Microbial Food Webs in an Artificially Divided Acidic Bog Lake

The microbial loop of a naturally acidic bog lake, Große Fuchskuhle (Northeastern Germany), that had been artificially divided into 4 basins, was investigated. In the northeast (NE) and southwest (SW) basins, which differ strongly in chemistry and primary production, we conducted intensive studies of the main carbon fluxes through microbial food webs. In the less acidic, NE basin, much higher phytoplankton as well as bacterial biomass and production were found in parallel with negligible numbers of larger zooplankters. Weakly top-down controlled populations of protists were characterized by an exceptionally low numerical proportion of heterotrophic nanoflagellates (HNF) to ciliates (-1.5-3.5). The ciliate community was dominated by a scuticociliate, Cyclidium sp. (>95% of total ciliates), with an estimated grazing rate equal to 46–80% of heterotrophic bacterial production. In contrast, in the more humic, SW basin, both phyto- and bacterioplankton dynamics seemed to be top-down controlled by abundant populations of small fine-filter feeding cladocerans, Ceriodaphnia quadrangula and Diaphanosoma brachyurum. Consequently, ciliates disappeared from the food web structure of the SW basin, HNF dropped to negligible numbers and bacteria showed very uniform morphology, dominated by small cocci or short rods. Our investigations have shown that the division of the lake into separate compartments can lead to very different microbial food web structures with extreme species compositions.     

Prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients

An experiment designed to examine food preferences of heterotrophic nanoflagellates (HNF) grazing on bacterioplankton was performed in the freshwater Rímov reservoir (Czech Republic). Water samples were size-fractionated to obtain < 5 microm filtrate containing bacteria and HNF. To manipulate resource availability, < 5 microm treatments were incubated in dialysis bags submerged in the barrels filled with the unfiltered reservoir water amended with either orthophosphate or glucose or combination of both. We employed rRNA-targeted probes to assess HNF prey preferences by analysing bacterial prey in HNF food vacuoles compared with available bacteria. Actinobacteria (the HGC69a probe) were avoided by HNF in all treatments. Cytophaga-Flavobacterium-Bacteroidetes bacteria (the CF319a probe) were positively selected mainly in treatments in which bacteria were heavily grazed, the < 5 microm treatments, but this trend was less pronounced towards the end of the study. The members of a small subcluster of Betaproteobacteria (the R-BT065 probe) were mostly positively selected. The nutrient amendments differentially affected bacterioplankton dynamics in almost all treatments, and together with the size fractionation, altered HNF overall bacterivory as well as prey selection. Analyses of bacterivores in unfiltered treatments allowed to detect the effect of different protists on shifts in HNF selectivity observed in < 5 microm compared with unfiltered treatments.     

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.     

Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes

The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha- and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south-west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria-related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas- and Rhodobacter-like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter-rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium-related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.     

Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater community

We present a detailed analysis of the effects of distinct bacterial mortality factors, viral lysis and heterotrophic nanoflagellates (HNF) bacterivory, associated with the development of filamentous Flectobacillus populations. Reservoir bacterioplankton communities were subjected to additions of both HNF and viruses together, or HNF alone, and then incubated in situ in dialyses bags. For distinct bacterial groups, mortality or growth stimulation was analysed by examining bacterial prey ingested in HNF food vacuoles with fluorescence in situ hybridization (FISH) and via FISH with microautoradiography (MAR-FISH). We also developed a semi-quantitative MAR-FISH-based estimation of relative activities of Flectobacillus populations (targeted by the R-FL615 probe). Bacterial groups vulnerable to HNF predation (mainly clusters of Betaproteobacteria), or discriminated against (Actinobacteria), were detected. Bacterial lineages most vulnerable to virus-lysis (mainly the Betaproteobacteria not targeted by the R-BT065 probe, of the Polynucleobacter cluster) were identified by comparing treatments with HNF alone to HNF and viruses together. Filaments affiliated with the Flectobacillus cluster appeared in both treatments, but were about twice as abundant, long and active as in incubations with viruses and HNF as compared with HNF alone. Viruses appeared to selectively suppress several bacterial groups, perhaps enhancing substrate availability thus stimulating growth and activity of filamentous Flectobacillus.     

