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Applied and Environmental Microbiology, April 2004, p. 2052-2060, Vol. 70, No. 4
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.4.2052-2060.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Centre de Recherche, de Développement et de Transfert Technologique Acéricole Inc.,1 Centre de Recherche et de Développement sur les Aliments, Agriculture et Agro-alimentaire Canada, St-Hyacinthe, Quebec J2S 8E3,2 Département de Pathologie et de Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec J2S 7C6, Canada3
Received 21 August 2003/ Accepted 14 January 2004
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- and ß-Proteobacteria, respectively, were the most frequently encountered genera. Gram-positive bacteria were also observed, and Staphylococcus, Plantibacter, and Bacillus were the most highly represented genera. The sampling period corresponding to 50% of the cumulative sap flow percentage presented the greatest bacterial diversity according to its Shannon diversity index value (1.1).
-Proteobacteria were found to be dominant almost from the beginning of the season to the end. These results are providing interesting insights on maple sap microflora that will be useful for further investigation related to microbial contamination and quality of maple products and also for guiding new strategies on taphole contamination control. |
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Since these pioneer works on maple sap microbiology, maple syrup production operations have significantly changed (10). Tapping procedures now use smaller spouts made of plastic materials instead of larger metallic spouts. Maple sap collection procedures also differ from historical ones by using plastic tubing and vacuum instead of metal buckets. Added to the evolution of the sugarbush operations is the fact that the microbiological identification methods have also considerably evolved over the years. Molecular tools for the identification of microorganisms are now in common use, and 16S rRNA gene analysis is intensively used in phylogeny studies. Among the 16S rRNA gene analysis methods is amplified ribosomal DNA restriction analysis (ARDRA). This molecular technique has been successfully used for bacterial community analysis in a great variety of environments, including food (2, 7, 22, 23).
All these changes are contributing to the need for updated information on the microbial ecology of maple sap. Therefore, the aim of this work was to analyze the cultivable bacterial community of maple sap coming out of the taphole by molecular techniques. Better knowledge of bacterial composition in sap will undoubtedly contribute to improvement of control strategies for prevention of taphole contamination.
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Bacterial counts and culture isolation.
Bacterial counts were performed on each maple sap sample. Total aerobic counts were obtained by diluting the samples in 0.1% peptone water (Difco Laboratories, Detroit, Mich.) and spread plating in duplicate on plate count agar (Difco Laboratories) supplemented with 0.5% of sucrose. Incubation was performed at 30°C for 48 h followed by 7°C for 10 days to increase the differences in colony appearance. Bacterial isolates were obtained from plate count agar plates presenting between 30 and 150 colonies (from one to eight colonies per sample). The isolates were picked to represent the widest variation of colony appearance (form, color, and texture) and then purified by three successive cultivations on tryptic soy agar (Difco) at 30°C for 24 to 48 h. Stock cultures were prepared in brain heart infusion medium (Difco) supplemented with glycerol and kept frozen at 80°C prior to use.
Total DNA extraction.
The DNA of bacterial isolates was prepared according to the procedures of Vincent et al. (27) with the exception that for gram-negative bacteria, no mutanolysin was used. The concentration of purified DNA was measured using Hoechst 33258 dye and a fluorometer (Hoefer DyNA Quant 200; Pharmacia Biotech, Piscataway, N.J.).
PCR amplification.
The amplified 16S rRNA gene was obtained from each isolate and reference strain by PCR with the universal primers F27 (5'-AGAGTTTGATCMTGGCTCAG-3') (3) and R1492 (5'-TACGGYTACCTTGTTACGACTT-3') (28), which are targeted to universally conserved regions and permit the amplification of an approximately 1,500-bp fragment. PCR amplification was carried out in a GeneAmp PCR System 9600 thermocycler (Perkin-Elmer Corporation, Norwalk, Conn.). Reaction tubes contained 25 ng (5 µl) of DNA extract, 1 U of Taq DNA polymerase (Pharmacia Biotech), 1x buffer (10 mM Tris-HCl [pH 9.0], 1.5 mM MgCl2, 500 mM KCl), 10 mM deoxynucleoside triphosphate, and 20 pmol of each primer/µl. Initial DNA denaturation and enzyme activation steps were performed at 95°C for 4 min, followed by 35 cycles of denaturation at 94°C for 30 s, annealing at 56°C for 1 min and extension at 72°C for 1 min, and a final extension at 72°C for 10 min. The presence and yield of specific PCR product (16S rRNA gene) was monitored by 1% agarose (wt/vol) (BioShop Canada) gel electrophoresis at 200 V for 1 h in 1x Tris-acetate-EDTA buffer and made visible by ethidium bromide staining and UV transillumination.
ARDRA procedure.
