Regulation of bacterial assemblages in oligotrophic plankton systems: results from experimental and empirical approaches

Bacteria are relevant members of planktonic food webs, both in terms of biomass and production share. The assessment and comprehension of the factors that control bacterial abundance and production are, thus, necessary to understand how carbon and nutrients circulate in planktonic food webs. It is commonly believed that bacterial abundance, activity and production are either determined by the available nutrient levels (‘bottom-up’ control) or by the effect of predators (‘top-down’). These factors have also been shown to regulate the internal structure (the physiological and phylogenetic structure) of the bacterioplankton black box. We present here different empirical and experimental ways in which the factors that control bacterial communities are assessed, among them, the direct comparison of the rates of bacterial growth and losses to grazing. Application of several of these methods to open ocean data suggests that bacteria are regulated by resources at the largest scales of analysis, but that this overall regulation is strongly modulated by predators in all types of systems. In the most oligotrophic environments, bacterial abundance and growth are regulated by predators, while in the richest environments it is bacterial (phylogenetic, size, activity) community composition that is most affected by protist predators, while abundance can be influenced by metazoans. Because changes in bacterial community composition require that bacteria have enough nutrient supply, the overall effect of these regulations is that bacterial growth appears to be top-down regulated in the most nutrient-poor environments and bottom-up regulated in the richer ones. This revised version was published online in August 2006 with corrections to the Cover Date.     

Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom

The vernal successions of phytoplankton, heterotrophic nanoflagellates (HNF) and viruses in temperate lakes result in alternating dominance of top-down and bottom-up factors on the bacterial community. This may lead to asynchronous blooms of bacteria with different life strategies and affect the channelling of particular components of the dissolved organic matter (DOM) through microbial food webs. We followed the dynamics of several bacterial populations and of other components of the microbial food web throughout the spring phytoplankton bloom period in a pre-alpine lake, and we assessed bacterial uptake patterns of two constituents of the labile DOM pool (N-acetyl-glucosamine [NAG] and leucine). There was a clear genotypic shift within the bacterial assemblage, from fast growing Cytophaga-Flavobacteria (CF) affiliated with Fluviicola and from Betaproteobacteria (BET) of the Limnohabitans cluster to more grazing resistant AcI Actinobacteria (ACT) and to filamentous morphotypes. This was paralleled by successive blooms of viruses and HNF. We also noted the transient rise of other CF (related to Cyclobacteriaceae and Sphingobacteriaceae) that are not detected by fluorescence in situ hybridization with the general CF probe. Both, the average uptake rates of leucine and the fractions of leucine incorporating bacteria were approximately five to sixfold higher than of NAG. However, the composition of the NAG-active community was much more prone to genotypic successions, in particular of bacteria with different life strategies: While 'opportunistically' growing BET and CF dominated NAG uptake in the initial period ruled by bottom-up factors, ACT constituted the major fraction of NAG active cells during the subsequent phase of high predation pressure. This indicates that some ACT could profit from a substrate that might in parts have originated from the grazing of protists on their bacterial competitors.     

Trophic interactions between viruses, bacteria and nanoflagellates under various nutrient conditions and simulated climate change

Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top-down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom-up control (nutrients) under various simulated climatic conditions (temperature and UV-B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl-Pak bags exposed to an increase of 3°C and 20% UV-B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV-B radiation effect on the bacterial dynamics. These results show that top-down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short-term simulated climate changes are only a secondary effect controlling microbial processes.     

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.     

Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing

We analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran Daphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal of Daphnia and doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the class Proteobacteria and the Cytophaga-Flavobacterium cluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of the Proteobacteria increased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 microm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure.     