Bacterioplankton Growth on Fractions of Dissolved Organic Carbon of Different Molecular Weights from Humic and Clear Waters

The ability of fractions of dissolved organic carbon (DOC) of different molecular weights (MW) to support bacterial growth was studied in batch culture experiments. Natural pelagic bacteria were inoculated into particle-free (0.2-μm filtered) water, taken from 10 oligotrophic lakes of differing humic content, and either used without further treatments or ultrafiltered to remove DOC of >10,000 MW or >1,000 MW. Stationaryphase abundance of bacteria in the cultures was used as an estimate of bacterial carrying capacity. High-MW DOC (>10,000) comprised an increasing fraction of total DOC with increasing total DOC and humic content of the lakes. High-MW DOC was generally more available to bacteria (i.e., more bacteria were produced per unit of organic carbon initially present) than low-MW (<10,000) DOC. The availability to bacteria of this high-MW DOC decreased with increasing humic content. However, although less available in humic lakes than in clearwater lakes, the higher abundance of high-MW DOC made it quantitatively more important as a bacterial substrate; i.e., a larger fraction of the total bacterial yield of the cultures was due to high-MW DOC compounds in humic lakes than in clearwater lakes. On the average, 48% of bacterial growth occurred at the expense of DOC of <10,000 MW. DOC of <1,000 MW was responsible for an average of 22% of bacterial growth, with no significant correlation to humic content and DOC concentration of lakes. The DOC which supports bacterial growth, as well as the total DOC, is of different quality in humic and clearwater lakes.     

Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir

We investigated net growth rates of distinct bacterioplankton groups and heterotrophic nanoflagellate (HNF) communities in relation to phosphorus availability by analysing eight in situ manipulation experiments, conducted between 1997 and 2003, in the canyon-shaped Rímov reservoir (Czech Republic). Water samples were size-fractionated and incubated in dialysis bags at the sampling site or transplanted into an area of the reservoir, which differed in phosphorus limitation (range of soluble reactive phosphorus concentrations--SRP, 0.7-96 microg l-1). Using five different rRNA-targeted oligonucleotide probes, net growth rates of the probe-defined bacterial groups and HNF assemblages were estimated and related to SRP using Monod kinetics, yielding growth rate constants specific for each bacterial group. We found highly significant differences among their maximum growth rates while insignificant differences were detected in the saturation constants. However, the latter constants represent only tentative estimates mainly due to insufficient sensitivity of the method used at low in situ SRP concentrations. Interestingly, in these same experiments HNF assemblages grew significantly faster than any bacterial group studied except for a small, but abundant cluster of Betaproteobacteria (targeted by the R-BT065 probe). Potential ecological implications of different growth capabilities for possible life strategies of different bacterial phylogenetic lineages are discussed.     

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.     

Genetic pattern of the recent recovery of European otters in southern France

We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otter Lutra lutra in a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cévennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter.     

Growth of Bream,Abramis brama L., in Two Outside Basins of Different Trophic State of Lake Balaton

Age-composition, size-distribution, length/weight relationships and growth both in length and weight of bream stocks were studied on fishes collected in NE and SW basins of Lake Balaton during 1982/83. Stocks consisting of 10 to 12 age-groups were observed at the two lake areas. The linear growth and weight-gain in the SW-basin were annually faster than in the NE-basin, however, the growth of bream in Lake Balaton was slow as compared to that observed 10 years ago. Parallel with progressive eutrophication, the density of bream stocks increased by some 5–10 % especially at hypertrophic lake areas (SW) and consequently their growth was transformed to densitydependent. In the appearance of strong year-classes some cyclicism could be observed especially in the SW-basin.     

No difference in colony formation of Scenedesmus obliquus exposed to lakes with different nutrient levels

The algal genus Scenedesmus is famous for its highly phenotypic plasticity in response to various environmental factors. In laboratory, axenic cultures of Scenedesmus often fail to form colonies and remain in unicellular morph. To examine whether unicellular Scenedesmus can form colonies after exposure to natural lakes, dialysis bags and plastic bottles which contained the precultured Scenedesmus obliquus were exposed in two lakes with different nutrient levels for four weeks. Results showed S. obliquus grew well in dialysis bags but not in plastic bottles; S. obliquus can form colonies when incubated in dialysis bags which allow exchange with the aquatic environment of the substances, regardless of the nutrient levels of the two lakes. However, no colonies were observed in S. obliquus incubated in plastic bottles exposed in both lakes. This suggested that active growth and zooplankton infochemicals contributed together to the colony formation of S. obliquus exposed in situ environment.     