Three restriction enzymes were selected on the basis of simulated digests of the complete 16S rRNA gene sequences of chosen reference strains retrieved from GenBank. These strains are listed along with the accession numbers in Table 1. The selection of the reference strains was based on a preliminary study performed in our laboratory on bacterial population of maple sap from which different isolates were identified (data not shown) using the API 20E and 20NE strips (Biomerieux, Marcy-l'Etoile, France). The enzymatic reactions were simulated via the NEB cutter software, version 1.0, of the New England BioLabs website, using all commercially available enzymes. For digest experiments, cost-effective combinations of three enzymes were chosen, revealing clearly different (and thus by agarose gel electrophoresis clearly resolvable) restriction site polymorphisms in the reference strain sequences. Unpurified PCR products were each digested with the three selected restriction enzymes in separated reactions. The chosen enzymes were RsaI, HaeIII, and AluI. The digestions were performed for 2 h at 37°C in 20-µl reaction volumes containing 10 µl of the PCR product solution, 2 µl of the commercially supplied incubation buffer, 7.5 µl of water, and 0.5 µl (10 U/µl) of the restriction enzyme. Reaction products (10 µl) were run on a 2% agarose 1000 gel (GibcoBRL, Life Technologies Inc., Burlington, Ontario, Canada) in 1x Tris-borate-EDTA buffer for 4 h at 250 V under refrigeration. Gels were stained with ethidium bromide, made visible by UV transillumination, and digitalized with the gel print 2000i system (Bio/Can Scientific Inc., Mississauga, Ontario, Canada). The images were analyzed with the GelCompar software (Molecular Analyst Software Fingerprinting Plus; Bio-Rad Laboratories, Hercules, Calif.). The background was subtracted by the rolling disk method, and the normalized patterns obtained with each enzyme were combined to obtain a single pattern for each isolate or reference strain. The patterns were used to construct a dendrogram by using the unweighted pair group method using arithmetic averages (UPGMA) clustering algorithm using the Pearson correlation coefficient along with the fine optimization option. Bacterial isolates showing the same banding pattern were assembled to form a group. After distribution of the isolates according to their group and the sampling period (Table 2), the bacterial diversity was calculated for each sampling period by the Shannon diversity index (H) (17). For the diversity index calculation (see Fig. 5), the following equation was used: H = 1/N
(logNi logN) Ni, in which N represents the total number of isolates in a sampling period and Ni is the number of isolates for a single group.
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TABLE 1. List of reference strains and accession numbers used for ARDRA method development
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TABLE 2. List of bacterial isolates obtained in this study representing each ARDRA group and their closest affiliation according to the V1, V2, and V6 hypervariable regions (8) partial sequencing (525 bp) of 16S rRNA gene.
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FIG. 5. Change in the maple taphole bacterial composition over the sap flow season. Composition of the taphole bacterial community is described by the different classes of bacteria and the Shannon diversity index (H) for each sampling period (cumulative sap flow percentage).
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16S rRNA gene partial sequencing and sequence analysis.
PCR products obtained from 48 cloned bacterial isolates were sequenced using an Applied Biosystems 310 sequencer (ABI 310 DNA sequencer, Big Dye Terminator cycle sequencing ready kit; Perkin-Elmer). Sequences of the PCR products (each 1,500 bp) obtained with the F27 and R1492 primers were partially sequenced using primers M13F (Invitrogen), 342R (16), and 800R (1). The partial sequences used to determine similarities were analyzed from the F27 primer to the conserved region corresponding to the sequence 5'-GTGCCAGCMGCCGCGGTAATAC-3', thus giving an approximately 525-bp fragment. The 16S rRNA gene sequences which have been determined in the present study were deposited in the National Center for Biotechnology Information database and are available under the accession numbers shown in Table 2. The FASTA database of the European Bioinformatics Institute (EMBL), accessible on the internet (http://www.ebi.ac.uk/fasta/) was used to find nearly identical sequences for the 16S rRNA gene sequences determined. The ClustalW program, from the European Bioinformat-ics Institute (EMBL), accessible on the net (http://www.ebi.ac.uk/clustalw/), was used to align the sequences. Sequence dissimilarities were converted to evolutionary distances according to the method of Jukes and Cantor (13). The construction of neighbor-joining tree (see Fig. 4) (24) and bootstrap analysis of 500 resamplings (6) were performed using Mega 2 software (molecular evolutionary genetics analysis, version 2.1).
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FIG. 4. Phylogenetic tree of 48 maple sap bacterial isolates based on 16S rRNA gene partial sequences. The bootstrap consensus tree (50% cutoff value) was constructed by using the UPGMA.
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FIG. 1. Change in the contaminating bacterial population of the sap obtained from maple tree tapholes during the 2001 and 2002 seasons. Average results (n = 10) are presented with standard deviations (bars) for each sap flow cumulative percentage.
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FIG. 2. Agarose gel-generated ARDRA dendrogram illustrating the relationship (percent similarity) between different reference bacterial strains obtained from American Type Culture Collection that were used for ARDRA method development. ARDRA banding patterns were obtained by independent digestion of the amplified 16S rRNA gene with RsaI, HaeIII, and AluI endonucleases. The dendrogram was constructed with Molecular Analysis Software Fingerprinting Plus and grouped with the UPGMA.
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-Proteobacteria, Flavobacteria, and Sphingobacteria. Actinobacteria and
-Proteobacteria encountered the highest number of different ARDRA groups, with 12 and 9, respectively.