Correlations between plant phylogenetic and functional diversity in a high altitude cold salt desert depend on sheep grazing season: Implications for range recovery

Environmental impact alters assemblages by increasing species relatedness, thus reducing phylogenetic and functional diversity. We assessed whether different controlled grazing regimes influenced the recovery of plant phylogenetic diversity (Average Taxonomic Distinctness, ATD) and functional diversity based on plant growth habit (GH) and life cycle duration (LCD) [Shannon-Weiner Index (H’), ?ln(Simpson's Index, D)] in pastures from previously unmanaged and highly overgrazed conditions. Plant presence/absence data were collected during August 2006 from a high altitude cold salt desert in south-western Utah, where controlled grazing has been maintained for over 70 years to study range restoration. Winter-spring and spring grazed pastures were examined at four grazing levels: ungrazed, light, medium, and heavy, with each level differing in the number of animal use days per hectare relative to available forage biomass. For winter-spring, animal use days were divided equally between the two seasons. Winter-spring grazing promoted recovery of plant phylogenetic and functional diversity compared to spring grazing as reflected by the consistently higher values of ATD, and the stability of species composition within each ecological trait and their similarity to values for ungrazed pastures. Spring grazing was detrimental to recovery efforts and resulted in the reduction of palatable non-grass species, ATD, and functional diversity with increased grazing intensity. Many significant positive correlations between phylogenetic and functional diversity indices existed during spring, but not winter-spring grazing. While H’(GH) was uncorrelated with ATD during winter-spring, it was positively correlated in spring, suggesting species in the plant community (based on growth habit) during spring were randomly assembled without influence from local species interactions, and that different growth habits are conserved within lineages so that communities randomly assembled from more lineages will have a greater diversity of growth habits than communities assembled from fewer lineages. H’(LCD) was negatively correlated with ATD during winter-spring, suggesting local species interactions naturally influence assemblage composition regarding life cycle duration. As such, species within the same lineage likely interact (compete) more for scarce resources because they share similar life cycle durations, thus leading to greater trait variation in communities with fewer lineages than in those with many lineages. Yet, this correlation was positive during spring, suggesting an overriding effect from grazing rather than local species interactions. Hence, sheep grazing at the DER appears to be a season-dependent driver of plant phylogenetic and functional diversity, and the correlations between them. We recommend Average Taxonomic Distinctness and functional diversity based on growth habit and life cycle duration be considered as significant developments in the construction of practical rapid assessment tools for biomonitoring and feedback regarding grazing impacts in similar ecosystems.     

Interaction of Nutrient Limitation and Protozoan Grazing Determines the Phenotypic Structure of a Bacterial Community

We examined the impact of nutrient conditions (carbon and phosphorus limitation) and grazing by protozoans on the phenotypic community structure of freshwater bacteria in continuous culture systems. Lakewater bacteria were grown on mineral medium, which was supplemented with glucose and amino acids and adjusted by different phosphorus concentrations to achieve either carbon or phosphorus limitation. Each nutrient treatment was inoculated with the same bacterial community and consisted of a nongrazing and a grazing treatment, to which the heterotrophic nanoflagellates Spumella sp. and Ochromonas sp. were added. We found that nutrient conditions alone resulted in differences in the phenotypic structure of the bacterial community: small and motile bacteria dominated under C limitation while large, elongated, and capsulated bacteria were characteristic for P limitation. The genotypic community composition as measured by T-RFLP (terminal restriction fragment length polymorphism) was not severely influenced by the two nutrient treatments. In the presence of flagellate predators, grazing-resistant bacteria developed under both nutrient conditions, but with different survival mechanisms: highly motile bacteria prevailed under C limitation, whereas the P-limited grazing treatment was dominated by filamentous forms. T-RFLP analysis revealed only moderate changes in bacterial community composition due to grazing, which were most pronounced under P limitation. Analysis by video microscopy revealed that high swimming speed is an efficient nonmorphological survival mechanism for bacteria to reduce the capture success of the flagellate predator. The rejection of optimal-sized, nonmotile bacteria under P limitation suggests the importance of other nonmorphological, surface-located cell properties. Our results illustrate that the realized mechanisms of grazing resistance are linked to the actual limitation conditions, and that the combined effects of nutrient limitation and grazing are major determinants of bacterial community structure.     

