisella – six clones (in PB7’96, PBo6S, PxS, P112), Micrococcus – six clones (in P234, PB8, PxS, P112), Nocardioides – five clones (in PB7’96, PBo6s, PxS), Ralstonia – three clones (in PBo6S, PB8), Corynebacterium – three clones (in PBo6S, PxS), Lactobacillus – three clones (in PBo6S, PxS), Acidobacteria – two clones (in P234, PB7’96), Paenibacillus – two clones (in P112), Acinetobacter – two clones (in P234), Streptomyces – two clones (in PBo6S), Legionella – one clone (PxS), Finegoldia – one clone (PxS), Sporosarcina – one clone (PxS), Streptococcus – one clone (PBo6S), Kocuria – one clone (PB8), Lactococcus – one clone (PB8), Delftia – one clone (P234), Pectobacterium – one clone (P234), Oryzihumus – one clone (P234), Tumebacillus – one clone (P234), Achromobacter – one clone (P112), Herbaspirillum – one clone (PB7’96), Citrococcus – one clone (PxS), Sphingomonas – one clone (PB7’96). The detailed number of identified clones with the most similar strains from NCBI database is presented in Table II. Phylogenetic tree of representatives of all identified genotypes with most similar sequences from NCBI database is presented in Fig. 4. As an out-group sequence, the Thermosipho sp. MV1063 (AJ419874) was used. The detailed number of identified clones with the most similar strains from NCBI database is presented in Table II.

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

GenusSimilarity based on 700 bp sequence of the 16S rRNA geneNumber of clonesOrigin P. ostreatus strains
The most closely related strain in NCBINCBI accession number(% of similarity)USAJapanPoland
PUSASPB8PB7’96PBo6SP234PxSPB63SP112
EscherichiaE. coli DA33137CP029579 (100)64110000000
E. coli 2012C-4502CP027440 (100) 210000000
E. coli 2015C-3125CP027763 (100) 310000000
E. coli 2013C-3342CP027766 (100) 10000000
CurvibacterCurvibacter sp. clone Z2_KL_466-12KP967473 (100)3806846425
Curvibacter sp. clone CX 18.4KX260804 (99) 00100011
PropionibacteriumPropionibacterium sp. clone 12L_77KP183061 (100)1400112223
P. granulosum JCM 6498113367 (99) 00000101
Propionibacterium sp. clone JPL-2_O14FJ957593 (99) 00000001
BacillusBacillus sp. CHORDb1MG995009 (100)1302012003
Bacillus sp. clone DJX505089 (99) 00000002
Bacillus sp. 1NLA3ECP005586 (99) 00001000
Bacillus sp. R-66632KT185191 (99) 00100000
Bacillus megaterium Y103MH368091 (99) 01000000
CupriavidusC. metallidurans Ni-2CP026544 (100)1222132002
Cupriavidus sp. EF11(2012)JX912460 (99) 00010000
PseudomonasPseudomonas sp. 09C 129CP025261 (100)1202001101
P. fuorescens PF85MF838663 (100) 00200000
P. simiae 4G1010KY939757 (100) 01000010
P. fuorescens L228CP015639 (100) 00000001
P. fuorescens 2F9KT695813 (100) 00100000
P. lurida MYb11CP023272 (100) 00100000
