Molecular characterisation of Halobacillus strains isolated from different medieval wall paintings and building materials in Austria

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  • International Biodeterioration & Biodeg

    aa

    Du

    aDepartment of Medical/Pharmaceutical Chemistry, University of Vienna, UZAII, 2B522, Althanstr, 14, A-1090 Vienna, Austriab

    geographical locations may indicate that this group of bacteria is common in salt-affected ruins.

    r 2006 Elsevier Ltd. All rights reserved.

    complexity and diversity of the bacterial communitiespresent in such habitats has increased enormously in recentyears because of the use of molecular techniques such as

    detected microorganisms.Several investigations based on culture-independent

    (Rolleke et al., 1998; Pinar et al., 2001a, b) as well as on

    ARTICLE IN PRESSculture-dependent techniques (Heyrman et al., 1999; Laizet al., 2000; Saiz-Jimenez and Laiz, 2000) have demon-strated that monuments where salt eforescences on the

    0964-8305/$ - see front matter r 2006 Elsevier Ltd. All rights reserved.

    doi:10.1016/j.ibiod.2006.05.004

    Corresponding author. Tel.: +43 1 4277 55116; fax: +43 1 4277 55120.E-mail address: guadalupe.pinar@univie.ac.at (G. Pinar).Keywords: Wall paintings; Halobacillus sp.; DGGE; RAPD-PCR; ITS-HHP

    1. Introduction

    Microorganisms play a crucial role in the deteriorationprocesses of building materials and objects of art,particularly if such materials are exposed to the open air(Bock and Sand, 1993; Ciferri, 1999; Herrera and Videla,2004; Peraza-Zurita et al., 2005). Knowledge about the

    denaturing gradient gel electrophoresis (DGGE) analysis(Rolleke et al., 1998; Gurtner et al., 2000; Gonzalez andSaiz-Jimenez, 2005). The information revealed by analysesof 16S rDNA sequences directly obtained from ampliedenvironmental DNA allows the detection of bacteria notyet cultivated. These data can be then used to designspecic culture media for the cultivation of the previouslyReceived 12 July 2005; received in revised form 20 March 2006; accepted 24 May 2006

    Available online 4 August 2006

    Abstract

    We previously reported on the detection and isolation of an indigenous population of Halobacillus from salt-damaged medieval wall

    paintings and building materials of Herberstein castle in St. Johann bei Herberstein in Styria, Austria. Several moderately halophilic,

    Gram-positive, endospore-forming Halobacillus-like bacteria could be again isolated by conventional enrichment from salt eforescences

    collected in the medieval St. Virgils chapel in Vienna. Comparative 16S rDNA sequence analyses showed that the St. Virgil isolates are

    most closely related (498.5% sequence similarity) to Halobacillus trueperi, Halobacillus litoralis, and to our previous halobacilli strainsobtained from the castle Herberstein. Based on 16S rDNA sequence analysis, the strains could be clustered in three different groups.

    Group I: St. Virgil strains S3, S4, S21, and S22 (99.8100% sequence similarity); group II: Herberstein strains K3-1, I7, and the St. Virgil

    strain S20 (99.399.7% sequence similarity); and group III: Herberstein strains I3, I3A, and I3R (100% sequence similarity). Molecular

    typing by denaturing gradient gel electrophoresis (DGGE), random amplied polymorphic DNA (RAPD-PCR), and internal

    transcribed spacer-homoduplexheteroduplex polymorphism (ITS-HHP) ngerprinting showed that all isolates are typeable by each of

    the methods. RAPD was the most discriminatory method. With respect to their physiological characteristicsi.e., growth in the presence

    of 520% (w/v) NaCl, no growth in the absence of NaCl, optimum growth at 37 1C in media containing 510% (w/v) NaCl, andoptimum pH around 7.58.0the St. Virgil isolates resembled our previously isolated strains. However, the St. Virgil strains showed

    some differences in their biochemical properties. St. Virgil isolates hydrolysed Tween 80, two isolates reduced nitrate, and no isolate

    liqueed gelatine. The recurrent isolation of halobacilli from salt eforescences on historic buildings and monuments at two differentInstitute of Bacteriology, Mycology and Hygiene, University of Veterinary Medicine Vienna, Veterinarplatz 1, A-1210 Vienna, AustriaMolecular characterisation of Hdifferent medieval wall paintings