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FIG. 3. Dendrogram of maple sap bacterial isolates representing each ARDRA group. ARDRA banding patterns were obtained after independent restriction digestion of the amplified 16S rRNA gene with three different enzymes (RsaI, HaeIII, and AluI). The dendrogram was constructed with Molecular Analysis Software Fingerprinting Plus and grouped with the UPGMA.
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-Proteobacteria class dominated from 25% of cumulative sap flow to the end of the season. Diversity, as indicated by the Shannon diversity index (H), was highest at 1.1 at midseason and was less at the beginning and at the end, according to data in Fig. 5. |
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TABLE 3. Maple taphole bacterial isolates distribution according to ARDRA groups, restriction patterns, and the evolution of the season as determined by the cumulative sap flow percentage
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In this way, results obtained in this study have demonstrated the great bacterial diversity of the maple taphole. Gram-negative organisms were among the prevailing bacteria, and
-Proteobacteria, including the Pseudomonas genus, were most frequently encountered. This observation was also made by Sheneman and Costilow (25), who have found that P. geniculata, now known as Pseudomonas fluorescens biotype G, was dominant in the maple taphole when old techniques of production were applied. The presence of P. geniculata in maple sap has already been found to enhance the characteristic flavor of maple syrup (20, 29). Our results showed that the ARDRA method was able to differentiate the Pseudomonas genus from others and that it was also useful for the discrimination of other genera and species of bacteria. The presence of the genus Pseudomonas was expected due to its importance in natural ecosystems, in relation notably with the degradation of xenobiotic compounds, its effect as a plant pathogen, and its plant growth-promoting activities (9, 12). Our study also reports the important presence at the maple tree taphole of ß-proteobacteria from the genus Ralstonia (group 7), observed throughout the season. This genus was not reported in previous publications. The only reported genus closed to Ralstonia was Achromobacter, which is also part of the ß-Proteobacteria class (25).
A total of 32 patterns were identified among the 190 isolates from maple taphole. The 32 ARDRA patterns represented organisms belonging to six bacterial divisions, namely Actinobacteria, bacilli, ß- and
-Proteobacteria, Flavobacteria, and Sphingobacteria. Actinobacteria and
-Proteobacteria encountered the highest number of ARDRA groups. The community diversity in maple sap was observed by determining phylotype richness, distribution, and similarity for 32 16S rRNA gene clones from each ARDRA group. Our results are in agreement with those of previous studies using conventional microbiological methods. Looking at our results, some analogies could be made with the bacterial community of maple sap and those observed for the forest soils. For instance, Morselli and Whalen (18) have demonstrated that the wood tissue of a healthy maple tree is sterile or practically sterile, suggesting that contamination of the taphole would necessarily come from the surrounding environment of the tree. Thus, microorganisms encountered in the forest soil could possibly contaminate the tree bark and find their way into the taphole and consequently into maple sap. The rhizosphere is a dynamic niche containing complex microbial communities, and microbial members may participate in a variety of beneficial and detrimental interactions with plants. Bacterial community members of rhizosphere from British Columbia (Canada) forest soils were characterized by DNA sequence analysis of 16S rRNA gene fragments following direct DNA isolation from soil, PCR amplification, and cloning. Phylogenetic analyses revealed that 85% of 709 16S rRNA gene clones were classified as
-, ß-,
-, and
-Proteobacteria, Actinobacteria, Cytophaga-Flexibacter-Bacteroides group, Acidobacterium, and Verrucomicrobia. Members of the Proteobacteria had an important contribution, representing 55% of the clone library (4).
In addition, the predominant presence of proteobacteria and gram-positive bacteria, such as bacilli and staphylococci, isolated from the maple taphole may be due in part to the use of aerobic-growth media. Kasahara and Ahttori (14) observed that in a study of two soils in Japan, 71% of the isolates that formed visible colonies within 18 h of incubation were members of the gram-positive species. As the length of the incubation period increased, the relative abundance of gram-positive organisms in the total collection of isolates decreased. This observation might explain in part our results on dominant members of maple sap microflora and on its diversity.
This study examined the cultivable bacterial community of maple sap by using the ARDRA method and 16S rRNA gene fragment sequencing. Results showed the great diversity of this bacterial community by the large number of ARDRA patterns observed in relation to the evolution of the sap flow season. After partial 16S rRNA gene sequencing, identities of ARDRA group representatives were revealed. Although sugaring operations have significantly changed since earlier studies on maple taphole microflora, the members of the genus Pseudomonas are still dominant in this environment. Dominance of the genus Ralstonia was also observed, which has not been reported before. Our results also show a greater bacterial diversity than previous work. For instance, an analogy was made between the bacterial community profile of the maple taphole and the bacterial community of the forest soil rhizosphere. These results provide interesting insights into maple taphole microflora that will be useful for further investigations of phenomena related to microbial contamination and quality of maple products and also of microbial control strategies.
We thank Carmen Charron, Mélissa Cournoyer, and René Desruisseaux for their technical work on sample collection and microbial counts.
Present address: Department of Food Science and Nutrition, Laval University, Qc. G1K 7P4, Canada. ![]()
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