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Applied and Environmental Microbiology, March 2006, p. 1932-1938, Vol. 72, No. 3
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.3.1932-1938.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Great Lakes WATER Institute, University of WisconsinMilwaukee, Milwaukee, Wisconsin 53204
Received 30 September 2005/ Accepted 3 January 2006
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The occurrence of Cladophora in nearshore Lake Michigan habitats may have significant public health and ecological importance (18, 43) and could also potentially decrease recreational activities on beaches. There is evidence that the algae provide food and shelter for epiphytes, invertebrates, and small fish (7, 33, 40, 43) and could provide a niche for pathogenic bacteria from gull droppings, sewage overflow, or runoff from urban and agricultural sources (14, 43). The presence of Cladophora has been associated with high levels of Escherichia coli and enterococcal bacteria in beach sand and swimming waters of the Great Lakes (18, 43), which may diminish the relationship between indicator organisms and actual pollution and potentially complicate beach-monitoring efforts.
Cladophora mats that become stranded on beaches produce a noxious odor as the organic material decays. It has been suggested that activities of sulfate-reducing bacterial (SRB) populations on algae play a dominant role in the anaerobic processes in aquatic environments (15, 16), accounting for about 50% of the biomineralization of organic matter (17, 31). In general, the abundance and activities of SRB have been observed to increase with an increase in the supply of organic nutrients (34, 41). Sulfate-reducing bacteria belonging to the
subdivision of the Proteobacteria have been shown to account for significant portions of bacterial populations on microbial mats in lakes (34, 35). In a study of Lake Cadagno (Switzerland), Tonolla et al. (35) found that 24% of the 4',6'-diamidino-2-phenylindole (DAPI)-stained cells were sulfate reducers by using fluorescent in situ hybridization, which corroborated the results of previous studies that documented the dominance of these bacterial groups in freshwater systems (12, 25).
Although the public health and ecological importance of microbial communities on Cladophora mats in freshwater environments have been documented, the structure and composition of such communities remain largely uncharacterized. Therefore, in this study, we employed both culture-based and molecular analyses to examine and characterize microbial communities associated with Cladophora mats collected along the shoreline of Lake Michigan. The primary objective of our study was to determine the abundance and persistence of the fecal indicator bacterium E. coli and the SRB phylogenetic group on Cladophora mats. Additionally, this study was also designed to examine the compositions of microbial communities associated with Cladophora mats using 16S rRNA gene sequencing.
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FIG. 1. Map of counties along Lake Michigan where Cladophora mats and water samples were collected from beaches from July to November 2004 and from June to September 2005.
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Sample collection.
Cladophora samples were collected on 10 sampling days from July through November 2004 and on six sampling days from June through September 2005 to determine the prevalence of E. coli on stranded mats along the shores of Lake Michigan. In all, 63 samples were collected at 11 beach sites. Cladophora mats were obtained from the waterline at each beach site and placed in sterile Whirl-Pak bags. At Bradford Beach, McKinley Beach, and Atwater Beach, the three beach sites used for microcosm studies, as well as several other beach sites, water samples were also collected using a 1-liter grab sampler and transferred to autoclaved sample bottles. Both the Cladophora mats and matching water samples were placed on ice and taken immediately to the laboratory, where they were stored at 4°C until they were analyzed.
Enumeration of E. coli on Cladophora mats from beaches.
E. coli densities on the Cladophora mats and in the matching water samples were determined by membrane filtration using a U.S. Environmental Protection Agency (USEPA) modified method (36). For Cladophora samples, 50 g of algal material was placed in a sterile 1-liter beaker with 600 ml of 0.85% sterile saline and vigorously stirred for 10 min to elute the bacteria from the mats. Then 1 and 10 ml of the supernatant were removed for membrane filtration; for samples in which colonies were too numerous to count, 1 ml of a 1:10 or 1:100 dilution was used. For analysis of water samples, 10 ml and 100 ml were filtered through 0.45-µm nitrocellulose membrane filters, placed on modified m-TEC medium (BD Diagnostics, Sparks, MD), and incubated at 44.5°C overnight. Colonies that exhibited ß-glucuronidase activity, as indicated by a purple color, were counted as E. coli colonies.
Determination of bacterial abundance and persistence on Cladophora mats in microcosm studies.