StaphylococcusS. epidermidis FDAARGOS_161CP014132 (99)901002002
S. epidermidis TWSL_19KT184899 (100) 00000100
S. caprae OZK14KT591476 (99) 00000100
Staphylococcus sp. JCE 11LT899997 (100) 00000001
Staphylococcus sp. clone 12L_53KP183056 (100) 01000000
PelomonasP. saccharophila ATCC 15946NR_115049 (99)902102301
AcidovoraxAcidovorax sp. clone M_KL_81_14KP967499 (100)400100012
Acidovorax sp. clone CSC28JN541150 (100)300010020
WeissellaW. cibaria BM2CP027427 (99)600120100
W. confusa SM10KU060300 (100) 00000002
MicrococcusM. luteus JGTA-S5KT805418 (100)600001000
Micrococcus sp. cpRA422KJ510213 (100) 01000000
Micrococcus sp. EF1B-B144KC545358 (99) 00000100
Micrococcus sp. strain CAU1456MG214549 (99) 00000001
M. terreus IHBB 9339KU921566 (99) 00001100
ParacoccusParacoccus sp. clone SL36HQ264096 (100)600011210
P. yeei TWCC 57946LC371258 (100) 00100000
NocardioidesN. terrigena DS-17NR_044185 (99)500220000
Nocardioides sp. clone EHFS1_S02aEU071473 (99) 00000100
RalstoniaR. solanacearum RSCMCP02598 (99)301010000
Ralstonia sp. clone DVBSW_M180KF755496 (100) 00010000
CorynebacteriumC. ureicelerivorans IMMIB RIV-2301CP009215 (99)300010000
Corynebacterium sp. clone YHSS1EF658675 (100) 00010000
Corynebacterium sp. clone OD-12KX379256 (100) 01000000
LactobacillusL. sakei FAM18311CP020459 (99)300010000
L. sakei PR11KX139193 (99) 00000100
L. sakei DS4CP025839 (99) 00000100
AcidobacteriaAcidobacteria clone SEW_08_293HQ598999 (99)200001000
Acidobacteria clone SEW_08_084HQ598816 (99) 00100000
PaenibacillusP. typhae xj7NR_109462 (99)200000001
P. marchantiophytorum R55NR_148618 (99) 00000001
AcinetobacterAcinetobacter sp. SWBY1CP026616 (99)200001000
A. towneri MTCC11368TKM070563 (99) 00001000
StreptomycesS. rishiriensis JCM 4686LC002811 (99)200010000
Streptomyces sp. 111013air4KP262513 (99) 00010000
LegionellaLegionella sp. L-29AB856218 (98)100000100
FinegoldiaF. magna JCM 1766NR_113383 (99)100000100
SporosarcinaS. psychrophila DSM 6497CP014616 (100)100000100
StreptococcusS. pneumoniae 11ACPO18838 (99)100010000
KocuriaK. rhizophila 3330KP345929 (100)101000000
LactococcusL. garvieae MJFO10MH057260 (100)101000000
DelfiaD. lacustris SH2MHO 14970 (100)100001000
PectobacteriumP. carotovorum subsp. brasiliense BC1CP009769 (100)100001000
OryzihumusO. leptocrescens S32011-bAB649006 (100)100001000
TumebacillusTumebacillus sp. 7B-408KF441681 (99)100001000
AchromobacterA. mucicolens OZK37KT716268 (100)100000001
HerbaspirillumHerbaspirillum sp. WW2KU495919 (100)100100000
CitricoccusCitricoccus sp. PL13f_S6JF274870 (99)100000100
SphingomonasSphingomonas sp. CAU-S5MF113252 (99)100100000
Number of diferent clonesXXX51516171817817
Number of genusXX322913131513512
Number of unidentified clones of BacteriaXX740610141015712

