Flavobacteria blooms in four eutrophic lakes: linking population dynamics of freshwater bacterioplankton to resource availability

Heterotrophic bacteria are major contributors to biogeochemical cycles and influence water quality. Still, the lack of representative isolates and the few quantitative surveys leave the ecological role and significance of single bacterial populations to be revealed. Here we analyzed the diversity and dynamics of freshwater Flavobacteria populations in four eutrophic temperate lakes. From each lake, clone libraries were constructed using primers specific for either the class Flavobacteria or Bacteria. Sequencing of 194 Flavobacteria clones from 8 libraries revealed a diverse freshwater Flavobacteria community and distinct differences among lakes. Abundance and seasonal dynamics of Flavobacteria were assessed by quantitative PCR with class-specific primers. In parallel, the dynamics of individual populations within the Flavobacteria community were assessed with terminal restriction fragment length polymorphism analysis using identical primers. The contribution of Flavobacteria to the total bacterioplankton community ranged from 0.4 to almost 100% (average, 24%). Blooms where Flavobacteria represented more than 30% of the bacterioplankton were observed at different times in the four lakes. In general, high proportions of Flavobacteria appeared during episodes of high bacterial production. Phylogenetic analyses combined with Flavobacteria community fingerprints suggested dominance of two Flavobacteria lineages. Both drastic alterations in total Flavobacteria and in community composition of this class significantly correlated with bacterial production, emphasizing that resource availability is an important driver of heterotrophic bacterial succession in eutrophic lakes.     

Regulation of bacterial secondary production in two eutrophic lakes and in experimental enclosures

Bacterial cell number and secondary production of bacterioplanktonwere measured during two periods of 14 and 19 days, respectively,in experimental enclosures of lake water (each containing about5–7 m³ and in two Danish, eutrophic lakes. Additions ofphosphate and planktivorous fish to some of the enclosures inducedrapid changes in the phytoplankton biomass, primary productionand release of extracellular organic carbon (EOC). In some ofthe enclosures containing fish, release of EOC from phytoplanktoncon stituted from 36 to 55% of the bacterial secondary productiondetermined by means of [³H]thymidine incorporation into DNA.In others, such a relationship was not found, suggesting thatphytoplankton species-specific release rates of compositionof EOC might play a role in the microbial response. In enclosureswithout fish, released dissolved organic carbon from zooplanktongrazing activities could Sustain     

Activity profiles of bacterioplankton in a eutrophic river

1. The significance of microbial diversity in processing dissolved organic matter (DOM) is largely unknown. We investigated the range of functional diversity in the bacterioplankton from a eutrophic river by profiling extracellular enzyme activities (EEA) and substrate-induced respiration (SIR) patterns.
2. The EEA profiles consisted of assays for 21 hydrolases, measured using fluorogenic substrates arrayed on 96-well microplates. Commercially available BiOLOG^® GN and ECO plates, which contained 120 different substrates, were used for the SIR profiles.
3. The EEA data were more dynamic than the SIR. Five enzymes, leucine aminopeptidase, alkaline phosphatase, alanine aminopeptidase, arginine aminopeptidase and β-glucosidase, showed consistently high activity; ten others were ubiquitous at lower activity levels; the remainder were detected intermittently. The SIR data showed less temporal variability. With one exception (citrate), the 20 substrates that generated the largest responses were all saccharides or their derivatives.
4. The EEA and SIR data did not generally correlate. Both methods were effective for ordinating bacterioplankton although, unlike the SIR, the EEA ordination followed a clear temporal trajectory.
5. Because the SIR profiles are based on a culture response, whilst the EEA profiles measure activity of the extant community, the latter appear to be more directly linked to the mechanics of DOM processing.     