Temperature and biotic factors influence bacterial communities associated with the cyanobacterium Microcystis sp

Cyanobacterial blooms represent a nutritious niche for associated bacteria including potential pathogens for humans as well as livestock. We investigated bacterial community composition associated with Microcystis sp. using different approaches: batch experiments on Microcystis sp. or its enriched exudates, field enclosures (dialysis bags) and field sampling during natural blooms in freshwaters. Bacterial community composition associated with Microcystis sp. differed significantly with temperature, bacterial source community and number of incubated cyanobacterial strains. Interestingly, Actinobacteria of the AcI cluster were only present in the 20°C treatments and disappeared at higher incubation temperatures. Moreover, Archaea were present in all field samples but did not show any regional patterns, which is consistent with bacteria. Absence of Archaea in the experimental treatments indicates reduced growth under experimental conditions. In contrast, members of the genus Sphingomonas (Alphaproteobacteria), which includes species known as human pathogens, occurred in almost all samples. Thus Sphingomonadales seem to be an integral element of Microcystis sp. blooms - even affecting concentrations of microcystins as a result of their breakdown of the toxins. Depending on environmental conditions such as temperature, light, currents and nutrients, the role of heterotrophic Bacteria associated with Cyanobacteria can greatly vary by either increasing (pathogens) or decreasing (breakdown of toxins) health risks caused by mass developments of potentially toxic Cyanobacteria.     

Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-Rich Aggregates (“Iron Snow”)

Microbial ferrous iron [Fe(II)] oxidation leads to the formation of iron-rich macroscopic aggregates (“iron snow”) at the redoxcline in a stratified lignite mine lake in east-central Germany. We aimed to identify the abundant Fe-oxidizing and Fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their pH values. Nucleic acid- and lipid-stained microbial cells of various morphologies detected by confocal laser scanning microscopy were homogeneously distributed in all iron snow samples. The dominant iron mineral appeared to be schwertmannite, with shorter needles in the northern than in the central basin samples. Total bacterial 16S rRNA gene copies ranged from 5.0 × 10⁸ copies g (dry weight)⁻¹ in the acidic central lake basin (pH 3.3) to 4.0 × 10¹⁰ copies g (dry weight)⁻¹ in the less acidic (pH 5.9) northern basin. Total RNA-based quantitative PCR assigned up to 61% of metabolically active microbial communities to Fe-oxidizing- and Fe-reducing-related bacteria, indicating that iron metabolism was an important metabolic strategy. Molecular identification of abundant groups suggested that iron snow surfaces were formed by chemoautotrophic iron oxidizers, such as Acidimicrobium, Ferrovum, Acidithiobacillus, Thiobacillus, and Chlorobium, in the redoxcline and were rapidly colonized by heterotrophic iron reducers, such as Acidiphilium, Albidiferax-like, and Geobacter-like groups. Metaproteomics yielded 283 different proteins from northern basin iron snow samples, and protein identification provided a glimpse into some of their in situ metabolic processes, such as primary production (CO₂ fixation), respiration, motility, and survival strategies.     

Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan

We investigated the diversity and distribution of archaeal and bacterial 16S rRNA gene sequences in deep aquifers of mid‐ to late Miocene hard shale located in the northernmost region of the Japanese archipelago. A major fault in the north‐west–south‐east (NW–SE) direction runs across the studied area. We collected three groundwater samples from boreholes on the south‐west (SW) side of the fault at depths of 296, 374 and 625 m below ground level (m.b.g.l.) and one sample from the north‐east (NE) side of the fault at a depth of 458 m.b.g.l. The groundwater samples were observed to be neutral and weakly saline. The total microbial counts after staining with acridine orange were in the order 10⁵?10⁶ cells mL^?1 and 10³ cells mL^?1 in the aquifers to the SW and to the NE of the fault, respectively. A total of 407 archaeal and bacterial 16S rRNA gene sequences (204 and 203 sequences, respectively) were determined for clone libraries constructed from all groundwater samples. Phylogenetic analyses showed that the libraries constructed from the SW aquifers were generally coherent but considerably different from those constructed from the NE aquifer. All of the archaeal clone libraries from the SW aquifers were predominated by a single sequence closely related to the archaeon Methanoculleus chikugoensis, and the corresponding bacterial libraries were mostly predominated by the sequences related to Bacteroidetes, Firmicutes and δ‐Proteobacteria. In contrast, the libraries from the NE aquifer were dominated by uncultured environmental archaeal clones with no methanogen sequences and by β‐proteobacterial clones with no sequences related to Bacteroidetes and δ‐Proteobacteria. Hence, the possible coexistence of methanogens and sulphate reducers in Horonobe deep borehole (HDB) on the SW side is suggested, particularly in HDB‐6 (374 m.b.g.l.). Moreover, these organisms might play an important geochemical role in the groundwater obtained from the aquifers.     

Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir

Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-microm treatment) or enhance (<5-microm treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. Time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan grazing, viral abundance, and frequency of visibly infected cells. Shifts in bacterial community composition (BCC) were examined by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rDNA genes from the different treatments, and fluorescence in situ hybridization (FISH) with previously employed and newly designed oligonucleotide probes. Changes in bacterioplankton characteristics were clearly linked to changes in mortality rates. In the reservoir, where bacterial production about equaled protist grazing and viral mortality, community characteristics were nearly invariant. In the "grazer-free" (0.8-microm-filtered) treatment, subject only to a relatively low mortality rate (approximately 17% day(-1)) from viral lysis, bacteria increased markedly in concentration. While the mean bacterial cell volume was invariant, DGGE indicated a shift in BCC and FISH revealed an increase in the proportion of one lineage within the beta proteobacteria. In the grazing-enhanced treatment (5-microm filtrate), grazing mortality was approximately 200% and viral lysis resulted in mortality of 30% of daily production. Cell concentrations declined, and grazing-resistant flocs and filaments eventually dominated the biomass, together accounting for >80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage. Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity.     

Effects of drying regime on microbial colonization and shredder preference in seasonal woodland wetlands

1. Energy budgets of wetlands in temperate deciduous forests are dominated by terrestrially derived leaf litter that decays under different drying conditions depending on autumn precipitation. We compared decay rates and microbial colonization of maple leaves under different inundation schedules in a field experiment, and then conducted a laboratory study on shredder preference. In the field, litter bags either remained submerged (permanent), were moved to a dried part of the basin once and then returned (semi-permanent), or were alternated between wet and dry conditions for 8 weeks (temporary).
2. There was no difference in decay rates among treatments, but leaves incubated under permanent and semi-permanent conditions had higher fungal and bacterial biomass, and lower C : N ratios than those incubated under alternating drying and wetting conditions.
3. To determine the effects of these differences in litter nutritional quality on shredder preference, we conducted a laboratory preference test with larvae of leaf-shredding caddisflies that inhabit the wetland. Caddisflies spent twice as much time foraging on permanent and semi-permanent litter than on litter incubated under temporary conditions.
4. There is considerable variation among previous studies in how basin drying affects litter breakdown in wetlands, and no previous information on shredder preference. We found that frequent drying in a shallow wetland reduces the nutritional quality of leaf litter (lower microbial biomass and nitrogen content), and therefore preference by invertebrate shredders. These results suggest that inter-annual shifts in drying regime should alter detritus processing rates, and hence the mobilization of the energy and nutrients in leaf litter to the wetland food web.     

Diel changes in the specific growth rate and mean cell volume of natural bacterial communities in two different water masses in the Irish sea

Diel changes in the specific growth rates of natural bacterial communities as a whole and of different groups within the communities were followed over 2 days during July 1982, in stratified waters in the vicinity of a shallow sea tidal mixing front in the Irish Sea. Waters well above (4 m) and below (60 m) the thermocline were enclosed in dialysis bags and incubated in situ. The results show that there were periods of altered growth rates of the whole bacterial community and synchronous cell division of morphological groups. An increase in mean cell volume within both 4 and 60 m communities preceded an increase in specific growth rates, with a resultant decrease in the mean cell volume. Above the thermocline the whole bacterial community, as well as the rod and coccoid forms, doubled in number once a day. The doubling time of the whole bacterial community at 60 m was 2 days and slower than that at 4 m. This was due to a slower doubling time (3 days) for the coccoid forms. Rod forms at the two depths had a similar doubling time (1 day). The time of day when maximum division rate occurred was also different in the two water masses. At 4 m more coccoid forms divided during the night, whereas at 60 m more divided during the day. Conversely, at 4 m more rod forms divided during the day, whereas at 60 m more divided at night.These data indicate that the bacterial community and members of the community may be adapted to exploit the diurnal rhythms of dissolved organic carbon (DOC) release by other organisms and that portions of the bacterial community may therefore be more active at certain times of the day. The diurnal growth of the bacterial community may thus vary between different water masses and largely reflects the differences in the chemical and biological characteristics of the two water masses investigated.     