Microcosm experiments were carried out with freshly collected Cladophora mats to specifically evaluate the persistence of E. coli, sulfate-reducing bacterial, and total bacterial populations in microbial communities in the mats. Approximately 100-g (wet weight) portions of mats were placed in sterile beakers along with 800 ml of lake water collected at the site. Matching water samples that contained no Cladophora were analyzed concurrently to examine the persistence of E. coli over time. The beakers were kept in the dark at room temperature to reduce or prevent photosynthetic activity. Subsamples were collected and examined for the presence of different bacterial populations. For E. coli, microcosms were vigorously stirred, and aliquots were analyzed as described above. Approximately 1 g of algal mat from each sampling site was weighed and added to 5 ml of sterile deionized water. Bacterial cells on the Cladophora mats were detached by sonication (model 2210 sonicator; Branson, Danbury, CT) at 40 kHz for 5 min in 30 ml of 0.1% tetrasodium pyrophosphate (Na4P2O7 · 10H2O) before total bacteria and SRB were counted as described below.
DAPI staining.
The total number of bacteria was determined by concentrating samples under a 15-kPa vacuum onto 0.2-µm-pore-size, black polycarbonate filters (GE Osmonics, Minnetonka, MN), which were stained with 200 µl of 15-µg/µl DAPI for 3 min, rinsed with sterile water, and mounted on glass slides with type FF immersion oil (28). Cells in 10 fields were counted using epifluorescence microscopy (model BX60 microscope; Olympus, Melville, NY).
Fluorescent in situ hybridization.
The abundance of SRB on the Cladophora mats was determined using fluorescent in situ hybridization as described by Manz et al. (20) and Olapade and Leff (23). SRB populations were detected using the SRB385 probe designed to specifically target the
subdivision of the Proteobacteria, as described by Amann et al. (2), which is the phylogenetic group containing most sulfur-reducing bacteria (6, 31, 35); however, this probe also hybridizes with several gram-positive bacteria, such as Clostridium (30). Briefly, samples were concentrated onto 0.2-µm-pore-size polycarbonate filters, rinsed with deionized water, and treated with 1 ml of 0.1% Nonidet P-40 (Sigma-Aldrich, St. Louis, MO). The filters were placed in petri plates and treated with 40 µl of the Texas Red-labeled probe, which was used at a concentration of 5 ng/µl in hybridization buffer consisting of 6x SSC, 0.02 M TRIZMA base (pH 7.0), 0.1% sodium dodecyl sulfate, and 0.01% poly(A) (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate). The filters and probe were incubated at 53°C for 4 h. The sequence of the SRB385 probe was 5'CGGCGTCGCTGCGTCAGG3' (Sigma Genosys, The Woodlands, TX). After incubation, the filters were washed twice with 400 µl of wash buffer, incubated with 80 µl of wash buffer for 10 min at the hybridization temperature, and then rinsed twice with 400 µl sterile deionized water. Cells that hybridized to the SRB385 probe were enumerated using epifluorescence microscopy by counting between 50 and 100 fields on duplicate slides.
DNA extraction and PCR amplification.
Total DNA was extracted from the Cladophora samples in microcosm studies using a QIAamp DNA extraction kit, as described by the manufacturer (QIAGEN, Valencia, CA). DNA was extracted from multiple beakers representing the three beach sites at the start of the experiments. DNA was eluted in 75 µl of sterile, deionized water before the concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Bacterial DNA in a sample was amplified by PCR by targeting the (approximately) full-length 16S rRNA gene with the universal bacterial primers 8F (5'AGAGTTTGATCCTGGCTCAG3') and 1492R (5' GGTTACCTTGTTACGACTT 3') (Sigma Genosys, The Woodlands, TX). The PCR amplification protocol included DNA denaturation at 95°C for 1 min, annealing at 50°C for 1 min, and extension 72°C for 1 min for 30 cycles and a final extension for 5 min at 72°C, using a thermal cycler from MJ Research (Watertown, MA). The amplification products were evaluated on a 1.5% agarose gel. The PCR products were purified with a QIAquick PCR purification kit (QIAGEN, Valencia, CA) before they were utilized for cloning and sequencing assays.
Cloning and sequencing.
Clone libraries from 16S rRNA gene amplification were constructed using a TOPO TA cloning kit (Invitrogen, Carlsbad, CA). Plasmid DNA was isolated using a QIAGEN plasmid mini kit (QIAGEN, Valencia, CA). Sequencing of the 16S rRNA gene was performed with a CEQ 8000 automated sequencer, using the chain terminator technique with dye-labeled dideoxynucleotides, according to the manufacturer's instructions (Beckman Coulter, Fullerton, CA).