    Katrin Ripkaa, Ewald B.M.Werner Lubitza, Gradation 58 (2006) 124132

    lobacillus strains isolated fromnd building materials in Austria

    ennerb, Astrid Michaelsena,adalupe Pinara,

    www.elsevier.com/locate/ibiod

  • 2.3. Bacterial strains

    catalase, nitrate reduction, oxidative-fermentative metabolism of glucose

    dTTP, 3mM MgCl2) was diluted to 1 and 12.5 pmol of each primer

    2.5.2. DGGE

    ARTICLE IN PRESSratisurfaces are a common phenomenon, as a result ofchanging physical parameters, may be a habitat forextremely salt-tolerant and moderately halophilic micro-organisms. The molecular detection and isolation ofHalobacillus species in deteriorated wall paintings andbuilding materials of the Catherine chapel at Herbersteincastle (Styria, Austria) (Pinar et al., 2001c) promptedfurther studies to focus on this group of bacteria notpreviously reported from stoneworks. In the past, haloba-cilli were overlooked due to the use of unsuitable culturemedia with inadequate salt concentration, and/or the longincubation time required for the growth of this group ofbacteria under laboratory conditions.Recently, we cultivated Halobacillus-like bacteria from

    stonework samples of a medieval building in Austria (St.Virgils chapel, Vienna). Here we report on the molecularcharacterisation of Halobacillus strains from wall paintingsand building materials.

    2. Materials and methods

    2.1. Description of the site and sampling

    This study was carried out in two different locations, the Catherine

    chapel at Herberstein castle (Styria, Austria) and the St. Virgil Chapel

    (Vienna, Austria). The Catherine chapel at Herberstein castle is decorated

    with several frescoes from the 14th century. The wall paintings were

    discovered and partly exposed around 1930, but restoration did not start

    before the 1940s. However, after restoration, the chapel was neglected and

    used as storage room until the mid-90s. The location is exposed to

    humidity uctuation at irregular intervals. Two samples were collected

    from different areas of the wall paintings: sample H1 was taken below the

    chancel east wall window where a brownish biolm was observed; sample

    H6 was taken from the chancel north wall, from a zone of the painting

    with an intense rosy discoloration. An additional sample (m7) was taken

    outside the chapel, from a limestone wall also showing an intense rosy

    discoloration.

    The St. Virgil Chapel dates back to the beginning of the 14th century. It

    is located under the ruins of St. Mary Magdaleine Chapel. St. Virgil

    Chapel was originally created as a tomb. After the Chapel of St. Mary

    Magdaleine was destroyed in 1781 by a re and demolished, the

    underground room was abandoned. The chapel was rediscovered during

    an excavation in 1972. The rectangular room is 10.5m long and 6m wide.

    The mortar and rubble walls are 1.5m thick, containing six recesses with

    pointed arches, one of which was removed to open the present-day

    entrance. They are decorated with large red crosses painted onto white

    plaster. The whole chapel walls are encrusted with salt eforescences

    visible to the naked eye. A sample (S3) was directly taken from a salt

    eforescence.

    All samples were collected with sterile scalpels and vials by scraping off

    surface material and plaster to a depth of 13mm. Samples were used

    within a few hours for conventional enrichment and cultivation.

