Bottom-up versus top-down effects on ciliate community composition in four eutrophic lakes (China)

Previous studies have shown that ciliate plankton is generally controlled by food resources (e.g., algae) and predators (e.g., metazooplankton). Among lakes with similar trophic levels but different distributions of phyto- and metazooplankton, the main forces acting on ciliate assemblages may be different. We investigated the relationship between ciliate communities and bottom-up versus top-down variables based on a survey of four subtropical eutrophic lakes (China). Two of the lakes (Chaohu, Taihu) are located on the Mid-lower Yangtze Plain near sea level, and the other two (Dianchi, Xingyunhu) on the Yunnan-Kweichow Plateau at 1700 m above sea level. Blooms of cyanobacteria developed during summer in Lakes Chaohu and Taihu and throughout the year in Lakes Dianchi and Xingyunhu. Ciliate functional feeding groups differed significantly between lakes. The results of canonical correspondence analysis (CCA) and variation partitioning showed that cyanobacteria significantly influence ciliate species, whereas ‘edible’ algae (cryptophytes, diatoms) and cladocerans were the important variables in explaining the ciliate community structure of Lakes Dianchi and Xingyunhu compared with Lakes Taihu and Chaohu. Our results highlight the importance of consistent cyanobacterial blooms in shaping the ciliate community in subtropical eutrophic shallow lakes by interacting with top-down and bottom-up factors.     

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.     

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.     

Bottom-up and cascading top-down control of macroalgae along a depth gradient

On marine rocky shores, macroalgal herbivory is often intense, such that the cascading effects of fish predation may contribute to the control of algal communities. To estimate the magnitudes of top-down and bottom-up control on a macroalgal community, we manipulated the access of carnivorous fish to macroalgal colonization substrates, as well as nutrient availability, at two sub-littoral depths. There were three levels of fish manipulation: natural fish community, no fish and the enclosure of one common species, the perch, Perca fluviatilis. We found a clear cascade effect of fish predation on both the total density and several individual species of macroalgae, which was more pronounced in deep than shallow water. The density of the dominant grazers, i.e. snails, increased in nutrient-enriched conditions; perch were inefficient in controlling herbivores, and had therefore no cascading effect on algal densities under such conditions. Although nutrients enhanced the growth of opportunistic algae, herbivores, in the absence of fish, inhibited this response. While algal diversity was higher in shallow than in deep water, the enrichment effect was opposite at the two depths with lowered diversity in the shallows and increased at depth. Our results indicate that fish predation is an efficient regulator of meso-herbivores and that its effect thereby cascades onto the producer trophic level such that both perennial and opportunistic algae benefit from the presence of fish. This cascade effect is probably stronger at depth where predation efficiency is less disturbed by wave motion.     

The annual cycle of heterotrophic freshwater nanoflagellates: role of bottom-up versus top-down control

The population dynamics of heterotrophic nanoflagellates (HNF)were analyzed in pre-alpine Lake Constance over three consecutiveyears. A recurrent seasonal pattern led to the identificationof five seasonal phases: winter, spring, clear-water, summerand autumn. HNF biomass was lowest in winter and highest m latespring several weeks after the phytoplankton spring bloom. Theaverage biomass of HNF was 5–12% of bacterial biomassand 13–34% of ciliate biomass respectively. The largestHNF cells were recorded during the spring phase, whereas theaverage cell size was reduced to one-third during the subsequentclear-water phase. The pronounced differences in the mean cellsize were attributed mainly to varying grazing impact on HNFThroughout most of the year, HNF production was balanced bygrazing of microzooplankton, namely ciliates, within the microbialloop. During the dear-water phase, however, the grazing impactwas mainly due to rotifers and daphnids. Changing grazing impactwas primarily responsible for the observed 2-fold interannualdifference m the mean biomass of HNF Overall, top-down controlby grazing was more important in governing the population dynamicsof HNF than bottom-up control by bacterial food supply.     

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.     

Epiphytic bacterial community composition on two common submerged macrophytes in brackish water and freshwater

Background  

Plants and their heterotrophic bacterial biofilm communities possibly strongly interact, especially in aquatic systems. We aimed to ascertain whether different macrophytes or their habitats determine bacterial community composition. We compared the composition of epiphytic bacteria on two common aquatic macrophytes, the macroalga Chara aspera Willd. and the angiosperm Myriophyllum spicatum L., in two habitats, freshwater (Lake Constance) and brackish water (Schaproder Bodden), using fluorescence in situ hybridization. The bacterial community composition was analysed based on habitat, plant species, and plant part.     

Patterns in the top-down versus bottom-up regulation of heterotrophic nanoflagellates in temperate lakes

The importance of resources versus that of predators in determiningthe abundance of organisms is modulated by several factors whichvary over time and space. Here, we evaluate the abundance ofheterotrophic nanoflagellates (HNF), the main predators of planktonicbacteria, in the plankton of 16 Quebec lakes as a function ofthe abundance of resources and zooplankton (predators). We analyzethe data at two different scales: among lakes varying in resourcesupply and within lakes. Resource factors (total phosphorus,chlorophyll, bacterial concentration) best explained the abundancesof HNF among lakes differing in resource availability. Whenthe effect of resource availability was removed, the biomassof cladocerans became an important determinant of HNF abundance,with abundance declining and the ratio of bacteria per flagellateincreasing, as the cladocerans increased. Within lakes, HNFabundance was not a direct function of resource concentration.Multiple regression models based on data for many lakes showedthat both bottom-up (food) and top-down (predation) variablespredicted HNF abundance quite well. An examination of the seasonalpattern among individual lakes showed each group of variablesdiffering in importance: bottom-up variables were more importantin spring and top-down variables in midsummer. An examinationof the effects of different assemblages of zooplankton on HNFshowed cladocerans to exert the highest negative impact on HNFand to be responsible for keeping low HNF numbers during mostof the summer with that probably affecting the pathways of energyflux in those lakes dominated by cladocerans versus those dominatedby other zooplankton. The absolute, as well as the relative,importance of the different biotic and abiotic factors examinedin predicting the abundance of HNF is a function of the scaleof the investigation. Among lakes varying greatly in resourcesupply, resources are found to better correlate with HNF abundance.When the analysis is performed at another scale, within lakes,the relative importance of resources and predation in determiningHNF abundances changes depending on the variability superimposedby other factors (seasonality and lake food web structure).     

Geochemistry of suspended and settling solids in two freshwater lakes

This study describes the 1987–1992 time variationof the bulk chemical composition, levels of heavymetals, arsenic, nitrogen and phosporous insuspended and settling solids in Lake Volkerak andLake Zoom (The Netherlands). Suspended and setlingsolids were collected with continuous flowcentrifuges and sediment traps, respectively. Therelations between solids characteristics and metalconcentrations in the particles were investigatedusing correlation and factor-analysis. Heavy metals,except manganese, were associated with clay contentof the particles and with organic carbon which wasmainly determined by phytoplankton growth. Manganesewas correlated with Org-C only. Clay and organicmatter with associated heavy metals showed negativetrends on all locations, and a seasonality due toalgal biomass dilution. It is concluded that thetrophic state significantly affects trace metalcycling. Sediment traps collect different types ofparticles than continuous flow centrifuges. Thetraps collect particles with higher clay content,lower Org-C concentrations and higher Org-C/Nelemental ratios than the centrifuges. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effect of grazers and viruses on bacterial community structure and production in two contrasting trophic lakes

Background

Over the last 30 years, extensive studies have revealed the crucial roles played by microbes in aquatic ecosystems. It has been shown that bacteria, viruses and protozoan grazers are dominant in terms of abundance and biomass. The frequent interactions between these microbiological compartments are responsible for strong trophic links from dissolved organic matter to higher trophic levels, via heterotrophic bacteria, which form the basis for the important biogeochemical roles of microbial food webs in aquatic ecosystems. To gain a better understanding of the interactions between bacteria, viruses and flagellates in lacustrine ecosystems, we investigated the effect of protistan bacterivory on bacterial abundance, production and structure [determined by 16S rRNA PCR-DGGE], and viral abundance and activity of two lakes of contrasting trophic status. Four experiments were conducted in the oligotrophic Lake Annecy and the mesotrophic Lake Bourget over two seasons (early spring vs. summer) using a fractionation approach. In situ dark vs. light incubations were performed to consider the effects of the different treatments in the presence and absence of phototrophic activity.

Results

The presence of grazers (i.e. < 5-μm small eukaryotes) affected viral production positively in all experiments, and the stimulation of viral production (compared to the treatment with no eukaryotic predators) was more variable between lakes than between seasons, with the highest value having been recorded in the mesotrophic lake (+30%). Viral lysis and grazing activities acted additively to sustain high bacterial production in all experiments. Nevertheless, the stimulation of bacterial production was more variable between seasons than between lakes, with the highest values obtained in summer (+33.5% and +37.5% in Lakes Bourget and Annecy, respectively). The presence of both predators (nanoflagellates and viruses) did not seem to have a clear influence upon bacterial community structure according to the four experiments.

Conclusions

Our results highlight the importance of a synergistic effect, i.e. the positive influence of grazers on viral activities in sustaining (directly and indirectly) bacterial production and affecting composition, in both oligotrophic and mesotrophic lakes.     

Bottom-up and top-down regulation of decomposition in a tropical forest

The soil nutrients, microbes, and arthropods of tropical forests are patchy at multiple scales. We asked how these three factors interact to generate patterns of decomposition in 450 100 cm² litterbags arrayed along a 50 m ridge top in a Panama rainforest. We tested top-down (via grazing by microbivores like collembola and diplopods) and bottom-up (via added N and P) effects on the decomposition of cellulose. By using a 1,000-fold gradient in mesh size we generated a two-fold gradient in arthropod grazing. Microbivore grazing first retarded then ultimately enhanced decomposition rates. Micropulses of N and P (simulating concentrated urine) enhanced neither decomposition rates nor microbivores but increased the abundance of predacious ants. Decomposition rates also varied across the ridge, and were lowest in a plot with the deepest litter and highest soil moisture. These data generate the working hypothesis that N and P cascade upward at grains of 100 cm² to enhance a major predator in the litter; predators then absorb any increases in microbivores attracted to the extra fungal growth. These population interactions are in turn embedded in mesoscale variability generated by individual tree canopies that drive changes in litter quality and soil moisture. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

应用DGGE法对青海相邻两盐湖中细菌多样性的快速检测

分别对青海相邻两盐湖柯柯盐湖、茶卡盐湖土样、泥样进行富集培养后,从中提取的DNA用两套不同的细菌通用引物进行扩增,分别得到包含V8和V9高变区的16SrDNA片断。经变性梯度凝胶电泳(DGGE)分析,结果显示这两个盐湖富集样品中细菌多样性具有较大的差异,而且同一盐湖不同性质样品中的细菌多样性差异也较大,两湖的泥样富集样品中均表现出了稍丰富的多样性。     

Diversity of bacterial community in freshwater of Woopo wetland

Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.     

Changes in freshwater bacterial community composition during measurements of microbial and community respiration

The respiration rates of a pelagic community and of its microbialfraction (< 1.2 µm) were measured at two depths inthe oxic layer of a meromictic alpine lake (Cadagno, Switzerland)using the oxygen technique. The duration of the incubationswere 12, 24 and 55 h. Bacterioplankton abundance (DAPI counts)and composition (whole cell hybridization using 11 group-specificrRNA-targeted oligonucleotide probes) were measured during theincubations. Respiration generally increased with time, especiallyin the microbial fraction, or remained similar. This resultwas not always consistent with changes in bacterial abundanceand cell volume. The composition of the community also changedduring the incubations. The abundance of ß-Proteobacteriaincreased during the course of all the experiments. These resultsextend the previous conclusions drawn in marine environmentsto fresh waters and demonstrate that, in addition to changesin bacterial abundance, cell volume and biomass, changes inthe taxonomic composition of the bacterial community can occurduring discrete incubations of freshwater planktonic communities.     

Top-down control of a meiobenthic community by two juvenile freshwater fish species

Top-down control of prey assemblages by fish predation has been clearly demonstrated for zooplankton and macroinvertebrates. However, in the benthic communities of freshwater ecosystems, the impact of fish predation on meiofaunal assemblages is nearly unknown. In this study, the predation effects of juvenile carp (Cyprinus carpio) and gudgeon (Gobio gobio) on meiofaunal abundance, biomass, community structure, and the diversity of nematodes were examined using microcosms that were sampled repeatedly over 64 days. Significant differences in abundance and biomass were found between the two fish treatments (carp and gudgeon) and their respective controls for nematodes, oligochaetes, and crustaceans (copepods, harpacticoids, ostracods, and cladocerans), but not for rotifers. These changes were consistent with top-down control of the freshwater meiofaunal assemblages in the microcosms over time. By contrast, small-bodied meiofauna was more abundant, suggesting indirect facilitation. Neither the species richness nor the diversity of the nematode community was affected by fish predation. The results indicate that predation by juvenile freshwater fish depresses the overall abundance and biomass of meiofaunal assemblages, except for rotifers, and alters the size structure of the meiofaunal community. Therefore, the meiofaunal assemblages of freshwater ecosystems may be influenced by bottom-feeding juvenile fish, e.g., carp and gudgeon, through top-down control of meiofaunal populations.     

Vertical profiles of water and sediment denitrifiers in two plateau freshwater lakes

The present study investigated the abundance, richness, diversity, and community composition of denitrifiers (based on nirS and nosZ genes) in the stratified water columns and sediments in eutrophic Dianchi Lake and mesotrophic Erhai Lake using quantitative PCR assay and high-throughput sequencing analysis. Both nirS- and nosZ denitrifiers were detected in waters of these two lakes. Surface water showed higher nosZ gene density than bottom water, and Dianchi Lake waters had larger nirS gene abundance than Erhai Lake waters. The abundance of sediment nirS- and nosZ denitrifiers in Dianchi Lake was larger than that in Erhai Lake. nirS richness and diversity and nosZ richness tended to increase with increasing sediment layer depth in both lakes. The distinct structure difference of sediment nirS- and nosZ denitrifier communities was found between in Dianchi Lake and Erhai Lake. These two lakes also differed greatly in water denitrifier community structure. Moreover, phylogenetic analysis indicated the presence of several different groups of nirS- or nosZ denitrifiers in both lakes. The novel nirS denitrifiers were abundant in both Dianchi Lake and Erhai Lake, while most of the obtained nosZ sequences could be affiliated with known genera.

     

Bottom-up rather than top-down processes regulate the abundance and activity of nitrogen fixing plants in two Connecticut old-field ecosystems

The maintenance of nitrogen limitation in terrestrial ecosystems remains a central paradox in biogeochemistry. Although plants that form a symbiotic association with nitrogen fixing bacteria should be at a competitive advantage over non-fixing plant species in N limited environments, N₂ fixing plants are uncommon in most mid- to high-latitude ecosystems. Theory and observation suggest that preferential grazing on N-rich tissues by herbivores, resource limitations to growth, reproduction and N₂ fixation, and temperature limitations to the activity of the N₂ fixing enzyme nitrogenase, explain the rarity of N₂ fixing plants. These ideas, however, have never been confronted by multifactor experiments in the field. In a 3 year field experiment, we found that the abundance, growth, reproductive output and fraction of plant-N derived from N₂ fixation in temperate, old-field ecosystems was constrained by the availability of phosphorus (P). Although the availability of light was crucial to the performance of old-field N₂ fixing plants, the largest gains in biomass and the rate of N₂ fixation were observed in the plots fertilized with P. By contrast, herbivory had no effect on the abundance, biomass and activity of N₂ fixing plants and inconsistent effects on foliar nitrogen concentrations (opposing directions, depending upon year), suggesting that herbivores do not affect the ecology of N₂ fixing plants in old field ecosystems, at least not over the course of 3 years. Together with a recent study demonstrating that C limitation explains the absence of N₂ fixing trees in temperate forests our analysis suggests that stand replacing disturbances shift the limitation on the abundance and activity of N₂ fixing plants from P early in secondary succession to light later in succession, as the forest canopy closes and incident light levels decline precipitously.