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Applied and Environmental Microbiology, December 2005, p. 7799-7805, Vol. 71, No. 12
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.12.7799-7805.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
College of Marine Studies, University of Delaware, Lewes, Delaware 19958
Received 1 June 2005/ Accepted 9 August 2005
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Previous studies have examined the uptake of glucose and EPS by the total microbial assemblage (22, 29), but little is known about the uptake of these compounds by specific bacterial groups. In the Atlantic Ocean, the alphaproteobacterial group SAR11 accounts for about 50% of glucose assimilation (29). The SAR11 clade and other Alphaproteobacteria are also important in the assimilation of other low-molecular-weight (LMW) compounds, such as amino acids and N-acetylglucos-amine, in Delaware coastal waters (11), and of dimethylsulfoniopropionate in the Gulf of Mexico, the northwestern Mediterranean, the coastal North Atlantic Ocean, and the Sargasso Sea (30, 31, 44). Uptake of EPS by specific bacterial groups has not been examined, but a few studies have considered other high molecular weight (HMW) compounds. Cytophaga-like bacteria appear to dominate protein and chitin use in Delaware coastal waters, whereas Alphaproteobacteria were less important in uptake of these compounds (11). Likewise, SAR11 bacteria accounted for much less of the protein assimilation than of the glucose assimilation in the North Atlantic Ocean (29).
Single-cell analyses of leucine and thymidine assimilation have provided some insights into the contributions of specific phylogenetic groups to bacterial production and thus to total DOM uptake. Cottrell and Kirchman (10) found that 50% of the variation in the assimilation of both leucine and thymidine by a bacterial group was explained by its abundance and that the contribution of the various phylogenetic groups to bacterial production followed the biogeography of these groups in the Delaware Estuary. Data from microautoradiography fluorescence in situ hybridization (micro-FISH) can also be used to examine the fraction of cells within each phylogenetic group assimilating leucine and thymidine (11). In the Delaware Estuary, there is no correlation between this fraction and the relative abundance of bacterial groups (except for Betaproteobacteria), suggesting that these groups are controlled by factors other than bottom-up ones. The relationship between abundance and assimilation of other organic compounds is unclear.
The goal of this study was to identify the main phylogenetic groups that participate in EPS and glucose assimilation in the Delaware Estuary. Polysaccharides are the main carbohydrate in the estuary, as glucose and other monosaccharides cannot be detected (<5 nM) (26), most likely because they are rapidly consumed by microbes. The bacterial community structure changes along the salinity gradient of the estuary, with Betaproteobacteria and Actinobacteria being abundant in the freshwater section while Alphaproteobacteria dominate the lower part of the estuary (10, 27). We hypothesized that the most abundant groups in each location dominate uptake of EPS and glucose. We found that abundance only partially explained the relative uptakes of these compounds, suggesting that bacterial communities are controlled by more than just bottom-up factors, such as DOM concentrations and composition.
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Sample collection and preparation.
Surface water was collected from four locations along the Delaware Estuary in July 2003 (salinities of 0, 13, 21, and 26 practical salinity units [PSU]) and June 2004 (28 PSU). Water samples (30 ml) were incubated with 2 nM [3H]glucose (33 Ci/mmol; Amersham) for 2 h or with 1.5 µM [3H]EPS (concentration in glucose equivalents) for 14 h. Both treatments were incubated at the in situ temperature in the dark. Paraformaldehyde (2% final concentration) was added to killed controls 15 min prior to the addition of the 3H-labeled compounds. At the end of the incubation, samples were fixed with paraformaldehyde (2% final concentration), and all samples were stored at 4°C for 24 h. Samples were then filtered onto 0.2-µm-pore-size polycarbonate filters, which were kept at 20°C until analysis.
FISH and microautoradiography analysis.