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.

The PCR reactions designed for detection of NifH, β-glucosidase and β-xylanase genes gave no product for all analyzed fungal strains. However, LMCO genes were detected (Fig. 5). LMCO is a complex of enzymes, which include laccases (EC 1.10.3.2) among others.

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.

Discussion

Yara et al. (1999, 2006) reported that bacteria or bacteria-like organisms could interact with only one strain of P. ostreatus. However, authors did not confirm the endocellular character of these bacteria, they described them only as bacteria associated with P. ostreatus G2 hyphae. Using fluorescent microscopy technique, which was described by Bianciotto et al. (2000), we found bacteria associated with all eight tested strains of P. ostreatus originating from different geographic zones (Japan, Poland, and the USA). Every specimen was prepared from living cells and their movement was possible to observe under a microscope. These observations and lack of growth of isolated organisms without the presence of host on microbiological media strongly suggested the endosymbiotic character of the observed bacteria. This hypothesis was also strongly supported by the fact that cultivation of the fungal strains on media with wide range of antibacterial antibiotics (ampicillin, neomycin, gentamicin, penicillin G, streptomycin, polymyxin B, kanamycin, ciprofloxacin, detreromycin, tobramycin (200 ppm), meropenem, and ceftadizine (30 ppm), data unpublished) did not eradicate bacteria from fungal mycelia. Similar techniques used for the isolation of bacteria from five strains of Lentinula edodes not revealed the presence of associated bacteria (data unpublished). Due to the fact that it was not possible to fully distinguish between endosymbiotic and associated bacteria among the isolates tested we decided to use in this study the term “bacteria associated with”. Literature of subject shows the presence of one or two species of bacteria associated with P. ostreatus. Yara et al. (2006) described bacteria associated with one strain of P. ostreatus belonging to B. cepacia complex, which is complex of at least 20 different species from Burkholderia genus (LiPuma 2005). In this work, we report the presence of bacteria related to at least 34 different genera living in association with eight P. ostreatus strains originating from different geographical regions. It was noticeable that bacteria from genus Curvibacter were isolated from almost all analyzed fungal strains. The only one strain that did not contain these bacteria was a PUSAS strain. This strain also was the only one associated with E. coli bacteria what is difficult to explain due to lack of knowledge of history of this strain, The bacteria from the Curvibacter genus were reported endosymbionts of Oryza sativa roots (Singh et al. 2006), similarly as an uncultured bacterium from Chlorella cultures (Otsuka et al. 2008) and tomato rhizosphere (Lioussanne et al. 2010) and the bacteria associated with Hydra, which serve as a protective factor against pathogen infections (Fraune et al. 2015). Bacteria of genera Bacillus and Pseudomonas are well-known plant growth-promoting bacteria due to competitive and antagonistic activity versus several pathogens (Compant et al. 2010). The occurrence of Curvibacter, Bacillus and Pseudomonas bacteria associated with P. ostreatus could be related to the known lower susceptibility of this edible mushroom when compare to Agaricus bisporus (J.E. Lange) Imbach. Gigasporacea sp. endosymbionts were described as N2 fixing bacteria (Bianciotto et al. 2003). However, our study did not show the presence of nitrogenase reductase genes using PolF and PolR primers; however, the occurrence of clones similar to Cupriavidus suggest that these bacteria could be N2-fixers associated with oyster mushroom. Strains of Cupriavidus taiwanensis, previously were isolated from nodules of Mimosa, can nodulate also legumes and fix N2. However, the nifH gene is only distantly related to other alphaproteobacterial rhizobial strains (Gyaneshwar et al. 2011), what was probably a reason that used primers were not specific in this case. The bacteria associated with P. ostreatus could also influence their hosts’ capability for lignocellulolytic substrates utilization. PCR reactions with specific primers for β-glucosidase, β-xylanase genes did not reveal their presence, which suggests that these bacteria did not play important role in degradation of polysaccharides. However, the presence of LMCO genes was identified in this study. Laccases are a group of enzymes able to use a variety of substrates, including lignin (Rekuc et al. 2006). This suggests that although oyster mushroom-associated bacteria were able to produce neither β-glycosidase nor β-xylanase, they still could be able to support the lignocellulolytic activity of the strains tested due to laccase activity.