Phylogenetic analysis.
Approximately 200 clones from three 16S rRNA clone libraries were randomly chosen for sequencing. The sequences obtained were trimmed for quality before alignment, using the Vector NTI software (Invitrogen, Carlsbad, CA). Neighbor-joining trees were constructed using ClustalW with 1,000 bootstrap iterations and NJ plot (27). The clone sequences were compared with previously published GenBank sequences using the BLAST system (1) in order to determine close relatives.
Statistical analyses.
Statistical analyses were carried out using SPSS, version 10.01 (SPSS Inc., Chicago, IL). Differences between numbers of bacteria were determined by Student t test analysis after normalization of all data sets by log10 transformation.
Nucleotide sequence accession numbers.
The partial 16S rRNA gene sequences have been deposited in the GenBank database under accession numbers DQ228212 to DQ228252.
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TABLE 1. E. coli densities on Cladophora mats collected from beach sites on Lake Michigan
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FIG. 2. Numbers of E. coli (log transformed) on Cladophora mats (A) and in lake water samples (B) collected from beach sites (McKinley Beach, Bradford Beach, and Atwater Beach) along the Lake Michigan shore. The values are averages for replicate samples from each microcosm. The standard errors were less than 6% of the E. coli values for Cladophora samples and less than 10% of the E. coli values for water samples.
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Numbers of total and sulfate-reducing bacteria.
In general, the numbers of total and sulfate-reducing bacteria on the Cladophora mats in microcosms were fairly similar for the three sites (Fig. 3A and 3B). The numbers of sulfate-reducing bacteria that hybridized to the SRB385 probe on freshly collected Cladophora mats ranged from 4.4 x 106 cells/g (6.64 log CFU/g) to 5.73 x 106 cells/g (6.76 log CFU/g) and remained consistently high after 7 days in microcosms (Fig. 3B). The SRB in the microbial communities accounted for between 20% and 27% of the total bacteria at the three sites.
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FIG. 3. Numbers of SRB (A) and percentages of DAPI-stained cells positive for the SRB385 probe (B) on Cladophora mats collected from McKinley Beach, Bradford Beach, and Atwater Beach in Wisconsin during survival studies conducted in microcosms. The values are averages for replicate samples from each microcosm.
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- and ß-Proteobacteria and accounted for 2.4% and 6.4% of the clone libraries (Table 2). Cluster 3 contained only three clones belonging to the
-Proteobacteria, representing <1.0% of the clone libraries, while the
subdivision of the Proteobacteria (cluster 4) accounted for 3.2% of the clone libraries. Clusters 5 and 6 accounted for 12.8% and 4.8% of the clone library and belonged to the low-G+C-content and high-G+C-content gram-positive bacteria, respectively. The largest cluster was the Cytophaga-Flavobacterium-Bacteroides (CFB) bacterial group, which accounted for about 40% of the total clone library.
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FIG. 4. Phylogenetic consensus tree based on neighbor-joining analyses of partial 16S rRNA gene sequences, showing the representative clones of predominant bacterial taxa.
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TABLE 2. Distribution of 200 cloned 16S rRNA gene sequences obtained from the epiphytic bacterial communities on Cladophora mats collected from three beach sites along Lake Michigan shores
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Abundance and persistence of sulfate-reducing bacteria on Cladophora mats.
Quantitative analysis of the microbial communities on the Cladophora mats using the SRB385 fluorescently labeled probe indicated that the numbers of sulfate-reducing bacteria were relatively high, perhaps higher than the numbers based on results obtained from clone libraries. The obvious disparity between the two methodological approaches could be attributed to the comparatively low coverage of this phylogenetic group by the sequencing approach. Overall, the sizes of the populations of bacteria belonging to the SRB functional group in the microbial communities examined in our study fell in the range that was previously documented in similar studies (31, 34). In a study in which a traditional most-probable-number approach was used, Teske et al. (34) found an average of 4.5 x 106 SRB cells/ml on the surface layer of cyanobacterial mats of Solar Lake (Sinai, Egypt). Also, Santegoeds et al. (31), using the same SRB385 probe that was used in our study, found an average of 64 x 106 SRB cells/ml on the surface of a 2-week-old artificially constructed bacterial biofilm. Cross-hybridization of the SRB385 probe with non-SRB members of the community also should be considered, as this probe has been shown to detect gram-positive bacteria, such as Clostridium spp. (30). The occurrence of bacteria belonging to the SRB functional group on Cladophora mats examined in this study may further corroborate the well-documented alga-bacterium association found in previous studies, based in part on the reliance of heterotrophic bacterial populations on alga-released dissolved organic carbon in surface-associated microbial communities (10, 23).