FISH analysis was done using the following Cy3-labeled probes: Eub338 for Eubacteria (3); Alf968 for Alphaproteobacteria (20); Bet42a and Gam42a for Beta- and Gammaproteobacteria, respectively (33); CF319a for Cytophaga-like bacteria (32); HGC96a for Actinobacteria (37); and a suite of four probes for SAR11 bacteria (34). Unlabeled competitor probes were used for Beta- and Gammaproteobacteria (33). In addition, a negative probe was used to determine nonspecific binding (24).
Following FISH analysis, samples were subjected to microautoradiography as described by Cottrell and Kirchman (10). Glucose samples were exposed for 12 to 24 h, while EPS samples were exposed for 3 to 6 days. These exposure times were set so that the percentage of total cells associated with silver grains was in the range of 15 to 20%. This range was chosen because that was the maximum percentage of cells assimilating EPS that could be detected. At the end of the exposure time, the slides were developed as described previously (10). The samples were mounted with a 4:1 mixture of Citifluor (Ted Pella) and Vectashield (Vector Labs) containing 0.5 ng/µl of 4',6'-diamidino-2-phenylindole (DAPI) stain and were covered with coverslips. Slides were stored at 20°C until microscopic analysis.
Total cells (DAPI stained), cells affiliated with a specific bacterial group (Cy3 labeled), and cells that assimilated the radiolabeled compound (with silver grains developed during microautoradiography) were counted using a semiautomatic microscope and image analysis as described previously (10). Data were collected from 30 fields of view, and the numbers of cells counted are indicated in Tables 1 and 2. To calculate the percentage of total silver grain area, the total silver grain area around the probe-positive cells was summed and divided by the sum of total silver grain area associated with DAPI-stained cells. Cell volumes were calculated using the algorithm described by Sieracki et al. (39).
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TABLE 1. Average cell sizes of bacteria that were active and inactive in EPS assimilation
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TABLE 2. Average cell sizes of bacteria that were active and inactive in glucose assimilation
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FIG. 1. Percentage of bacteria in each phylogenetic group assimilating radiolabeled DOM verses percentage of total silver grain area around these cells. The data for both EPS and glucose from all locations are included. The error bars in the upper left corner of the panel represent the averaged error bars of all data points. A 1:1 line bisects the graph.
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FIG. 2. Compositions of bacterial communities assimilating glucose (A) and EPS (B) in the Delaware Estuary. The contribution of each group was estimated from the silver grain area. Cytophaga-like bacteria were not detected in 0-PSU water. The glucose sample from 13 PSU could not be analyzed (ND, not determined) due to technical problems. , ß, represent Alpha-, Beta-, and Gammaproteobacteria, respectively, CF represents Cytophaga-like bacteria, and HGC represents Actinobacteria. Error bars indicate standard errors.
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In addition to broad phylogenetic groups, we also examined the contribution of the SAR11 clade, a subgroup of the Alphaproteobacteria (19), to assimilation of glucose and EPS. The SAR11 clade was abundant (20 to 33% of all prokaryotes) in the saline part of the estuary (Fig. 3) but was near detection limits in freshwater (27). Glucose assimilation by the SAR11 clade was significantly higher than that of EPS (25% and 15%, respectively) in two of three stations (t test, P < 0.05). However, SAR11 bacteria assimilated these compounds less than expected based on abundance (Fig. 3).
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FIG. 3. SAR11 clade abundance and contribution to glucose and EPS assimilation in the Delaware Estuary. Abundance is the percentage of all prokaryotes in the SAR11 clade. The contribution of SAR11 bacteria to glucose and EPS assimilation is expressed as a percentage of total silver grain area. For each salinity, significantly different percentages (t test, P < 0.05) are indicated by different letters. NA, not available. Error bars indicate standard errors.
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FIG. 4. Contributions of various phylogenetic groups to glucose (A) and EPS (B) assimilation in the Delaware Estuary. The percentage of the total silver grain area as a function of a phylogenetic group's abundance in the community is shown; 1:1 lines bisect the graphs. Numbers adjacent to the data points indicate the salinity. Error bars indicate standard errors.
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Importance of EPS and glucose assimilation to a phylogenetic group.