The origin of identified P. ostreatus-associated bacteria, their phylogenesis, and relationship with hosts were difficult to determine. In the natural environment, the oyster mushroom is a saprophyte, which develops on dead trunks and deciduous trees. Occasionally, it can develop in places of cuts on living trees. Such a variety of hosts may be the reason for the biodiversity of bacterial associations. Different non-pathogenic species probably inhabited mycelium of P. ostreatus during colonization of various hosts.

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.
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.
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.
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.

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.
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.
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 numberParent strainNumber of clonesThe most similar strains in NCBI database
Strain nameAccessing number and similarity (%)
KR779716PxS; PBo6S2Methylobacterium sp. 63JF905617 (99)
KR779718PBo6S1Corynebacterium ureicelerivorans IMMIB RIV-2301CP009215 (99)
KR779719PBo6S1Corynebacterium sp. clone YHSS1EF658675 (100)
KR779720PB81Corynebacterium sp. clone OD-12KX379256 (100)
KR779721PxS; PBo6S; PB7’964Weissella cibaria_BM2CP027427 (99)
MH424523P1122Weissella confusa SM10KU060300 (100)
KR779722PBo6S; PB63S; P234; PxS5Paracoccus sp. clone SL36HQ264096 (100)
MH424529PB7’961Paracoccus yeei TWCC 57946LC371258 (100)
KR779723P2341Bacillus sp. 1NLA3ECP005586 (99)
KR779725PB7’961Bacillus sp. R-66632KT185191 (99)
KR779726P234; PB8; P112; PBo6S8Bacillus sp. CHORDb1MG995009 (100)
MH424530P1122Bacillus sp. clone DJX505089 (99)
MH424531PB81Bacillus megaterium Y103MH368091 (99)
KR779727PxS1Nocardioides_sp. clone EHFS1_S02aEU071473 (100)
KR779728PBo6S; PB7’964Nocardioides terrigena DS-17NR_044185 (99)
KR779729PxS1Citricoccus sp. PL13f_S6JF274870 (99)
KR779730PxS1Micrococcus sp. EF1B-B144KC545358 (99)
MH424533P2341Micrococcus luteus JGTA-S5KT805418 (99)
MH424534PB81Micrococcus sp. cpRA422KJ510213 (100)
MH424535P1121Micrococcus sp. strain CAU1456MG214549 (99)
MH424536P234; PxS2Micrococcus terreus IHBB 9339KU921566 (99)
KR779731PxS; P112; PB7’96; P234; PB89Pelomonas saccharophila ATCC 15946NR_115049 (99)
KR779732P112; P234; PB85Staphylococcus epidermidis_FDAARGOS_161CP014132 (99)
MH424568PxS1Staphylococcus epidermidis TWSL_19KT184899 (100)
MH424569PxS1Staphylococcus caprae OZK14KT591476 (99)
MH424570P1121Staphylococcus sp. JCE 11LT899997 (100)
MH424571PB81Staphylococcus sp. clone 12L_53KP183056 (99)
KR779733PB8; PBo6S2Ralstonia solanacearum RSCMCP025986 (99)
MH426745PBo6S1Ralstonia sp. clone DVBSW_M180KF755496 (100)
KR779734PUSAS; PBo6S; P234; PB7’96; P11211Cupriavidus metallidurans Ni-2CP026544 (100)
MH424572PBo6S1Cupriavidus sp. EF11(2012)JX912460 (99)
KR779735PxS; P1122Propionibacterium granulosum JCM 6498NR_113367 (99)
MH424575P1121Propionibacterium sp. clone JPL-2_O14FJ957593 (99)
KR779736PB7’96; P112; PxS; P234; PB63S; Pbo6S11Propionibacterium sp. clone 12L_77KP183061 (99)
KR779737PxS; PB8; P234; P1125Pseudomonas sp. 09C 129CP025261 (100)
KR779738PB7’961Pseudomonas _uorescens 2F9KT695813 (100)
MH424593PB7’962Pseudomonas__uorescens_PF85MF838663 (100)
MH424580PB8; PB63S2Pseudomonas simiae strain 4G1010KY939757 (100)
MH424594P1121Pseudomonas _uorescens L228CP015639 (100)
MH424599PB7’961Pseudomonas lurida MYb11CP023272 (100)
KR779740P112; PB63S; PB7’964Acidovorax sp. clone M_KL_81_14KP967499 (100)
MH427201PB63S; PBo6S3Acidovorax sp. clone CSC28JN541150 (100)
KR779742PUSAS11Escherichia coli DA33137CP029579 (100)
MH427368PUSAS21Escherichia coli 2012C-4502CP027440 (100)
KR779743PUSAS31Escherichia coli 2015C-3125CP027763 (100)
MH427381PUSAS1Escherichia coli 2013C-3342CP027766 (100)
KR779745PxS1Lactobacillus sakei PR11KX139193 (99)
MH427585PxS1Lactobacillus sakei DS4CP025839 (99)
MH427654PB81Lactobacillus sakei FAM18311CP020459 (99)
KR779746PxS1Legionella sp. L-29AB856218 (98)
KR779747PxS1Finegoldia magna JCM 1766NR_113383 (99)
KR779748PxS1Sporosarcina psychrophila DSM 6497CP014616 (100)
KR779749PBo6S1Streptococcus pneumoniae 11ACP018838 (99)
KR779750PB81Kocuria rhizophila 3330KP345929 (100)
KR779751PB81Lactococcus garvieae MJF010MH057260 (100)
KR779752P2341Del_ia lacustris SH2MH014970 (100)
KR779753P2341Pectobacterium carotovorum subsp. brasiliense BC1CP009769 (100)
KR779754P2341Oryzihumus leptocrescens S32011-bAB649006 (100)
KR779755P2341Tumebacillus sp. 7B-408KF441681 (99)
KR779756P1121Achromobacter mucicolens OZK37KT716268 (100)
KR779757PB7’961Herbaspirillum sp. WW2KU495919 (100)
MH427999P234; PBo6S; PB8; PB63S; PxS; PB7’96; P11235Curvibacter sp. clone Z2_KL_466-12KP967473 (100)
MH428000PB63S, PB7’96; P1123Curvibacter sp. clone CX 18.4KX260804 (99)
MH428038P2341Acidobacteria clone SEW_08_293HQ598999 (99)
MH428102PB7’961Acidobacteria clone SEW_08_084HQ598816 (99)
MH428220P1121Paenibacillus typhae xj7NR_109462 (99)
MH428377P1121Paenibacillus marchantiophytorum R55NR_148618 (99)
MH428379P2341Acinetobacter sp. SWBY1CP026616 (99)
MH428572P2341Acinetobacter towneri MTCC11368TKM070563 (99)
MH428659PBo6S1Streptomyces rishiriensis JCM 4686LC002811 (99)
MH428674PBo6S1Streptomyces sp. 111013air4KP262513 (99)
MH428833PB7’961Sphingomonas sp. CAU-S5MF113252 (99)