    2.2. Cultivation strategy

    Two different media were used for enrichment: M2 medium

    (Tomlinson and Hochstein, 1976) and maintenance medium (MM)

    (Spring et al., 1996). Enrichments were conducted in 300mL Erlenmeyer

    asks containing 30mL medium. To avoid fungal growth, media were

    supplemented with 50 mgmL1 cycloheximide (Sigma). Flasks wereincubated aerobically at room temperature (2273 1C) and at 37 1C in a

    K. Ripka et al. / International Biodeteriowater bath by shaking using magnetic stirring bars. Over a total period of

    3 weeks, weekly aliquots of 100mL enrichments were plated onto fourDGGE was done as previously described (Muyzer et al., 1993) using a

    D GENE system (Bio-Rad) in 0.5 TAE (20mM Tris, 10mM acetate,0.5mM Na2EDTA; pH 7.8). Conditions used: lineal chemical gradient

    ranged from 25% to 60% (100% denaturant contains 7M urea and 40%

    v/v formamide). Gel electrophoretic separation was done at 60 1C andwere added. PCR was carried out in 25mL volumes and 2.5 mL templatewas added.

    Two different PCR reactions were carried out to amplify eubacterial

    16S rDNA fragments. For DGGE analysis, 200-bp fragments of the 16S

    rDNA were amplied using the eubacterial specic primer 341fGC

    (forward) to which a 40-base GC clamp was added to its 50 end (Muyzer etal., 1993). As reverse primer, the universal consensus primer 518r (Muyzer

    et al., 1993) was used. For sequencing analyses, 1500-bp 16S rDNAfragments were amplied using the forward primer 27f and the reverse

    primer 1492r (Lane, 1991). PCR reactions were performed using a

    Robocycler (Stratagene). PCR conditions: 5min denaturation (95 1C),followed by 30 cycles consisting of 1min denaturation (95 1C), 1minprimer annealing (55 1C) and 2min primer extension (72 1C), with a nalextension step of 72 1C for 5min.[O/F test], citrate utilisation, indole production, hydrolysis of casein and

    starch) were carried out as described by Smibert and Krieg (1994). Oxidase

    activity was tested using commercial test strips (Bactident oxidase;

    Merck).

    2.5. Molecular characterisation

    2.5.1. DNA extraction and PCR analysis

    Genomic DNAs were extracted according to the protocol provided by

    Ausubel et al. (1991). For PCR analysis, 2 PCR Master Mix (Promega)(50 units/mL of Taq DNA polymerase supplied in a proprietary reaction

    buffer (pH 8.5), 400mM dATP, 400mM dGTP, 400mM dCTP, 400mMStrains K3-1, I3, and I7 (Pinar et al., 2001c), and strains I3R and I3A

    were isolated from the chapel of Herberstein castle. Strains S3, S4, S20,

    S21, and S22 were isolated from the stonework of the chapel of St.Virgil in

    Vienna. All isolates were stored at 70 1C in MM broth containing 20%(w/v) glycerol as cryoprotectant. Bacterial inocula for all experiments were

    taken from cryopreserves, streaked onto MM plates and cultivated at

    37 1C for 48 h. Reference type strains of Halobacillus used in this studywere: Halobacillus karajensis DSM 14948T, Halobacillus halophilus DSM

    2266T, Halobacillus litoralis DSM 10405T, Halobacillus trueperi DSM

    10404T, Halobacillus locisalis DSM 16468T (DSMZ, Deutsche Sammlung

    von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany)

    and H. salinus JCM 11546T (JCM, Japanese Collection of Microorgan-

    isms, RIKEN BioResource Center, Japan).

    2.4. Phenotypic characterisation

    Growth at different NaCl concentrations (0%, 1%, 5%, 10%, 15%,

    20%, 25%, and 30% w/v) was determined on M2A agar (Denner et al.,

    1994); plates were incubated aerobically at 37 1C for 48 h. Cell morphologywas examined on a Leitz Diaplan (Germany) phase contrast microscope.

    Gram staining, KOH-lysis test and conventional biochemical tests (i.e.,different solid media: M2 medium (20% w/v NaCl), M2A medium (20%

    w/v NaCl) (Denner et al., 1994), Halococci medium (25% w/v NaCl), and

    LB medium (Atlas, 1995). All media were incubated aerobically at room

    temperature and at 37 1C.

    on & Biodegradation 58 (2006) 124132 125200V for 3.5 h. Subsequently, gels were stained with ethidium bromide

    and documented using a UVP gel documentation system.