The contribution of a specific phylogenetic group to DOM fluxes does not necessarily reflect the importance of a compound to that group. To explore this question, we calculated the fraction of bacteria in each group that assimilated glucose or EPS, i.e., probe-positive cells with silver grains compared with probe-positive cells in that particular group (with and without silver grains). This is different from the case for the previous sections, which present the contribution of each bacterial group to EPS or glucose assimilation, i.e., probe-positive cells with silver grains divided by all cells with silver grains. For example, Alphaproteobacteria accounted for 35% of EPS assimilation in 26-PSU water, but only 12% of Alphaproteobacteria used EPS in this region of the estuary.
Overall, the fraction of bacteria in each group assimilating glucose (15 to 30%) was significantly higher than the fraction assimilating EPS (5 to 20%) (Fig. 5) (paired t test, P < 0.05). More Actinobacteria assimilated glucose than EPS at all locations. Similar fractions of cells affiliated with Alphaproteobacteria assimilated glucose and EPS in 28-PSU water. However, a higher cell fraction of this group assimilated glucose at the other sites. The fractions for the other phylogenetic groups alternated with salinity. For example, more Betaproteobacteria assimilated EPS in 28-PSU water, while more cells of this group used glucose in 21-PSU water.
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FIG. 5. Fraction of bacteria in a group assimilating glucose verses fraction of bacteria in a group assimilating EPS. The line bisecting the graph is the 1:1 line. Numbers adjacent to the data points indicate the salinity. Error bars indicate standard errors.
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FIG. 6. Relative abundance of each bacterial group as a function of the fraction of bacteria in phylogenetic groups assimilating either glucose (A) or EPS (B); 1:1 lines bisect the graphs. Error bars indicate standard errors.
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The ratios between the volumes of substrate-assimilating and nonassimilating cells indicate that bacteria taking up glucose and EPS were larger than nonassimilating bacteria (t test, P < 0.05). EPS-assimilating bacteria were larger than nonassimilating bacteria by 20 to 44% (Table 1). Cytophaga-like bacteria had the highest ratio of assimilating to nonassimilating cell volumes in the EPS treatment; assimilating cells were 62% larger than nonassimilating ones. This was also the case for Cytophaga-like bacteria cells assimilating glucose (Table 2), in which the assimilating Cytophaga-like bacteria were 57% larger than the nonassimilating cells affiliated with this group. The other phylogenetic groups had smaller differences (range of 10 to 35%) in the glucose treatment. Overall, EPS-assimilating bacteria were larger than glucose-assimilating cells by 10 to 30%.
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Unlike EPS assimilation, which occurred across a broad range of groups, glucose assimilation was generally dominated by a few major groups. In particular, Alphaproteobacteria dominated glucose assimilation in the saline part of the estuary, and this group assimilated glucose more than expected based on its relative abundance, while most of the bacterial groups assimilated glucose as expected based on their abundance. These data are consistent with previous studies suggesting that Alphaproteobacteria are important in the assimilation of LMW compounds such as amino acids, N-acetylglucosamine (11), and dimethylsulfoniopropionate (31). The ability to use various LMW DOM compounds perhaps explains the high abundance of this group. Alphaproteobacteria are abundant in marine environments (8, 20, 27), and LMW DOM can support a high fraction of bacterial production (25).
The SAR11 clade, a subgroup of the Alphaproteobacteria, is abundant in the oceans (29, 34) as well as in the Delaware Estuary (27). Although the SAR11 clade accounts for about 50% of glucose assimilation in the Sargasso Sea (29), it accounted for only 15 to 20% of glucose assimilation in the Delaware. The SAR11 clade is a very diverse group (1, 18), and the phylotypes of this group in the Delaware Estuary probably differ from those in the Sargasso Sea. The Sargasso Sea is oligotrophic, while the Delaware Estuary is eutrophic. This difference probably selects for different phylotypes with diverse metabolisms.