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

GenusSimilarity based on 700 bp sequence of the 16S rRNA geneNumber of clonesOrigin P. ostreatus strains
The most closely related strain in NCBINCBI accession number(% of similarity)USAJapanPoland
PUSASPB8PB7’96PBo6SP234PxSPB63SP112
EscherichiaE. coli DA33137CP029579 (100)64110000000
E. coli 2012C-4502CP027440 (100) 210000000
E. coli 2015C-3125CP027763 (100) 310000000
E. coli 2013C-3342CP027766 (100) 10000000
CurvibacterCurvibacter sp. clone Z2_KL_466-12KP967473 (100)3806846425
Curvibacter sp. clone CX 18.4KX260804 (99) 00100011
PropionibacteriumPropionibacterium sp. clone 12L_77KP183061 (100)1400112223
P. granulosum JCM 6498113367 (99) 00000101
Propionibacterium sp. clone JPL-2_O14FJ957593 (99) 00000001
BacillusBacillus sp. CHORDb1MG995009 (100)1302012003
Bacillus sp. clone DJX505089 (99) 00000002
Bacillus sp. 1NLA3ECP005586 (99) 00001000
Bacillus sp. R-66632KT185191 (99) 00100000
Bacillus megaterium Y103MH368091 (99) 01000000
CupriavidusC. metallidurans Ni-2CP026544 (100)1222132002
Cupriavidus sp. EF11(2012)JX912460 (99) 00010000
PseudomonasPseudomonas sp. 09C 129CP025261 (100)1202001101
P. fuorescens PF85MF838663 (100) 00200000
P. simiae 4G1010KY939757 (100) 01000010
P. fuorescens L228CP015639 (100) 00000001
P. fuorescens 2F9KT695813 (100) 00100000
P. lurida MYb11CP023272 (100) 00100000
StaphylococcusS. epidermidis FDAARGOS_161CP014132 (99)901002002
S. epidermidis TWSL_19KT184899 (100) 00000100
S. caprae OZK14KT591476 (99) 00000100
Staphylococcus sp. JCE 11LT899997 (100) 00000001
Staphylococcus sp. clone 12L_53KP183056 (100) 01000000
PelomonasP. saccharophila ATCC 15946NR_115049 (99)902102301
AcidovoraxAcidovorax sp. clone M_KL_81_14KP967499 (100)400100012
Acidovorax sp. clone CSC28JN541150 (100)300010020
WeissellaW. cibaria BM2CP027427 (99)600120100
W. confusa SM10KU060300 (100) 00000002
MicrococcusM. luteus JGTA-S5KT805418 (100)600001000
Micrococcus sp. cpRA422KJ510213 (100) 01000000
Micrococcus sp. EF1B-B144KC545358 (99) 00000100
Micrococcus sp. strain CAU1456MG214549 (99) 00000001
M. terreus IHBB 9339KU921566 (99) 00001100
ParacoccusParacoccus sp. clone SL36HQ264096 (100)600011210
P. yeei TWCC 57946LC371258 (100) 00100000
NocardioidesN. terrigena DS-17NR_044185 (99)500220000
Nocardioides sp. clone EHFS1_S02aEU071473 (99) 00000100
RalstoniaR. solanacearum RSCMCP02598 (99)301010000
Ralstonia sp. clone DVBSW_M180KF755496 (100) 00010000
CorynebacteriumC. ureicelerivorans IMMIB RIV-2301CP009215 (99)300010000
Corynebacterium sp. clone YHSS1EF658675 (100) 00010000
Corynebacterium sp. clone OD-12KX379256 (100) 01000000
LactobacillusL. sakei FAM18311CP020459 (99)300010000
L. sakei PR11KX139193 (99) 00000100
L. sakei DS4CP025839 (99) 00000100
AcidobacteriaAcidobacteria clone SEW_08_293HQ598999 (99)200001000
Acidobacteria clone SEW_08_084HQ598816 (99) 00100000
PaenibacillusP. typhae xj7NR_109462 (99)200000001
P. marchantiophytorum R55NR_148618 (99) 00000001
AcinetobacterAcinetobacter sp. SWBY1CP026616 (99)200001000
A. towneri MTCC11368TKM070563 (99) 00001000
StreptomycesS. rishiriensis JCM 4686LC002811 (99)200010000
Streptomyces sp. 111013air4KP262513 (99) 00010000
LegionellaLegionella sp. L-29AB856218 (98)100000100
FinegoldiaF. magna JCM 1766NR_113383 (99)100000100
SporosarcinaS. psychrophila DSM 6497CP014616 (100)100000100
StreptococcusS. pneumoniae 11ACPO18838 (99)100010000
KocuriaK. rhizophila 3330KP345929 (100)101000000
LactococcusL. garvieae MJFO10MH057260 (100)101000000
DelfiaD. lacustris SH2MHO 14970 (100)100001000
PectobacteriumP. carotovorum subsp. brasiliense BC1CP009769 (100)100001000
OryzihumusO. leptocrescens S32011-bAB649006 (100)100001000
TumebacillusTumebacillus sp. 7B-408KF441681 (99)100001000
AchromobacterA. mucicolens OZK37KT716268 (100)100000001
HerbaspirillumHerbaspirillum sp. WW2KU495919 (100)100100000
CitricoccusCitricoccus sp. PL13f_S6JF274870 (99)100000100
SphingomonasSphingomonas sp. CAU-S5MF113252 (99)100100000
Number of diferent clonesXXX51516171817817
Number of genusXX322913131513512
Number of unidentified clones of BacteriaXX740610141015712

Bertaux J, Schmid M, Prevost-Boure NC, Churin JL, Hartmann A, Garbaye J, Frey-Klett P. In situ identification of intracellular bacteria related to Paenibacillus spp. in the mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N. Appl Environ Microbiol. 2003;69(7):4243–4248. doi:10.1128/AEM.69.7.4243–4248.2003 MedlineBertauxJSchmidMPrevost-BoureNCChurinJLHartmannAGarbayeJFrey-KlettPIn situ identification of intracellular bacteria related to Paenibacillus spp. in the mycelium of the ectomycorrhizal fungus Laccaria bicolor S238NAppl Environ Microbiol200369(7):42434248. doi:10.1128/AEM.69.7.4243–4248.2003MedlineOpen DOISearch in Google Scholar

