Bacterioplankton Community Composition in Five Lakes Differing in Trophic Status and Humic Content

Abstract To investigate the relation between lake type and bacterioplankton community composition, five Swedish lakes, which differed from each other in nutrient content and water color, were studied. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA was used to examine community composition. The DGGE-patterns of the different samples were analyzed in relation to physical, chemical, and biological data from the lakes by canonical correspondence analysis (CCA). The three variables found to most strongly correlate with the DGGE patterns were biomasses of microzooplankton, cryptophytes, and chrysophytes, suggesting that these biota had an impact on bacterioplankton community structure. Two of the three factors were, in turn, significantly correlated to parameters associated with the trophic status of the lakes, indicating that the nutrient content of the lakes, at least indirectly, influenced the structure of the bacterioplankton community. The relation to water color was less pronounced. Received: 16 February 2000; Accepted: 27 April 2000; Online Publication: 18 July 2000     

Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms

The bacterioplankton community composition in two Finnish forest lakes with different content of humic substances was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of the major bands. The same dominant bacterial phylotypes were detected in the bacterioplankton communities of clear-water Lake Ahvenlammi and humic Lake Sammalisto. For 4 years, in every water layer, Actinobacteria was the dominant and Verrucomicrobia the second most common phylum. In the hypolimnion, other dominant phyla were also found. We set up a mesocosm experiment to assess the effect of a sudden load of allochthonous humus extract to the bacterioplankton community composition. Changes in the bacterial communities were followed in four control and four humus extract-added mesocosms for 50 days. In the humic mesocosms the phylotypes of allochthonous Proteobacteria arriving with the humus extract were initially prevalent but disappeared during the first weeks. After this the Actinobacteria-dominated communities resembled the bacterioplankton communities of the control mesocosms and Lake Ahvenlammi. Towards the end of the experiment the community patterns in all the mesocosms started to change slightly because of erratic occurrence of new proteobacterial phylotypes. Thus the effects of a sudden load of allochthonous humic material and bacteria to the bacterioplankton community composition were transient.     

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America

Metacommunity studies on lake bacterioplankton indicate the importance of environmental factors in structuring communities. Yet most of these studies cover relatively small spatial scales. We assessed the relative importance of environmental and spatial factors in shaping bacterioplankton communities across a > 6000 km latitudinal range, studying 48 shallow lowland lakes in the tropical, tropicali (isothermal subzone of the tropics) and tundra climate regions of South America using denaturing gradient gel electrophoresis. Bacterioplankton community composition (BCC) differed significantly across regions. Although a large fraction of the variation in BCC remained unexplained, the results supported a consistent significant contribution of local environmental variables and to a lesser extent spatial variables, irrespective of spatial scale. Upon correction for space, mainly biotic environmental factors significantly explained the variation in BCC. The abundance of pelagic cladocerans remained particularly significant, suggesting grazer effects on bacterioplankton communities in the studied lakes. These results confirm that bacterioplankton communities are predominantly structured by environmental factors, even over a large‐scale latitudinal gradient (6026 km), and stress the importance of including biotic variables in studies that aim to understand patterns in BCC.     

pH Influences the Importance of Niche-Related and Neutral Processes in Lacustrine Bacterioplankton Assembly

pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.     

Dissolved Organic Carbon as Major Environmental Factor Affecting Bacterioplankton Communities in Mountain Lakes of Eastern Japan

Relationships between environmental factors and bacterial communities were investigated in 41 freshwater lakes located in mountainous regions of eastern Japan. Bacterioplankton community composition (BCC) was determined by polymerase chain reaction-denaturing gradient gel electrophoresis of the 16S rRNA gene and then evaluated on the basis of physicochemical and biological variables of the lakes. Canonical correspondence analysis revealed that BCC of oligotrophic lakes was significantly influenced by dissolved organic carbon (DOC) content, but its effect was not apparent in the analysis covering all lakes including mesotrophic and eutrophic ones. The generalized linear model showed the negative association of DOC on the taxon richness of bacterioplankton communities. DOC was positively correlated with the catchment area per lake volume, suggesting that a large fraction of DOC supplied to the lake was derived from terrestrial sources. These results suggest that allochthonous DOC has a significant effect on bacterioplankton communities especially in oligotrophic lakes. The genus Polynucleobacter was detected most frequently. The occurrence of Polynucleobacter species was positively associated with DOC and negatively associated with total phosphorus (TP) levels. In addition, TP had a stronger effect than DOC, suggesting that oligotrophy is the most important factor on the occurrence of this genus.     

Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure

The phylogenetic composition of bacterioplankton communities in the water column of four shallow eutrophic lakes was analyzed by partially sequencing cloned 16S rRNA genes and by PCR-DGGE analysis. The four lakes differed in nutrient load and food web structure: two were in a clearwater state and had dense stands of submerged macrophytes, while two others were in a turbid state characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had very high nutrient levels (total phosphorus > 100 microg/l), while the other lakes were less nutrient rich (total phosphorus < 100 microg/l). Cluster analysis, multidimensional scaling and ANOSIM (analysis of similarity) were used to investigate differences among the bacterial community composition in the four lakes. Our results show that each lake has its own distinct bacterioplankton community. The samples of lake Blankaart differed substantially from those of the other lakes; this pattern was consistent throughout the year of study. The bacterioplankton community composition in lake Blankaart seems to be less diverse and less stable than in the other three lakes. Clone library results reveal that Actinobacteria strongly dominated the bacterial community in lake Blankaart. The relative abundance of Betaproteobacteria was low, whereas this group was dominant in the other three lakes. Turbid lakes had a higher representation of Cyanobacteria, while clearwater lakes were characterized by more representatives of the Bacteroidetes. Correlating our DGGE data with environmental parameters, using the BIOENV procedure, suggests that differences are partly related to the equilibrium state of the lake.     

Comparative analysis of bacterioplankton assemblages from maritime Antarctic freshwater lakes with contrasting trophic status

The bacterioplankton assemblages of eight maritime Antarctic lakes with a wide range of trophic status and geographic span (six lakes from Hope Bay, Antarctic Peninsula and two from Potter Peninsula, King George Island) were described using denaturing gradient gel electrophoresis and band sequencing during two consecutive austral summers (2003–2004). Analyses of the gels identified a total of 230 bands spread across 57 different positions. Among those bands, 14 were shared between lakes from Hope Bay and Potter Peninsula, 17 were observed only in particular lakes, and 17 were registered both years in the same lake. We successfully reamplified and sequenced 43 bands located in 36 different positions belonging to Bacteroidetes, Actinobacteria, Betaproteobacteria and Cyanobacteria. The closest matches for 63% of the sequenced bands were from Antarctic or from other cold environment clones and sequences already in the databases, suggesting the widespread dominance of microbial communities adapted to cold habitats. The results of the multivariate analyses (Cluster Analysis and CCA) indicated that the nutrient status of the lake influences the bacterioplankton assemblages. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Impact of UV radiation on bacterioplankton community composition

The potential effect of UV radiation on the composition of coastal marine bacterioplankton communities was investigated. Dilution cultures with seawater collected from the surface mixed layer of the coastal North Sea were exposed to different ranges of natural or artificial solar radiation for up to two diurnal cycles. The composition of the bacterioplankton community prior to exposure was compared to that after exposure to the different radiation regimes using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA and 16S ribosomal DNA. Only minor changes in the composition of the bacterial community in the different radiation regimes were detectable. Sequencing of selected bands obtained by DGGE revealed that some species of the Flexibacter-Cytophaga-Bacteroides (FCB) group were sensitive to UV radiation while other species of the FCB group were resistant. Overall, only up to approximately 10% of the operational taxonomic units present in the dilution cultures appeared to be affected by UV radiation. Thus, we conclude that UV radiation has little effect on the composition of coastal marine bacterioplankton communities in the North Sea.     

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.     