Influence of the bacterioplankton community of a tropical eutrophic lagoon on the bacterial community of its neighbouring ocean

The Rodrigo de Freitas lagoon (RFL) is a tropical eutrophic coastal ecosystem located in the urban area of Rio de Janeiro, Brazil. This environment consists of freshwater but has communication with the ocean through a channel (Jardim de Alah’s Channel). The aim of this study was to evaluate the influence of lagoon water on the nearby ocean using molecular and traditional microbiological methods. We hypothesised that due to the eutrophic low-salinity environment, the bacterioplankton community from the RFL would have a native “brackish” composition influenced by both freshwater and marine phylotypes, and that bacterial phylotypes of this community would be detected in oceanic samples closer to the channel between the lagoon and the ocean. The cultivation and microscopy experiments clearly showed this influence. Bacterial cell counts revealed that the greater amounts of bacterial cells present in the lagoon increased the observed values seen at oceanic stations near the channel. The Denaturing gradient gel eletrophoresis community profiles also showed a clear influence of Rodrigo de Freitas lagoon waters on the adjacent beaches. The band patterns found for the stations near the channel showed that these communities were mixtures of the communities of the lagoon and sea, and as the distance from the channel increased, the samples became more similar to ocean bacterial communities. A 16S rRNA gene clone library was constructed using a sample acquired from the connection point between the lagoon and the ocean. Around 52% of the sequences in the library showed similarity to the genus Proteobacteria (1% Alpha, 21% Beta, 19% Gamma and 29% unclassified Proteobacteria), and the second most abundant genus was Bacteroidetes, with 15% of the total clones. The results showed that the structure of the bacterial community had both freshwater and marine characteristics.     

Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes

Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 micro g liter(-1)) while the other lakes had relatively low nutrient levels (total phosphorus, <100 micro g liter(-1)). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (Daphnia and Ceriodaphnia) was significantly related to changes in the bacterial community in the clearwater lakes. Our results suggest that in eutrophic shallow lakes, seasonality of bacterial community structure is dependent on the dominant substrate source as well as on the food web structure.     

Wave exposure related growth of epiphyton: implications for the distribution of submerged macrophytes in eutrophic lakes

The distribution of submerged macrophytes in eutrophic lakes has been found to be skewed towards sites with intermediate exposure to waves. Low submerged macrophyte biomass at exposed sites has been explained by, for instance, physical damage from waves. The aim of this study was to investigate if lower biomass at sheltered sites compared to sites with intermediate exposure to waves can be caused by competition from epiphyton.Investigations were performed in eutrophic lakes in southern Sweden. Samples of submerged macrophytes and epiphytic algae on the macrophytes were taken along a wave exposure gradient. The amount of epiphyton (AFDW) per macrophyte biomass decreased with increased exposure. Biomass of submerged macrophytes, on the other hand, increased with increased exposure until a relatively abrupt disappearance of submerged vegetation occurred at high exposures. Production of epiphytic algae was monitored on artificial substrates from June to September at a sheltered and an exposed site in three lakes. It was higher at sheltered sites compared with exposed sites.We suggest that epiphytic algae may be an important factor in limiting the distribution of submerged macrophytes at sheltered sites in eutrophic lakes.     

对虾养殖围隔生态系统浮游细菌的呼吸与生产

The study on the respiration and production of bacterioplankton in five shrimp cultural enclosure ecosystems showed that the production and respiration fluctuated from 90 to 909 and 248 to 1785 μgC· L^-1. d^-l, respec-tively. There existed a significant positive relationship between production and respiration. The daily P/B ratio of bacterioplancton averaged 0.93 d^-l, and its production efficiency averaged 0.34.     

Seasonal variability of N:P ratios in eutrophic lakes

The ratios of different forms of nitrogen to phosphorus (particulate, total, total dissolved, and dissolved inorganic N : P) from four eutrophic lakes are presented to assess their variability during two consecutive growing seasons. Particulate and total N : P ratios showed the lowest amplitude of fluctuations, while the total inorganic N : P ratios showed the highest. All N : P forms demonstrated substantial variations and seasonal pattern over the growing period April-October. It was the short-lasting spring minima of the N : P ratios, ranging from less than 1: 1 to 6 : 1, which triggered the onset of nitrogen-fixing cyanophyte blooms. Seasonal mean values were as high as 20: 1 to 30: 1 and misleading in assessing nitrogen limitation. The nitrogen fixation rapidly restored the N : P values to normal levels (TN: TP of 15: 1 and over).     

Environmental predictors of electroactive bacterioplankton in small boreal lakes

Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.     

Distribution of viruses and their impact on bacterioplankton in mesotrophic and eutrophic reservoirs

Spatial distribution of planktonic viral particles (virioplankton) and mortality of heterotrophic bacteria caused by viral lysis were studied in the eutrophic Ivan’kovskoe and mesotrophic Uglichskoe reservoirs (the Upper Volga). During the summer peak of phytoplankton, the number of viral particles was higher in the Ivan’kovskoe Reservoir ((55.1 ± 9.5) × 10⁶ ml⁻¹ on average) than in the Uglichskoe Reservoir ((42.9 ± 5.1) × 10⁶ ml⁻¹ on average). The ratio of viral to bacterial abundances ranged from 2.5 to 7.0. The average number of mature phages in infected heterotrophic bacteria varied from 17 to 109 particles/cell. Most of the infected bacterial cells in the Ivan’kovskoe Reservoir were rod-shaped, and, in the Uglichskoe Reservoir, they were mainly vibrio-shaped. In the Ivan’kovskoe Reservoir, from 8.3 to 22.4% of planktonic bacteria were infected by phages, suggesting phage-induced mortality of bacterioplankton equal to 10.5–34.8% (19.1% on average) of the daily bacterial production. In the Uglichskoe Reservoir, from 9.4 to 33.5% of bacteria were phage-infected, suggesting phage-induced bacterial mortality of 13.7–40.2% (23.5% on average) of the daily bacterial production. The obtained results testify to an important role of autochthonous viruses in the regulation of bacterioplankton abundance and production in the reservoirs.     

Genetic diversity of cyanobacteria in four eutrophic lakes

Recent studies indicate genetic diversity of cyanobacteria in eutrophic lakes is not represented well by culture collections or morphology. Yet, few studies have investigated genetic richness and evenness of cyanobacteria using culture-independent methods. We compared the genetic structure of cyanobacteria supported by four neighboring eutrophic lakes during the ice-free season. The partial phycobilincpcB/A genes plus intergenic spacer (PC-IGS) was used as a genetic marker.Sequences were phylogeneticallygrouped by maximum likelihood into genotypes representing sub-genera of the major taxa. Genotypes fell into genera commonly observed by microscopy in these lakes including Microcystis, Aphanizomenon, Chroococcus, Anabaena, and Cylindrospermopsis. Only three genotypes were shared among all four lakes, despite significant water flowage between lakes.A Parsimony P-test indicated lakes were significantly (p=0.01) clustered on the maximum likelihood tree. Pairwise differences using Unifrac distance were moderately or not significant. Analysis of molecular variance (AMOVA) indicated genetic variation among all genotypes (φ=0.06, p<0.001) and 94% of variability occurred within lakes rather than between lakes (6%), explaining the lack of pairwise differences between lakes. Lorenze curves of genotype abundance in each lake showed genetic structure was only moderately uneven (Gini coefficients of 0.37-0.5) indicating lakes did not support dominant genotypes. Overall, results from this study suggest diversity of cyanobacteria is shaped by heterogeneity within lakes (temporally or spatially) and relatively even population structures.     

富营养化湖泊溶解性有机碳生物可利用性研究进展

富营养化湖泊溶解性有机碳(DOC)包括内源和外源性碳源,不同来源碳源在物质化学结构组成和分子量级等方面具有显著差异,进而影响到对细菌的生物可利用性和碳素在食物网中的传递效率。根据国内外文献,综述了内外源DOC在碳稳定同位素值域上的显著差异,建议通过对DOC碳稳定同位素的分析来识别富营养化湖泊中DOC的主要来源;通过对比内外源DOC在碳水化合物、结合态中性糖和腐殖质含量上的差异,并结合细菌生长参数如细菌二级生产力、细菌呼吸作用及细菌生长效率来分析内外源DOC对细菌的生物可利用性。从富营养化湖泊DOC来源的角度探讨其生物可利用性和碳素传递效率,有助于了解富营养化湖泊食物网中碳素循环特征,加强对湖泊生态学的认识,为湖泊环境治理与保护提供科学依据。     

Causes and consequences of the success of bream in Dutch eutrophic lakes

In the last decennia eutrophication has caused a shift in the species composition of fish communities in Dutch fresh waters. The changes have led to the disappearance of vegetation in lakes and ponds; zooplankton and chironomids are now the most abundant food organisms for fish. In the turbid, open waters bream and pikeperch are the dominant fish species. Only small bream is vulnerable to predation, but because bream grows much faster than the other cyprinids the time span in which the fish is vulnerable is the shortest. The large bream (>20 cm) can coexist with pikeperch since it is not vulnerable to predation and still utilizes the food organisms efficiently. Eutrophication is accelerated if both bream populations are composed of small-sized specimens preventing large-sized zooplankton to develop, and if they are composed of large-sized individuals which can efficiently stir up the bottom sediments.     

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.     

Nutrient limitation of bacterioplankton and phytoplankton in humic lakes in northern Sweden

1. Two small humic lakes in northern Sweden with concentrations of dissolved organic carbon (DOC) between 15 and 20 mg L^–1 were fertilized with inorganic phosphorus (P) and inorganic nitrogen (N), respectively. A third lake was unfertilized and served as a control. In addition to this lake fertilization experiment, data from different regional surveys were used to assess the role of different limiting factors.
2. The P fertilization had no effects on bacterioplankton or phytoplankton, while phytoplankton were significantly stimulated by N fertilization. Inorganic nutrient limitation of bacterioplankton was a function of DOC concentration in water of the investigated region and nutrient-limited bacteria were found only in lakes with DOC concentrations less than around 15 mg L^–1
3. The fertilization experiments demonstrated that the DOC-rich experimental lakes contained a bioavailable pool of P that was not utilized to its full potential under natural conditions. The overall mobilization of energy (bacterioplankton plus phytoplankton) in the experimental lakes was restricted by lack of inorganic N.     

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     

Seasonal development of bacterioplankton in two forest lakes in central Sweden

Bacteria were counted with acridine orange epifluorescence technique in two humic lakes during 3 years. Less than 1% of the cells were found attached to detritus aggregates. 73% of the total number and 48% of the total volume were smaller than 1 µm. The mean cell volume ranged from 0.10 to 0.35 µm³ with the highest cell volumes occurring during early summer contemporarily with the growth of the bacterial biomass and probably indicating favourable growth conditions. The mean density of bacteria in oligotrophic brown-water lakes is higher than in oligotrophic clear-water lakes. The development of bacterial biomass showed a regular and seasonally dependent pattern with maxima during early summer and autumn. The importance of different factors for the regulation of bacterial biomass is discussed. Three different approaches were used to estimate bacterial production. These resulted in an average production rate of 15–60 µg C · l^?1 · d^?1 during the growing season. It was concluded that allochthonous sources comprised a significant part of the energy supply to the bacteria in the two humic lakes.     

Seasonal modulation of bacterioplankton community at a temperate eutrophic shallow lake

At the present time, there is still a lack of information about environmental parameters modulating variations on bacterial diversity in temperate lakes, particularly from Portugal. Fermentelos Lake (Central Portugal) is a shallow water body that sustains an important wetland area. The strong nutrient inputs from agriculture and industrial runoffs have led to its current eutrophic status. The present work aimed to understand which factors modulate the seasonal bacterioplankton diversity at this lake using 16S rRNA PCR-denaturing gradient gel electrophoresis (DGGE) and multivariate analysis. Environmental data demonstrated eutrophic features throughout all samples with nitrate concentrations reaching 12.0 mg N (NO₃ ⁻) l⁻¹ in March 2006, while the highest conductivity (609 μS cm⁻¹), soluble reactive phosphorus (0.37 mg l⁻¹), total suspended solids (87.2 mg l⁻¹) and chlorophyll a (286.6 μg l⁻¹) levels were recorded in August 2007. Over the past two decades there was a general increase in nitrate, pH and conductivity levels at this lake, suggesting the eutrophication process is still in progress. Multivariate analysis showed that summer versus winter DGGE patterns could be established for bacterial assemblages and were mainly defined by water temperature and chlorophyll a. Actinobacteria were dominant throughout the study period although a general preference for higher temperature, pH, total suspended solids, conductivity, soluble reactive phosphorus (SRP) and chlorophyll a levels was observed. The highest concentrations of nitrogen sources were related to Bacteroidetes and phototrophic eukaryote (cryptophycean) dominance. The expansion of Betaproteobacteria, Alphaproteobacteria and Cyanobacteria phylotypes was generally associated to high temperature, pH, conductivity and SRP values.     

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.