Bacterial community composition on the Cladophora mats.
The cloned sequences obtained from the epiphytic bacterial communities on Cladophora mats belonged to various phylogenetic groups in the domain Bacteria, including the CFB cluster, the high- and low-G+C-content gram-positive bacteria, and the
, ß,
, and
subdivisions of the Proteobacteria. Several of the clones used in this study were most closely related to sequences that were characterized as previously unclassified or uncultured bacteria based on sequences in the GenBank database, suggesting that a high number of phenotypically undescribed bacterial species were present in the community, as observed in other studies of bacterium-alga interactions (9).
The CFB phylogenetic group was the most abundant clone group obtained from the Cladophora mats, which corroborated the results of previous studies that documented that there were high levels of bacterial species belonging to the CFB cluster in similar alga-bacterium associations in aquatic systems (9, 42). In general, bacterial species belonging to the CFB cluster have been reported to account for a high percentage of biofilm bacteria in aquatic systems (24) because they possess unique phenotypic characteristics that enable them to attach to particles, exhibit surface-dependent gliding motility, and utilize various complex macromolecules (44). The high percentage of clones in this phylogenetic group perhaps reflects the active degradation of high-molecular-weight organic carbon (i.e., cellulose) and various other macromolecules on the Cladophora mats.
The relatively high numbers of bacteria belonging to the high-G+C-content gram-positive group in the microbial communities on the algal mats were not too surprising, despite the fact that this group usually occurs at fairly low levels in aquatic systems (3). We expected high levels of bacteria belonging to both the CFB cluster and the gram-positive bacteria in the microbial communities on the Cladophora mats, since both of these bacterial groups typically comprise species that can thrive under both the oxic and anoxic conditions (29) commonly found on cyanobacterial mats located in freshwater environments (34).
The four subdivisions of Proteobacteria (i.e.,
, ß,
, and
subdivisions) that were found in this study accounted for a relatively high proportion of the total cloned sequences in the microbial communities on the algal mats. Among these bacterial groups, bacteria belonging to the ß-Proteobacteria generally predominated; this finding is consistent with the results of previous studies that showed that there were high proportions of ß-Proteobacteria in aquatic biofilms (5, 22, 32). Although bacteria belonging to the
-Proteobacteria accounted for the lowest proportion of sequences in our study, a high number of bacterial species with the ability to reduce sulfate belong to this subdivision and have been found previously in bacterial biofilms in other studies (31, 34).
Ecological and public health significance and future directions.
There has been increased emphasis on beach water quality in recent years by both the USEPA and the public health sector, and as a result, more beaches are being monitored for fecal pollution (38). Cladophora accumulation at the shoreline, a common occurrence at Great Lakes beach sites, might be a major complicating factor in assessing beach sites for fecal pollution. The potential for Cladophora mats to harbor pathogens, as well as indicator bacteria, warrants further study.
Typically, a person's initial perception of water quality is based entirely on the esthetic characteristics of the water and the surrounding environment (26). Decaying Cladophora emits a noxious odor which frequently can be mistaken for sewage contamination. The bacteria belonging to the CFB cluster in the microbial communities are most likely responsible for the majority of cell material breakdown on the algal mats and may produce the anoxic environment required for SRB, which are mainly obligate anaerobes (19). The metabolic activity of members of the SRB functional group, especially organisms belonging to the
-Proteobacteria, may contribute the most to the noxious odor that is characteristic of the beach sites along Lake Michigan. Additionally, the presence of SRB on the Cladophora mats suggests that the availability of sulfate is high and that the sulfate is metabolized, releasing hydrogen sulfide gas, which has a characteristic pungent odor. There is a need for studies examining this and establishing a direct correlation between populations of bacteria belonging to the SRB group on Cladophora mats and hydrogen sulfide production in order to further understand the ecological importance of the mats.
We thank Meredith Van Dyke, Joshua Harris, Marcia Silva, and Pat Bower for their assistance with various laboratory assays and Kiara Caldwell for assistance with fieldwork. We also appreciate the contributions to the sequence analysis made by Giles Goetz. We especially thank Harvey Bootsma for providing expertise and discussions concerning Cladophora in the Great Lakes environment.
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