Impact of UV Radiation on Bacterioplankton Community Composition

The potential effect of UV radiation on the composition of coastal marine bacterioplankton communities was investigated. Dilution cultures with seawater collected from the surface mixed layer of the coastal North Sea were exposed to different ranges of natural or artificial solar radiation for up to two diurnal cycles. The composition of the bacterioplankton community prior to exposure was compared to that after exposure to the different radiation regimes using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA and 16S ribosomal DNA. Only minor changes in the composition of the bacterial community in the different radiation regimes were detectable. Sequencing of selected bands obtained by DGGE revealed that some species of the Flexibacter-Cytophaga-Bacteroides (FCB) group were sensitive to UV radiation while other species of the FCB group were resistant. Overall, only up to ≈10% of the operational taxonomic units present in the dilution cultures appeared to be affected by UV radiation. Thus, we conclude that UV radiation has little effect on the composition of coastal marine bacterioplankton communities in the North Sea.     

Bacterial community structure in a latitudinal gradient of lakes: the roles of spatial versus environmental factors

1. We analysed the latitudinal variation of bacterioplankton in 45 freshwater environments (lakes, shallow lakes and ponds) across a transect of more than 2100 km stretching from Argentinean Patagonia (45°S) to Maritime Antarctica (63°S), to determine the factors that mainly determine bacterioplankton community structure. 2. Bacterioplankton community composition (BCC) was assessed by a fingerprinting method (denaturing gradient gel electrophoresis) followed by band sequencing, whereas the abundances of total bacteria and picocyanobacteria were estimated by epifluorescence microscopy. 3. Bacterioplankton community composition was controlled by a combination of spatial (latitude and longitude) and environmental [e.g. phosphate, light diffuse attenuation coefficient (K_d) and dissolved organic carbon] factors. Total bacterioplankton abundance declined with latitude. A multiple regression analysis showed that phosphate, K_d and latitude had significant effects on total bacterioplankton abundance. 4. Of 76 operational taxonomic units identified in the studied lakes, 45 were shared between Patagonian and Antarctic water bodies, 28 were present only in Patagonian lakes and three were restricted to the Antarctic lakes. Significant differences were found in BCC between Patagonia and Antarctica. Among the sequences, 54% were similar (>97% sequence similarity) to others reported from cold habitats elsewhere on the planet (glaciers, high mountain lakes, Arctic). 5. Our results provide new evidence that supports the hypotheses of biogeographic patterns of bacterial assemblages and suggest that both spatial and environmental factors control bacterioplankton community structure.     

Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes

We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes) . Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes.     

Biomass and structure of planktonic communities along an air temperature gradient in subarctic Sweden

1. Air temperature will probably have pronounced effects on the composition of plankton communities in northern lake ecosystems, either via indirect effects on the export of essential elements from catchments or through direct effects of water temperature and the ice‐free period on the behaviour of planktonic organisms. 2. We assessed the role of temperature by comparing planktonic communities in 15 lakes along a 6 °C air temperature gradient in subarctic Sweden. 3. We found that the biomass of phytoplankton, bacterioplankton and the total planktonic biomass were positively related to air temperature, probably as a result of climatic controls on the export of nitrogen from the catchment (which affects phytoplankton biomass) and dissolved organic carbon (affecting bacterioplankton biomass). 4. The structure of the zooplankton community, and top down effects on phytoplankton, were apparently not related to temperature but mainly to trophic interactions ultimately dependent on the presence of fish in the lakes. 5. Our results suggest that air temperature regimes and long‐term warming can have strong effects on the planktonic biomass in high latitude lakes. Effects of temperature on the structure of the planktonic community might be less evident unless warming permits the invasion of fish into previous fishless lakes.     

A method to study bacterioplankton community structure in Antarctic lakes

A method to study bacterioplankton community structure in Antarctic freshwater lake samples is described. Small samples (between 300 and 1000 ml) taken in remote field locations were used for crude DNA extraction, followed by PCR amplification of 16S rRNA gene fragments using group-specific primers. The amplification products of the PCR reaction were then separated using denaturing gradient gel electrophoresis to produce a profile of the bacterioplankton community. Whilst the technique is only semi-quantitative, it readily differentiated communities from lakes of different trophic status and from vertical profiles within different lake types. The method offers a sensitive tool for screening and monitoring Antarctic freshwater environments as a precursor and adjunct to more detailed studies. Accepted: 14 November 1999     

Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance

A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.     

Differential response of high-elevation planktonic bacterial community structure and metabolism to experimental nutrient enrichment

Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and emphasize that evaluation of eutrophication in these habitats should incorporate heterotrophic microbial communities and processes.     

Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system

It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm communities from three microhabitats (open water, Nuphar and Phragmites sites) at within‐ and among‐pond scale in a set of 14 interconnected shallow ponds. Our results demonstrate that while bacterioplankton and biofilm communities are highly distinct, a similar hierarchy of ecological processes is acting on them. For both community types, most variation in community composition was determined by pond identity and environmental variables, with no effect of space. The highest β‐diversity within each community type was observed among ponds, while microhabitat type (Nuphar, Phragmites, open water) significantly influenced biofilm communities but not bacterioplankton. Mass effects among bacterioplankton and biofilm communities were not detected, as suggested by the absence of within‐site covariation of biofilm and bacterioplankton communities. Both biofilm and plankton communities were thus highly structured by environmental factors (i.e., species sorting), with among‐lake variation being more important than within‐lake variation, whereas dispersal limitation and mass effects were not observed.     

Composition and diversity of cyanobacteria-associated and free-living bacterial communities during cyanobacterial blooms

Lakes undergoing cyanobacterial blooms often exhibit differences between free-living (FL) and cyanobacteria-associated (CA) bacterial assemblages, but previous studies have not compared distinct FL and CA communities across multiple lakes. This project investigated whether FL and CA communities differ from each other in consistent ways across lakes. FL and CA communities were collected from three Ohio (USA) lakes on two sampling dates during cyanobacterial blooms. High-throughput sequencing was used to characterize the communities, and comparisons were made of the composition and diversity of FL and CA communities within and across lakes. Diversity estimates did not vary significantly among lakes nor between CA and FL assemblages. The taxonomic composition of CA communities differed significantly from that of FL communities in Buckeye and Harsha Lakes and in Maumee Bay on one of two sampling dates. CA communities from Buckeye and Harsha Lakes were more similar to each other than to their respective FL communities. Community composition in Maumee Bay on August 18 did not differ between FL and CA habitats. As the bloom progressed, the FL community remained similar in composition to samples collected on August 18, while the CA community became significantly dissimilar. This study is the first cross-lake comparisons of CA and FL communities, uncovering the impacts of habitat type, lake, and sampling date in determining community composition.     

Community structures of ammonia‐oxidising archaea and bacteria in high‐altitude lakes on the Tibetan Plateau

1. Community structures of planktonic ammonia‐oxidising archaea (AOA) and bacteria (AOB) were investigated for five high‐altitude Tibetan lakes, which could be classified as freshwater, oligosaline or mesosaline, to develop a general view of the AOA and AOB in lakes on the Tibetan Plateau. 2. Based on PCR screening of the ammonia monooxygenase α‐subunit (amoA) gene, AOA were present in 14 out of 17 samples, whereas AOB were detected in only four samples. Phylogenetic analyses indicated that the AOB communities were dominated by a unique monophylogenetic lineage within Nitrosomonas, which may represent a novel cluster of AOB. AOA, on the other hand, were distinct among lakes with different salinities. 3. Multivariate statistical analyses indicated a heterogeneous distribution of the AOA communities among lakes largely caused by lake salinity, whereas the uniform chemical properties within lakes and their geographical isolation may favour relatively homogeneous AOA communities within lakes. 4. Our results suggest a wide occurrence of AOA in Tibetan lakes and provide the first evidence of salinity‐related differentiation of AOA community composition as well as potential geographical isolation of AOA in inland aquatic environments.