In contrast to the case for glucose assimilation, several bacterial groups assimilated EPS. Potential reasons for this finding include the fact that polysaccharides and other EPS components may be more important carbon sources than glucose. Polysaccharides concentrations are relatively high, whereas the glucose concentration is too low to be measured (<5 nM) in the Delaware (26). Second, EPS originating from phytoplankton is a complex mixture of compounds, including polysaccharides, proteins, lipids, and perhaps even some LMW compounds (43). In addition, the polysaccharides in EPS are probably diverse and composed of various monosaccharides. Therefore, different bacterial groups may use different components of EPS, preventing a single group from dominating EPS assimilation and allowing a broad spectrum of groups to be involved.
One of our initial hypotheses was that Cytophaga-like bacteria would dominate assimilation of EPS. This hypothesis was based on previous findings that cultured representatives of this group degrade polymers such as cellulose (28). In addition, uncultured bacteria affiliated with this group contribute to the assimilation of protein and chitin in coastal waters (11). The high abundance of Cytophaga-like bacteria on particles (13, 17) also suggests that these bacteria might be especially important in the cycling of HMW DOM. However, Cytophaga-like bacteria dominated EPS assimilation only occasionally in the Delaware Estuary. Since Cytophaga-like bacteria shared EPS assimilation with other bacterial groups, this DOM component appears to be an important source of carbon for a variety of bacteria rather than for a specific group.
We expected that community composition is controlled in part by bottom-up factors. Bottom-up control by DOM is supported by the extent to which there is a correlation between group abundance and its contribution to DOM uptake. These correlations indicate that relative DOM uptake explains 30 to 55% of relative abundance and thus of community composition. Bottom-up control also implies that bacterial groups with high fractions of substrate-assimilating cells would be more abundant than groups with lower fractions. In contrast, most bacterial groups with high fractions of substrate-assimilating cells had low abundances in the community. Similarly, the relative abundances of bacterial groups did not follow thymidine-active bacteria (12) or the growth rates of specific groups in the Delaware Estuary (46), with one exception. The abundance of Betaproteobacteria followed both thymidine assimilation (12) and growth rate (46) in this estuary. These data are consistent with bottom-up control of Betaproteobacteria. However, we did not observe any trends with EPS and glucose assimilation, even for Betaproteobacteria, suggesting that bacterial community structure is not controlled solely by bottom-up factors. If so, then top-down factors such as predation and viral lyses may be the main forces shaping bacterial communities in the Delaware and perhaps other estuaries.
Predation and viral lyses can be important top-down factors determining the composition of bacterial communities in aquatic environments (21, 23, 40, 42). Susceptibility of bacteria to predation is affected by cell size and indirectly by level of activity (16, 38). This may explain why the more active bacteria in the Delaware Estuary were also less abundant (12; this study). Differential grazing (23) would also explain the differences in the sizes of assimilating and nonassimilating cells found in our study. The size of bacteria can also affect viral lysis, since viruses tend to attack the largest cells in the community (35, 45). Bacterial abundance is another factor. Thingstad and Lignell (42) postulated with their "killing-the-winner" hypothesis that viral lysis is highest for abundant bacterial groups. The combination of predation and viral lysis, therefore, affects the abundance, size distribution, and diversity of bacterial groups in aquatic communities.
Our understanding of the abundance and function of specific bacterial groups in the aquatic environment has increased over the last decade. Overall, it seems that abundant groups contribute the most to the use of different DOM components in various marine environments, with some important exceptions. Alphaproteobacteria are one of the most abundant bacterial groups in the marine environments and have an important role in the uptake of LMW organic compounds. In contrast, several groups appear to be capable of processing HMW compounds, a diversity that may be a reflection of the complexity of HMW DOM. These data suggests that there is some bottom-up control of the community, but the fractions of substrate-assimilating cells in the groups imply that other factors are involved. It is likely that a combination of bottom-up (e.g., DOM concentration and composition) and top-down (e.g., predation and viral lysis) factors determine bacterial community structure in the Delaware Estuary. Further investigations of these factors will contribute to the understanding of DOM cycling in the Delaware Estuary and elsewhere.
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