  • 2.5.3. 16S rDNA sequencing and phylogenetic analyses

    The individual 16S rDNA fragments (1400 bp) were puried with theQIAquick PCR Purication Kit (Qiagen) and sequenced as described

    previously (Pinar et al., 2001c). The sequences obtained were compared

    with known 16S rDNA sequences of prokaryotes contained in the

    Ribosomal Database Project (RDP) (Maidak et al., 1999) and the EMBL

    database. Initial sequence data base search was performed by the

    SIMILARITY-RANK tool of the RDP and the FASTA search option

    (Pearson, 1994). Pair-wise evolutionary similarities and distances were

    computed by using the phylogeny inference package (PHYLIP) (Cole

    et al., 2003) of the online analysis of the RDP-II. A total of 1262 bases

    were compared.

    2.5.4. Random amplified polymorphic DNA-polymerase chain reaction

    (RAPD-PCR)

    For RAPD analysis, PCR was performed with 10 different primers (see

    gels and electrophoresed in 1 TBE buffer (5 TBE/L: 54 g Tris; 27.5 gBorat, 20mL 0.5M EDTA; pH 8.0) for 7 h at 100V using a D GENE

    system (BioRad, Munich, Germany).

    3. Results

    3.1. 16S rDNA sequence analysis

    All strains isolated from wall paintings and buildingmaterials (n 10) investigated in this study clustered withspecies of the genus Halobacillus (97.599.0% similarity),most closely to H. trueperi (98.699.0% similarity) and toH. litoralis (98.698.9% similarity) (Spring et al., 1996).These high-sequence similarities clearly indicate that theyare phylogenetically closely related, but do not allow one tocondently evaluate whether they should be considered tobelong to a single species (Fox et al., 1992). The halobacillistrains clustered in three groups: group Istrains S3, S4,S21, and S22 (99.8100% similarity); group IIstrains K3-1, I7, and S20 (99.399.7% similarity); and group IIIstrains I3, I3A, and I3R (100% similarity). Group I showed98.698.9% and 99.299.3% similarity with groups II andIII, respectively. Group II showed 98.598.8% similaritywith group III.

    ARTICLE IN PRESSK. Ripka et al. / International Biodeterioration & Biodegradation 58 (2006) 124132126Table 1). To the 1 diluted Mastermix (Promega), primer concentrationsfrom 3 to 15 nM were applied. PCR was carried out in 25 mL volume towhich 2.5mL of template was added.

    When using 10-nt primers, PCR was performed under the following

    thermocycling conditions: 4 cycles of [94 1C, 5min; 36 1C, 5min; and72 1C, 5min], 30 cycles of [94 1C, 1min; 36 1C, 1min; and 72 1C, 2min]followed by a nal step for 10min at 72 1C (Williams et al., 1990).

    When primer oligos X17 nt were used, the cycling programme was 4cycles of [94 1C, 5min; 40 1C, 5min; and 72 1C, 5min; low stringencyamplication], 30 cycles of [94 1C, 1min; 55 1C, 1min; and 72 1C, 2min;high stringency amplication] and a nal elongation step for 10min at

    72 1C (Welsh and McClelland, 1990).The whole reaction batches were run in a 2% (w/v) agarose gel at 160V

    for 2 h, stained with ethidium bromide and visualised with an UVP gel

    documentation system.

    2.5.5. Intergenic transcribed spacer-homoduplexheteroduplex (ITS-HHP)

    PCR

    For PCR, 12.5 pmol of each primer, S-D-Bact-1494-a-S-20 and L-D-

    Bact-0035-a-A-15 (Daffonchio et al., 2003), was used. PCR was carried

    out in 50 mL, to which 3.5mL template was added. PCR conditions: 4mindenaturation at 94 1C, then 35 cycles [94 1C, 1min; 55 1C, 7min; and 72 1C,2min] with a nal extension step at 72 1C for 7min (Daffonchio et al.,2003).

    The PCR products were run on three different kinds of gel: rst, 25 mlof PCR product was run at 160V for 2 h in a 2% (w/v) agarose gel;

    second, 6% (w/v) acrylamide gels and mutation detection enhancement

    (MDE) gels were used for...

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