Predation-mediated shifts in size distribution of microbial biomass and activity during detritus decomposition

Many experimental studies on detritus decomposition revealed a comparable microbial succession after the addition of a substrate pulse: from small, freely suspended single bacteria at the beginning, to more complex and larger growth forms during a later stage, accompanied by the appearance of bacterivorous protists. We examined in three model experiments with different organic carbon sources whether this shift in bacterial size structure is linked to the grazing impact of bacterivores. In short‐term (8–10 d) microcosm experiments we added natural dissolved and particulate detritus (macrophyte leaves and leachate, dead phytoplankton cells) as an organic substrate source. By the use of size‐fractionated inocula and eucaryotic inhibitors we obtained treatments without protists, in which bacteria developed without predation. These were compared, by measurements of bacterial activity and microscopical analysis of bacterial size structure, to incubations in which either cultured heterotrophic nanoflagellates or a natural protist assemblage was included in the inoculum. The presence of bacterial grazers resulted in a 50–90% reduction of bacterial biomass compared to grazer‐free trials. The selective removal of freely suspended bacteria produced a very different relative composition of bacterial biomass: it became dominated by large, grazing‐resistant forms such as filaments and cells attached to particles or clustered in small aggregates. In grazer‐free treatments, bacterial biomass was always dominated (>80%) by free‐living, single bacterial cells. The time course of the bacterial development suggested different underlying mechanisms for the appearance of predation resistant filamentous and of aggregated or attached bacteria. As bacterial aggregates developed in approximately similar amounts with and without grazers no specific growth stimulation by protists could be detected. In contrast, concentrations of filamentous bacteria were 2–10 times higher in treatments with protists, thus indicating a stimulation of this growth form during enhanced grazing pressure. Measurements of ectoenzymatic activity and H‐leucine uptake indicated that microbial activity was also shifted to larger size fractions. In most cases more than 50% of bacterial activity in treatments with protists was associated with the size fraction>10 μm whereas this value was <2% without grazers. Grazing by protists also enhanced the specific activity of the bacterial assemblage which is in contrast to an assumed lower competitive ability of complex bacterial growth forms. The results imply that the selective force of bacterivory in nutrient‐rich environments changes the structure and possibly the function of aquatic bacteria and their position in the food web, making protist‐resistant bacteria more vulnerable to metazoan filter feeders and detritivores, and possibly also subject to sedimentation.     

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 μg liter⁻¹) while the other lakes had relatively low nutrient levels (total phosphorus, <100 μg 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.     

The effect of grazing and nutrient supply on periphyton associated bacteria

The effects of nutrient additions and grazing by macro-invertebrates on periphyton-associated algae and bacteria were studied by performing an enclosure experiment on three occasions from early spring to summer at mesotrophic Lake Erken and V?dd?, at the Swedish Baltic coast. There were significant interactions between nutrient additions and grazing on bacterial biomass and specific activity in Lake Erken. Thus, the importance of either bottom-up or top-down effects could not be singled out. Bacterial biomass increased with enrichment only in the absence of grazers. Grazer presence tended to increase bacterial biomass in ambient nutrient conditions, but to decrease bacterial biomass under enrichment. For specific activity the positive response to enrichment was restricted to grazer presence. Hence, grazing by macro-invertebrates may have an indirect positive effect on bacterial activity by enhancing nutrient conditions through their feeding activities and/or fecal pellets production. In addition, we found a significant relationship between bacterial production and chlorophyll a at both sites. This relationship weakened in the presence of macro-invertebrates. Thus, the importance of internal nutrient regeneration by bacteria and algae decreased, possibly due to increased nutrient availability, in the presence of macro-invertebrate grazers.     