Bianciotto V, Bandi C, Minerdi D, Sironi M, Tichy HV, Bonfante P. An obligately endosymbiotic mycorrhizal fungus itself harbors obligately intracellular bacteria. Appl Environ Microbiol. 1996;62(8):3005–3010. MedlineBianciottoVBandiCMinerdiDSironiMTichyHVBonfantePAn obligately endosymbiotic mycorrhizal fungus itself harbors obligately intracellular bacteriaAppl Environ Microbiol199662(8):30053010. Medline10.1128/aem.62.8.3005-3010.19961680878702293Search in Google Scholar

Bianciotto V, Lumini E, Lanfranco L, Minerdi D, Bonfante P, Perotto S. Detection and identification of bacterial endosymbionts in arbuscular mycorrhizal fungi belonging to the family Gigasporaceae. Appl Environ Microbiol. 2000;66(10):4503–4509. doi:10.1128/AEM.66.10.4503–4509.2000 MedlineBianciottoVLuminiELanfrancoLMinerdiDBonfantePPerottoSDetection and identification of bacterial endosymbionts in arbuscular mycorrhizal fungi belonging to the family GigasporaceaeAppl Environ Microbiol200066(10):45034509. doi:10.1128/AEM.66.10.4503–4509.2000MedlineOpen DOISearch in Google Scholar

Bianciotto V, Lumini E, Bonfante P, Vandamme P. ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi. Int J Syst Evol Microbiol. 2003; 53(1): 121–124. doi:10.1099/ijs.0.02382–0 MedlineBianciottoVLuminiEBonfantePVandammePCandidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungiInt J Syst Evol Microbiol200353(1): 121124. doi:10.1099/ijs.0.02382–0MedlineOpen DOISearch in Google Scholar

Bonfante P. Plants, mycorrhizal fungi and endobacteria: a dialog among cells and genomes. Biol Bull. 2003;204(2):215–220. doi:10.2307/1543562 MedlineBonfantePPlants, mycorrhizal fungi and endobacteria: a dialog among cells and genomesBiol Bull2003204(2):215220. doi:10.2307/1543562Medline12700157Open DOISearch in Google Scholar

Cañizares R, Benitez E, Ogunseitan OA. Molecular analyses of β-glucosidase diversity and function in soil. Eur J Soil Biol. 2011; 47(1):1–8. doi:10.1016/j.ejsobi.2010.11.002CañizaresRBenitezEOgunseitanOAMolecular analyses of β-glucosidase diversity and function in soilEur J Soil Biol201147(1):18. doi:10.1016/j.ejsobi.2010.11.002Open DOISearch in Google Scholar

Chelius MK, Triplett EW. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol. 2001;41(3): 252–263. doi:10.1007/s002480000087 MedlineCheliusMKTriplettEWThe diversity of archaea and bacteria in association with the roots of Zea mays LMicrob Ecol200141(3): 252263. doi:10.1007/s002480000087Medline11391463Open DOISearch in Google Scholar

Compant S, Clément C, Sessitsch A. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem. 2010;42(5): 669–678. doi:10.1016/j.soilbio.2009.11.024CompantSClémentCSessitschAPlant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilizationSoil Biol Biochem201042(5): 669678. doi:10.1016/j.soilbio.2009.11.024Open DOISearch in Google Scholar

Cruz AF, Horii S, Ochiai S, Yasuda A, Ishii T. Isolation and analysis of bacteria associated with spores of Gigaspora margarita. J Appl Microbiol. 2008;104(6):1711–1717. doi:10.1111/j.1365–2672.2007.03695.x MedlineCruzAFHoriiSOchiaiSYasudaAIshiiTIsolation and analysis of bacteria associated with spores of Gigaspora margaritaJ Appl Microbiol2008104(6):17111717. doi:10.1111/j.1365–2672.2007.03695.xMedlineOpen DOISearch in Google Scholar

Donlan RM, Costerton JW. Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev. 2002;15(2): 167–193. doi:10.1128/CMR.15.2.167–193.2002 MedlineDonlanRMCostertonJWBiofilms: survival mechanisms of clinically relevant microorganismsClin Microbiol Rev200215(2): 167193. doi:10.1128/CMR.15.2.167–193.2002MedlineOpen DOISearch in Google Scholar

Fraune S, Anton-Erxleben F, Augustin R, Franzenburg S, Knop M, Schröder K, Willoweit-Ohl D, Bosch TCG. Bacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. ISME J. 2015;9(7): 1543–1556. doi:10.1038/ismej.2014.239 MedlineFrauneSAnton-ErxlebenFAugustinRFranzenburgSKnopMSchröderKWilloweit-OhlDBoschTCGBacteria-bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistanceISME J20159(7): 15431556. doi:10.1038/ismej.2014.239Medline447869525514534Open DOISearch in Google Scholar

Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A. Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev. 2011;75(4):583–609. doi:10.1128/MMBR.00020–11 MedlineFrey-KlettPBurlinsonPDeveauABarretMTarkkaMSarniguetABacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologistsMicrobiol Mol Biol Rev201175(4):583609. doi:10.1128/MMBR.00020–11MedlineOpen DOISearch in Google Scholar

Gyaneshwar P, Hirsch AM, Moulin L, Chen WM, Elliott GN, Bontemps C, Estrada-de los Santos P, Gross E, dos Reis FB Jr, Sprent JI, et al. Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact. 2011;24(11):1276–1288. doi:10.1094/MPMI-06–11–0172 MedlineGyaneshwarPHirschAMMoulinLChenWMElliottGNBontempsCEstrada-de los SantosPGrossEdos ReisFBJrSprentJILegume-nodulating betaproteobacteria: diversity, host range, and future prospectsMol Plant Microbe Interact201124(11):12761288. doi:10.1094/MPMI-06–11–0172MedlineOpen DOISearch in Google Scholar

Hogan DA, Wargo MJ, Beck N. Bacterial biofilms on fungal surfaces, In: Kjelleberg S, Givskov M, editors. The biofilm mode of life: mechanisms and adaptations. Norfolk (United Kingdom): Horizon Scientific Press. 2007; p. 235–245.HoganDAWargoMJBeckNBacterial biofilms on fungal surfaces, In: KjellebergSGivskovM, editors. The biofilm mode of life: mechanisms and adaptationsNorfolk (United Kingdom)Horizon Scientific Press2007; p. 235245Search in Google Scholar

Kellner H, Luis P, Buscot F. Diversity of laccase-like multicopper oxidase genes in Morchellaceae: identification of genes potentially involved in extracellular activities related to plant litter decay. FEMS Microbiol Ecol. 2007;61(1):153–163. doi:10.1111/j.1574–6941.2007.00322.x MedlineKellnerHLuisPBuscotFDiversity of laccase-like multicopper oxidase genes in Morchellaceae: identification of genes potentially involved in extracellular activities related to plant litter decayFEMS Microbiol Ecol200761(1):153163. doi:10.1111/j.1574–6941.2007.00322.xMedlineOpen DOISearch in Google Scholar

Khandeparker R, Verma P, Deobagkar D. A novel halotolerant xylanase from marine isolate Bacillus subtilis cho40: gene cloning and sequencing. N Biotechnol. 2011;28(6):814–821. doi:10.1016/j.nbt.2011.08.001 MedlineKhandeparkerRVermaPDeobagkarDA novel halotolerant xylanase from marine isolate Bacillus subtilis cho40: gene cloning and sequencingN Biotechnol201128(6):814821. doi:10.1016/j.nbt.2011.08.001Medline21890005Open DOISearch in Google Scholar

Król MJ, Perzynski A. [Utilization of benzene as the sole carbon source in fixation of free nitrogen by Azospirillum spp. and Pseudomonas stutzeri strains of bacteria]. (in Polish). Pam Pulaw (Poland). 2005;140:103–115.KrólMJPerzynskiA[Utilization of benzene as the sole carbon source in fixation of free nitrogen by Azospirillum spp. and Pseudomonas stutzeri strains of bacteria]. (in Polish)Pam Pulaw (Poland)2005140103115Search in Google Scholar

LiPuma JJ. Update on the Burkholderia cepacia complex. Curr Opin Pulm Med. 2005;11(6):528–533. doi:10.1097/01.mcp.0000181475.85187.ed MedlineLiPumaJJUpdate on the Burkholderia cepacia complexCurr Opin Pulm Med200511(6):528533. doi:10.1097/01.mcp.0000181475.85187.edMedline16217180Open DOISearch in Google Scholar

Lioussanne L, Perreault F, Jolicoeur M, St-Arnaud M. The bacterial community of tomato rhizosphere is modified by inoculation with arbuscular mycorrhizal fungi but unaffected by soil enrichment with mycorrhizal root exudates or inoculation with Phytophthora nicotianae. Soil Biol Biochem. 2010;42(3):473–483. doi:10.1016/j.soilbio.2009.11.034LioussanneLPerreaultFJolicoeurMSt-ArnaudMThe bacterial community of tomato rhizosphere is modified by inoculation with arbuscular mycorrhizal fungi but unaffected by soil enrichment with mycorrhizal root exudates or inoculation with Phytophthora nicotianaeSoil Biol Biochem201042(3):473483. doi:10.1016/j.soilbio.2009.11.034Open DOISearch in Google Scholar

Otsuka S, Abe Y, Fukui R, Nishiyama M, Sendoo K. Presence of previously undescribed bacterial taxa in non-axenic Chlorella cultures. J Gen Appl Microbiol. 2008;54(4):187–193. doi:10.2323/jgam.54.187 MedlineOtsukaSAbeYFukuiRNishiyamaMSendooKPresence of previously undescribed bacterial taxa in non-axenic Chlorella culturesJ Gen Appl Microbiol200854(4):187193. doi:10.2323/jgam.54.187Medline18802317Open DOISearch in Google Scholar

Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M, Hertweck C. Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus. Int J Syst Evol Microbiol. 2007a;57(11):2583–2590. doi:10.1099/ijs.0.64660–0 MedlinePartida-MartinezLPGrothISchmittIRichterWRothMHertweckCBurkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporusInt J Syst Evol Microbiol2007a57(11):25832590. doi:10.1099/ijs.0.64660–0MedlineOpen DOISearch in Google Scholar

Partida-Martinez LP, Monajembashi S, Greulich KO, Hertweck C. Endosymbiont-dependent host reproduction maintains bacterial-fungal mutualism. Curr Biol. 2007b;17(9):773–777. doi:10.1016/j.cub.2007.03.039 MedlinePartida-MartinezLPMonajembashiSGreulichKOHertweckCEndosymbiont-dependent host reproduction maintains bacterial-fungal mutualismCurr Biol2007b17(9):773777. doi:10.1016/j.cub.2007.03.039Medline17412585Open DOISearch in Google Scholar

Pisarska K, Pietr SJ. Biodiversity of dominant cultivable endophytic bacteria inhabiting tissues of six different cultivars of maize (Zea mays L. ssp. mays) cropped under field conditions. Pol J Microbiol. 2015;64(2):163–170. MedlinePisarskaKPietrSJBiodiversity of dominant cultivable endophytic bacteria inhabiting tissues of six different cultivars of maize (Zea mays L. ssp. mays) cropped under field conditionsPol J Microbiol201564(2):163170. Medline10.33073/pjm-2015-024Search in Google Scholar

Pierce GE. Pseudomonas aeruginosa, Candida albicans, and device-related nosocomial infections: implications, trends, and potential approaches for control. J Ind Microbiol Biotechnol. 2005;32(7): 309–318. doi:10.1007/s10295–005–0225–2 MedlinePierceGEPseudomonas aeruginosa, Candida albicans, and device-related nosocomial infections: implications, trends, and potential approaches for controlJ Ind Microbiol Biotechnol200532(7): 309318. doi:10.1007/s10295–005–0225–2MedlineOpen DOISearch in Google Scholar

Rekuc A, Kruczkiewicz P, Kielczynski R, Jastrzembska B, Bryjak J. [Laccase production and its immobilation on selcted media]. (in Polish). Acta Sci Pol Biotechnol. 2006;1(05):3–15.RekucAKruczkiewiczPKielczynskiRJastrzembskaBBryjakJ[Laccase production and its immobilation on selcted media]. (in Polish)Acta Sci Pol Biotechnol20061(05):315Search in Google Scholar

Sarand I, Timonen S, Nurmiaho-Lassila EL, Koivula T, Haahtela K, Romantschuk M, Sen R. Microbial biofilms and catabolic plasmid harbouring degradative fluorescent pseudomonads in Scots pine mycorrhizospheres developed on petroleum contaminated soil. FEMS Microbiol Ecol. 1998 Oct;27(2):115–126. doi:10.1111/j.1574–6941.1998.tb00529.xSarandITimonenSNurmiaho-LassilaELKoivulaTHaahtelaKRomantschukMSenRMicrobial biofilms and catabolic plasmid harbouring degradative fluorescent pseudomonads in Scots pine mycorrhizospheres developed on petroleum contaminated soilFEMS Microbiol Ecol1998 Oct;27(2):115126. doi:10.1111/j.1574–6941.1998.tb00529.xOpen DOISearch in Google Scholar

Singh RK, Mishra RPN, Jaiswal HK, Kumar V, Pandey SP, Rao SB, Annapurna K. Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis. Curr Microbiol. 2006;52(2):117–122. doi:10.1007/s00284–005–0136–5 MedlineSinghRKMishraRPNJaiswalHKKumarVPandeySPRaoSBAnnapurnaKIsolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysisCurr Microbiol200652(2):117122. doi:10.1007/s00284–005–0136–5MedlineOpen DOISearch in Google Scholar

Yara R, Azevedo JL, Maccheroni W, Kitajima EW, Leite B. Mycoplasma associated with cultures of the ligno-cellulolytic fungus Pleurotus sp. Acta Microsc. 1999;8:851–852.YaraRAzevedoJLMaccheroniWKitajimaEWLeiteBMycoplasma associated with cultures of the ligno-cellulolytic fungus Pleurotus spActa Microsc19998851852Search in Google Scholar

Yara R, Maccheroni W Jr, Horii J, Azevedo JL. A bacterium belonging to the Burkholderia cepacia complex associated with Pleurotus ostreatus. J Microbiol. 2006;44(3):263–268. MedlinYaraRMaccheroniWJrHoriiJAzevedoJLA bacterium belonging to the Burkholderia cepacia complex associated with Pleurotus ostreatusJ Microbiol200644(3):263268. MedlinSearch in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo