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Applied and Environmental Microbiology, June 2008, p. 3710-3717, Vol. 74, No. 12
0099-2240/08/$08.00+0 doi:10.1128/AEM.02645-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
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Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, North Carolina 28557,1 Center for Coastal Fisheries and Habitat Research, National Ocean Service, NOAA, 101 Pivers Island Road, Beaufort, North Carolina 28516-97222
Received 21 November 2007/ Accepted 15 April 2008
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Because of the amount of environmental degradation and potential health problems associated with Lyngbya blooms, there is interest in managing their occurrence. An effective management strategy, however, may depend, in part, on knowing whether or not L. wollei comprises one or several species which may vary in their environmental requirements, physiological characteristics, and toxicity. The advent of molecular techniques has shown that morphologically defined species can, in fact, be multiple genetically distinct species which can have different habitat preferences (3). The specific sequences selected for analysis included regions of both the small-subunit (SSU) rRNA and nifH genes. SSU rRNA plays a crucial catalytic function in protein synthesis, and the corresponding gene has historically proven to be useful for the identification of cyanobacterial species (10, 24). Cyanobacterial SSU rRNA gene sequences collected from environmental samples are often classified into operational taxonomic units (OTUs), i.e., groups that are >97% similar (22, 27). The nifH gene encodes a crucial Fe protein subunit, dinitrogenase reductase, involved in N2 fixation and has also been used extensively for the taxonomic characterization of cyanobacterial species (29).
In this study, L. wollei samples were collected from geographically dispersed environments and sequenced. Geographically dispersed sampling made it possible to assess the coherence between the SSU rRNA and nifH gene subclusters, as well as the distribution of specific strains or species showing >97% SSU rRNA gene sequence similarity (OTUs). At the same time, cell measurements on filaments collected at various sites were made to determine whether or not they fell into the size range ascribed to L. wollei (19). To determine if what is normally identified in sampling programs as L. wollei encompassed distinct strains or species, samples were taken from a number of springs, lakes, and rivers for both morphometric analysis and sequencing. The morphometric measurements were used to determine if the samples collected met the published criterion for this species and for comparison with the resulting phylogenetic analysis (19). Further, environmental data, including flow rates (14, 18), soluble-nutrient concentrations (http://nwis.waterdata.usgs.gov/fl/nwis/qwdata), and major ion concentrations (18, 25, 26), were collected to determine if any of the identified OTUs exhibited habitat preferences.
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TABLE 1. Collection sites for the Lyngbya sp. samples used in this study
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100 mg (wet weight) in a tube containing glass beads. The samples were then alternated between an 80°C water bath for 1 h and at least 1 min in a bead beater (Biospec Products, Inc., OK) to lyse the cells. DNA was then purified with a DNeasy Plant Kit (Qiagen, Valencia, CA). A blank extraction control where reagents, but no cells, were extracted in the same manner as a normal sample was included during each DNA extraction to control for cross-contamination between samples. Single-filament extractions were performed as previously described (9).
PCR amplification.
From each genomic DNA extraction, both a 324-bp segment of the nifH gene and a 374-bp segment of the SSU rRNA gene were PCR amplified with cyanobacterium-specific primers (10, 11). PCR amplicons were gel purified, cloned into the pCR 2.1-TOPO vector (Invitrogen, San Diego, CA), and sequenced at the University of North Carolina at Chapel Hill Automated DNA Sequencing Facility with a model 373A DNA sequencer (Applied Biosystems, Foster City, CA) by the Taq DyeDeoxy Terminator Cycle Sequencing method (Applied Biosystems, Foster City, CA).
Phylogenetic analysis.
Sequences were aligned with the SeqLab program (GCG version 11.1; Accelrys Inc., San Diego, CA) and adjusted manually when individual nucleotides were obviously misaligned. Maximum-likelihood phylogenies were constructed with MrBayes (8, 13) by using the HKY-G model (Fig. 1a) and GTR+I+G (Fig. 2) for the SSU rRNA gene and the HKY model for nifH. These specific evolutionary models were selected as optimal after analysis of the alignments with the MrModelTest v. 2.2 program (distributed by J. A. A. Nylander). To simplify the graphical representation of the SSU rRNA gene and nifH phylogenies, the sequences that were 100% homologous or varied by relatively few base pairs were represented by a single sequence (Fig. 1; see also Table S1 in the supplemental material).
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FIG. 1. Phylogenetic distribution of L. wollei partial 374-bp SSU rRNA gene (a) and 324-bp nifH (b) DNA sequences obtained in this study on the basis of Bayesian inference of phylogeny under HKY-G (a) and HKY (b) evolutionary models. Values at nodes are clade posterior probabilities. Values in parentheses are the numbers of replicate sequences with >97% base pair matches from the same site (see Table S1 in the supplemental material for the accession numbers of the sequences represented). Letter-and-number combinations in parentheses are NCBI database accession numbers. Abbreviations: CL, City Lake, High Point; ALX, Alexander Springs; CHA, Chassahowitzka Springs; KB, Kings Bay; FER, Fern Hammock Springs; GAI, Gainer Springs; HOM, Homosassa Springs; ICH, Ichetucknee Springs; IND, Indian Springs; JUN, Juniper Springs; RAI, Rainbow Springs; SGS, Silver Glen Springs; SIL, Silver Springs; SJR, St. Johns River; WAK, Wakulla Spring; WAS, Washington Spring; WW, Weeki Wachee Spring; WEK, Wekiwa Springs; WLL, Williford Spring; WLS, Wilson Spring; WR, Withlacoochee River.
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FIG. 2. Phylogenetic distribution of cyanobacteria and six representative L. wollei partial 374-bp SSU rRNA gene sequences obtained in this study on the basis of Bayesian inference of phylogeny under a GTR+I+G evolutionary model. Node values are clade posterior probabilities. Letter-and-number combinations in parentheses are NCBI database accession numbers.
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TABLE 2. Cell measurements for Lyngbya sp. cells from each SSU rRNA gene (OTU) and nifH (S) sequence grouping
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FIG. 3. Relative ion concentrations, from lowest to highest (1 to 3) segregated according to their corresponding phylogenetic grouping (Fig. 1), at all of the Lyngbya sp. collection sites included in this study. Table 3 contains descriptions of the y-axis groupings. (a) OTU1 to -3 are delineations from Fig. 1 based on a phylogenetic analysis of partial L. wollei SSU rRNA gene sequences. (b) S1 to -3 are delineations from Fig. 1 based on a phylogenetic analysis of partial L. wollei nifH gene sequences. For definitions of abbreviations, see the legend to Fig. 1.
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TABLE 3. y-axis values for Fig. 3 based on previous spring categorization studies involving dominant ion concentrations and milliequivalents
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Statistical analysis.
Statistical analysis consisted of a one-way analysis of variance with SPSS 11.0 software (SPSS Inc., Chicago, IL). A posteriori multiple comparison of means was achieved with the Bonferroni procedure with
= 0.05.
Nucleotide sequence accession numbers.
The nucleotide sequences determined in this study were submitted to GenBank and assigned accession numbers EF397755 to EF397766, EF397768, EF397770, EF397772 to EF39845, EF39847 to EF397908, EF422067, EF450886, EF450892, EF450894, EF450896, EF450900 to EF450903, EF450907, EF450911, EF450912, EF450919, EF450920, EF450922, EF450923, EF450926, EF450928, EF450932, EF450933, EF450937 to EF450939, EF450941, EF450946 to EF450968, EF450975, EF450978, and EF450980 to EF450996.
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TABLE 4. Single-filament extraction sequences and their OTUs or clusters from the SSU rRNA gene and nifH phylogenetic analyses, respectivelya
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Once the length and width data from each sample were recorded, these data were also segregated on the basis of their SSU rRNA gene OTU1, -2, or -3 grouping (Table 2). This was done to determine if there were any significant differences in the sizes of cells belonging to the different OTUs. The average width and length of cells belonging to OTU3 were statistically greater than those of OTU1 and -2 cells (Table 2). Cells belonging to OTU1 and OTU2, however, were not distinguishable from each other morphologically.
When the cell length and width data were sorted on the basis of the specific SSU rRNA gene/nifH subcluster obtained from the same sample, it was apparent that cells belonging to the OTU3/nifH S3 subcluster in the phylogenetic analysis were significantly larger than cells associated with the other two subclusters. Cells belonging to the OTU1/S1 and OTU2/S2 subclusters, in turn, were similar in size and not distinguishable morphologically, despite being genetically distinct.
Environmental parameters.
Each collection site from which Lyngbya samples were obtained was placed in a category based on major ion concentrations as defined by Whitford (25), Woodruff (26), and Slack and Rosenau (18) (Table 3). The goal was to determine if the hardness of the water correlated with specific genetically defined clusters. Collection sites where OTU3/S3 sequences were recovered generally had lower ion concentrations. In contrast, the OTU1/S1 and OTU2/S2 subclusters were more often found in environments exhibiting moderate-to-high ionic concentrations (Fig. 3). None of the OTUs were consistently correlated with average ambient dissolved inorganic N or phosphate concentrations measured at the site or with a specific range of N/P ratios (Fig. 4). Florida springs that were not sampled were not included in this nutrient comparison.
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FIG. 4. N/P ratios and dissolved in organic N and P values for collection sites in this study. (a) OTU1 to -3 are delineations from Fig. 1 based on a phylogenetic analysis of partial L. wollei SSU rRNA gene sequences. (b) S1 to -3 are delineations from Fig. 1 based on a phylogenetic analysis of partial L. wollei nifH gene sequences. For definitions of abbreviations, see the legend to Fig. 1.
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FIG. 5. Spring and river sites within Florida. Each collection site is represented by a symbol that corresponds to an OTU and S designation. The OTUs represent OTUs within the Lyngbya SSU rRNA gene library that we established in this study, and subclusters within a phylogenetic comparison of Lyngbya nifH sequences are represented by S1, -2, or -3 (Fig. 1).
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As stated above, the morphological data were only consistent with the existence of two species. Specifically, the measured dimensions of both OTU1/S1 and OTU2/S2 cells fell within the 24- to 65-µm width and 2- to 12-µm length ranges used to morphologically define L. wollei (19). These data indicate that OTU1/S1 and OTU2/S2 represent what is classically defined as L. wollei (19) and that this morphologically defined taxon actually contains two cryptic species or subspecies. However, the cells of OTU3/S3 were, on average, significantly wider (56.5 µm versus
41 µm) and longer (7.4 µm versus
5.5 µm) than those of OTU1/S1 and OTU2/S2 (Table 2). This size difference, in combination with distinct genetic differences, supports the conclusion that this is a distinct species.
Preliminary evidence also suggests that the putative species represented by OTU3 prefers habitats with a lower average ion content than the other species or subspecies. OTU1 and OTU2, in contrast, were found to occur in environments exhibiting a wide range of ion concentrations and milliequivalents (Fig. 3). These survey data indicated that neither OTU1 nor OTU2 showed any preference for an environment with a particular ion concentration, and this result was consistent with their being more broadly distributed geographically (Fig. 5). Interestingly, none of the OTUs were correlated with the overall availability of residual dissolved inorganic N or P or with differences in average N/P ratios (Fig. 4). The nutrient data collected and compared were from sites that contained Lyngbya mats. The selection of nutrient collection sites was therefore not random. The lack of any consistent N concentration for each OTU is likely due to the fact that L. wollei has the ability to rapidly and efficiently acquire dissolved forms of inorganic N (6) or to fix N when ambient N concentrations are low (12). Extensive nutrient studies of major springs in northern Florida have failed to find a correlation between the occurrence of Lyngbya and either dissolved inorganic N or P concentrations (23). This suggests that, from a management standpoint, while inputs of limiting nutrients might control overall biomass, they do not appear to be the primary factor affecting the distribution of these species.
Since these species are not found in all of the Florida springs that have experienced nutrient enrichment, there may be other limiting factors besides nutrients, including light, grazing, and temperature. Many springs are in protected national or state forests, and there is therefore a limited amount of light that can penetrate the tree canopy to reach the spring surface. L. wollei photosynthesizes the most at low light levels (
31 microeinsteins m–2 s–1) below the mat's surface (21). Springs that are exposed to more light due to little or no tree canopy might support only limited or no Lyngbya growth because of photoinhibition. However, in this study we did not quantify tree canopy coverage nor did we find a previously existing record. With regard to the effects of grazing, a recent study suggests that the sheath that encases L. wollei cells is unpalatable and reduces herbivory (1). Therefore, grazing may not play a significant role in the limitation of L. wollei biomass. Temperature is also unlikely to be involved, as almost all Florida springs are consistently about 22°C.
Given the fact that OTU1 and -2 are widely distributed and do not seem to be limited by nutrients or the suite of environmental conditions associated with different average ionic concentrations or strengths, it is curious that these species or subspecies seldom occupy the same environment (Fig. 1). This raises the question of what may be responsible for this apparent broad but largely nonoverlapping distribution pattern. A possible answer is that the observed pattern is due to limited sampling in each given environment. However, for multiple samples that were taken at different places in a given environment, the same trend holds true. A wide geographic distribution limited in environmental diversity suggests that Lyngbya species have been randomly introduced into different environments. If this is so, it is possible that humans (or birds) may be accelerating the dispersal of filaments, as many of the environments where Lyngbya now occurs are used year-round by recreational swimmers and boaters. If these random Lyngbya introductions find suitable substrates on which to grow, then the final amount of biomass, and concomitant environmental degradation and toxin production, will depend on overall nutrient availability and light levels. Furthermore, if humans are the primary vector for Lyngbya distribution, then normal recreational activities are likely to continue spreading these species in an uncontrollable manner. The data also indicate that multiple species are involved and that at least two of them, commonly referred to as L. wollei, appear to have potentially different habitat preferences.
This study is one of the first to compare a large set of gene sequences (64 SSU rRNA gene sequences, 142 nifH sequences) from a single defined species from a large number of sites (21 freshwater sites). The original purpose of this study was to establish a set of SSU rRNA gene and nifH sequences that could be used to identify L. wollei accurately and relatively quickly. However, it has become apparent from our sequence analyses that the current definition of L. wollei includes a complex assemblage of species. The potential ramifications of this finding extend beyond taxonomy. For example, toxin production and nutrient management studies can now be targeted for each species. In terms of developing an effective management strategy for waters impacted by L. wollei, future work should be directed toward determining if the nutrient physiologies of these apparently distinct species are significantly different and, if so, whether specific phosphate input reductions or manipulation of the light environment would be required to control their abundance in differing ionic environments.
We thank R. Noble, S. Whalen, M. Alperin, and several anonymous reviewers for their critical assessments of the manuscript. T. Steppe, J. Dyble, and L. Cheshire provided technical and analytical assistance. J. Burns, M. Jeansonne, J. Stevenson, and A. Pinowska assisted in sample collection.
Published ahead of print on 25 April 2008. ![]()
Supplemental material for this article may be found at http://aem.asm.org/. ![]()
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