Comparison of growth rates of aerobic anoxygenic phototrophic bacteria and other bacterioplankton groups in coastal Mediterranean waters

Growth is one of the basic attributes of any living organism. Surprisingly, the growth rates of marine bacterioplankton are only poorly known. Current data suggest that marine bacteria grow relatively slowly, having generation times of several days. However, some bacterial groups, such as the aerobic anoxygenic phototrophic (AAP) bacteria, have been shown to grow much faster. Two manipulation experiments, in which grazing, viruses, and resource competition were reduced, were conducted in the coastal Mediterranean Sea (Blanes Bay Microbial Observatory). The growth rates of AAP bacteria and of several important phylogenetic groups (the Bacteroidetes, the alphaproteobacterial groups Roseobacter and SAR11, and the Gammaproteobacteria group and its subgroups the Alteromonadaceae and the NOR5/OM60 clade) were calculated from changes in cell numbers in the manipulation treatments. In addition, we examined the role that top-down (mortality due to grazers and viruses) and bottom-up (resource availability) factors play in determining the growth rates of these groups. Manipulations resulted in an increase of the growth rates of all groups studied, but its extent differed largely among the individual treatments and among the different groups. Interestingly, higher growth rates were found for the AAP bacteria (up to 3.71 day⁻¹) and for the Alteromonadaceae (up to 5.44 day⁻¹), in spite of the fact that these bacterial groups represented only a very low percentage of the total prokaryotic community. In contrast, the SAR11 clade, which was the most abundant group, was the slower grower in all treatments. Our results show that, in general, the least abundant groups exhibited the highest rates, whereas the most abundant groups were those growing more slowly, indicating that some minor groups, such the AAP bacteria, very likely contribute much more to the recycling of organic matter in the ocean than what their abundances alone would predict.     

Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Rímov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 microm), bacteria and heterotrophic nanoflagellates (<5 microm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of beta-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.     

Effects of decreased resource availability, protozoan grazing and viral impact on a structure of bacterioplankton assemblage in a canyon-shaped reservoir

We conducted a transplant experiment to elucidate the effects of different levels of grazing pressure, nutrient availability, especially phosphorus, and the impact of viruses on the changes in the structure of bacterioplankton assemblage in a meso-eutrophic reservoir. A sample taken from the nutrient-rich inflow part of the reservoir was size-fractionated and incubated in dialysis bags in both inflow and dam area. The structure of bacterial assemblage was examined by fluorescence in situ hybridization using oligonucleotide probes with different levels of specificity. In terms of the relative proportions of different bacterial groups, we found very few significant changes in the bacterioplankton composition after transplanting the treatments to the nutrient-poor dam area. However, we observed marked shifts in morphology and biomass towards the development of filaments, flocs and "vibrio-like" morphotypes of selected probe-defined groups of bacteria induced by increased grazing pressure. Despite the very high abundances of viruses in all the treatments, their effects on bacterioplankton were rather negligible.     

Direct and indirect influences of crustacean zooplankton on bacterioplankton of Lake Constance

Herbivorous crustacean zooplankton may influence bacterial populations of lakes directly by grazing on them or indirectly by grazing on algae. In Lake Constance a regularly observed decrease of bacterial density during periods of high abundance of cladocerans (clearwater phase) indicated bacterial grazing losses. However, cladoceran grazing on bacteria appeared to be less efficient than on algae. Moreover, cladocera reduced grazing pressure on bacteria by grazing on bacterivorous flagellates. Additionally, a shift of bacterial composition from an originally higher percentage of filamentous and aggregate growth forms towards a population of homogenously distributed small single celled bacteria was observed regularly at the beginning of the clearwater phase. Transient increases of bacterial abundance and productivity coinciding with the increase of cladocera at the end of the algal spring bloom were interpreted as field indications of indirect bacteria-zooplankton interactions due to crustacean grazing on phytoplankton. The release of organic carbon during grazing of crustacea on algae was considered as explanation for the observed stimulation of bacterial populations. Thereby, additional, otherwise inaccessible algal carbon would be made available to bacteria by zooplankton. Experimental support for this hypothesis was given by showing that bacteria were able to respond to crustacean grazing on algae by enhanced growth and activities. The possible impact of these direct and indirect crustacea-bacteria interactions on the abundance, activity and composition of bacterioplankton as well as on the structure and function of the total planktonic community is discussed.     

Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition

Quantitative and qualitative changes in bacterial communities from the Mediterranean Sea were compared in duplicate batch mesocosms with or without addition of inorganic nutrients. Methods including traditional microbial ecology techniques, molecular biology and flow cytometry were combined to determine abundances, production, cell size, activity, culturability and taxonomic diversity of bacterial cells. Addition of nutrients and confinement resulted in an increase of bacterial densities which were rapidly controlled by protozoan grazing. Changes in bacterial activity and morphology were observed during the growth phase of bacteria and under grazing pressure. The proportion of medium-size and culturable cells increased during the growth phase. These cells were preferentially consumed by grazers resulting in a strong limitation of bacterial production. As a consequence of the grazing pressure, large cells were produced and contributed to the remaining bacterial productivity after grazing. Grazing had an effect on the taxonomic composition of bacterial communities by preferentially eliminating gamma-Proteobacteria, alpha-Proteobacteria were preserved. It seems that some species from the genera Ruegeria and Cytophaga may have developed defence strategies to escape predation.     

Changing phosphorus concentration and subsequent prophage induction alter composition of a freshwater viral assemblage

1. The effects of nutrients on the temporal variation in viral assemblage composition, and in particular the occurrence of temperate phages, were assessed in mesotrophic Lake Erken over 5 months of the ice‐free period. The percentage of the bacterial community that contained inducible prophages (lysogenic bacteria, LB) changed over the season, being lowest in late spring and highest in early autumn. The most important variables for predicting LB were concentrations of total nitrogen (TN), total phosphorus (TP) and temperature. 2. The viral assemblage composition, as determined by pulsed‐field gel electrophoresis (PFGE), also changed over the season. Prophages were induced by incubations with mitomycin C and we show, for the first time for natural communities, that the resulting temperate phages could be detected using PFGE. 3. A substantial fraction (19%) of the number of detected operational taxonomic units (OTUs: defined as unique genome sizes) appeared unique to temperate phages and 41% of OTUs increased in relative abundance after treatment with mitomycin C. 4. Different viral OTUs were induced at different times during the season. The most important environmental factor covarying with viral assemblage composition over the period of study, as determined by multivariate analysis, was concentration of TP. In re‐growth cultures with natural bacteria and lowered viral abundance (VA) (decreased virus to bacteria ratio), addition of PO₄‐P induced prophages and resulted in subsequent production of temperate phages, as indicated by a decreased percentage of LB and increased VA. Incubations of natural bacterial communities with mitomycin C (field data) or PO₄‐P (experiment) changed the viral assemblage composition at a similar rate as the observed monthly changes in the lake.     

Microbial decomposition of dissolved organic matter in a hypertrophic pond

Planktonic heterotrophic bacteria in lakes utilize the labile fraction of dissolved organic carbon (DOC), although information about seasonal changes in labile DOC in hypertrophic lakes in terms of absolute amount and relative proportion of the total DOC is still limited. We conducted DOC decomposition experiments using GF/F filtrates in water samples from hypertrophic Furuike Pond, together with monitoring of DOC concentration and bacterial abundance in water samples from the pond, to examine seasonal changes in the amount of labile DOC and growth of bacteria on labile DOC. DOC concentrations fluctuated between 2.7 and 11 mg C l⁻¹, and bacterial abundance fluctuated between 1.5 × 10⁶ and 1.0 × 10⁸ cells ml⁻¹. In the DOC decomposition experiment when grazers of bacteria were removed, small portions of DOC (18% ± 12%) were labile for decomposition by bacteria, and the growth yield of bacteria on labile DOC ranged between 3.3% and 19%. Furthermore, addition of nitrogen to water samples enhanced bacterial growth. Thus, not only labile DOC but also nitrogen limited bacterial growth in the pond. Considering the results in the present study together with those of previous studies, bacterial abundance in Furuike Pond is subjected to bottom-up control, such as by limitation of DOC and nitrogen throughout the year, although top-down control of bacterial abundance such as by grazing is seasonally important. Received: May 1, 2001 / Accepted: July 22, 2001     

Structural and functional patterns of bacterial communities in response to protist predation along an experimental productivity gradient

Substrate supply and protist grazing are two of the most important forces that determine the composition and properties of bacterial assemblages. General ecological theory predicts that the relative importance of these factors is changing with the environmental productivity. In the present study, the interplay between bottom-up and top-down control was studied in a productivity gradient simulated in one-stage chemostats containing natural assemblages of freshwater bacteria and heterotrophic nanoflagellates. Bacterial assemblages in the chemostats differed strongly with respect to their morphological, physiological and compositional properties in the presence versus the absence of predators. However, theses differences were modified by the productivity gradient. Whereas in predator-free chemostats the mean abundance and biomass of bacteria increased proportionally with increasing substrate supply, in treatments that included flagellates bacterial production was largely channelled into predator biomass. The bacterial morphological diversity increased along the productivity gradient with increasing substrate input but even more so with predators. Proportional to the increasing substrate supply, predation shifted the remaining bacteria towards morphologically inedible forms. Predation also caused shifts in bacterial substrate-utilization profiles, and in bacterial community composition, as analysed by terminal restriction fragment length polymorphism of PCR-amplified 16S-rRNA genes. Without predators, bacterial richness increased along the productivity gradient whereas with predators bacterial richness was higher at intermediate substrate levels. In accordance with ecological theory, these results demonstrated that predators influence all of the major characteristics of bacterial assemblages but the magnitude of this effect is modulated by the productivity of the system.     

Trophic interactions within the microbial food web in a tropical floodplain lake (Laguna Bufeos, Bolivia)

Whether the primary role of bacterioplankton is to act as "remineralizers" of nutrients or as direct nutritional source for higher trophic levels will depend on factors controlling their production and abundance. In tropical lakes, low nutrient concentration is probably the main factor limiting bacterial growth, while grazing by microzooplankton is generally assumed to be the main loss factor for bacteria. Bottom-up and top-down regulation of microbial abundance was studied in six nutrient limitation and dilution gradient-size fractionation in situ experiments. Bacteria, heterotrophic nanoflagellates (HNF), ciliates and rotifers showed relatively low densities. Predation losses of HNF and ciliates accounted for a major part of their daily production, suggesting a top-down regulation of protistan populations by rotifers. Phosphorus was found to be strongly limiting for bacterial growth, whereas no response to enrichment with Nitrogen or DOC was detected. HNF were the major grazers on bacteria (g-0.43 d(-1)), the grazing coefficient increased when ciliates were added (g- 0.80 d(-1)) but decreased when rotifers were added (g- 0.23 d(-1)) probably due to nutrient recycling or top-down control of HNF and ciliates by rotifers.     

Nutrient control of phytoplankton production in Lake Naivasha,Kenya

Lake Naivasha, a shallow tropical lake in Kenya's Rift Valley, has an unstable water column and is moderately eutrophic. Nutrient (bottom-up) control of primary production is more important than grazing (top-down) control. Experimental nutrient enrichment was used to investigate bottom-up control in more detail. Minor nutrients were not found to be limiting, whilst nitrogen was more limiting than phosphorus with an algal preference for ammonium over nitrate. Sediments form a phosphorus sink but there is hypolimnetic release from the one area showing regular temporary stratification. This indicates that the rate of primary production in the water column could double if conditions change to allow lake-wide nutrient release from sediments. Both external and recycled nutrient regeneration are important.