Ruminal degradability of 15N labelled ribonucleic acid in grass

The ruminal degradation of RNA in rye grass (Lolium perenne) was studied using the bag method. A non-lactating cow (BW 550 kg) fitted with a rumen cannula was used and fed twice daily at maintenance level with a chopped grass hay-based ration containing 30% ground barley. Rye grass, labelled during growth by fertilization with 15N2-urea (9.5 atom% 15N, 20 g N/m2), was cut at seven stages of growth and maturity and freeze-dried. RNA-N represented 6 to 17% of total N. Labelled grass samples (milled to 5.0 mm screen, 5.0+/-0.1 g DM) were incubated in polyester bags (100 x 200 mm, pore size 50 microm) in the rumen for periods of 1, 3, 6, 9, 12, 24, and 48 h. Data of N and RNA disappearances from the bags were fitted to an exponential equation to estimate parameters of degradation. The effective degradability of RNA in the rumen averaged 90+/-4%, for N it was 11% units lower (P < 0.001). Degradability of RNA was correlated to that of N (R2 = 0.92). Degradability of RNA (R2 = 0.96) and N (R2 = 0.93) decreased with increasing fibre content of grass. Increasing the fibre content by 1% diminished the degradability of RNA and N by 1.1% units and 2.4% units, respectively (P < 0.001). Assuming a microbial protein synthesis in the rumen of 150 g/kg DOM, a N: RNA ratio of 1:1.35 in rumen microbes and a rumen outflow rate of 0.06 h(-1), a model calculation indicates that about 9 to 19% of duodenal RNA are of dietary origin in animals fed grass. This should be taken into account for the calculation of microbial N on the basis of RNA as marker.     

Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity

In a mesotrophic reservoir, we examined the effects on the bacterioplankton of distinct consumers of bacteria, viruses and heterotrophic nanoflagellates, both alone and combined in an experiment using natural populations and in situ incubations in dialysis bags. Ribosomal RNA-targeted probes were employed as well as 16S RNA gene based PCR denaturing gradient gel electrophoresis (DGGE) to enumerate bacterial groups and assess bacterial community composition. We employed probes for Actinobacteria (HGC69a probe), Cytophaga-Flavobacterium-Bacteroidetes bacteria (CF319a probe), BET42a probe ( Betaproteobacteria ) and a subgroup- Betaproteobacteria (R-BT065 probe). We found consumer-specific effects on bacterial activity and diversity (against a background of CF and BET dominating all treatments) suggesting distinct vulnerabilities to the two sources of mortality. For example, growth rate of Actinobacteria was only positive in the presence of flagellates, while towards the end of the experiment ( T _72−96 h) growth rate of R-BT was only positive in the viruses only treatment. More specific data on how viruses and flagellates influenced Flectobacillus are shown in the companion paper. Highest richness (number of DGGE bands) was found in the virus only treatment and lowest when both consumers were present. In addition, we found suggestions of both antagonistic and synergistic interactions between the two sources of bacterial mortality. Notably, bactivory by flagellates was associated with reductions in bacterial diversity and increases in viral production.     

Impacts of Labile Organic Carbon Concentration on Organic and Inorganic Nitrogen Utilization by a Stream Biofilm Bacterial Community

In aquatic ecosystems, carbon (C) availability strongly influences nitrogen (N) dynamics. One manifestation of this linkage is the importance in the dissolved organic matter (DOM) pool of dissolved organic nitrogen (DON), which can serve as both a C and an N source, yet our knowledge of how specific properties of DOM influence N dynamics are limited. To empirically examine the impact of labile DOM on the responses of bacteria to DON and dissolved inorganic nitrogen (DIN), bacterial abundance and community composition were examined in controlled laboratory microcosms subjected to various combinations of dissolved organic carbon (DOC), DON, and DIN treatments. Bacterial communities that had colonized glass beads incubated in a stream were treated with various glucose concentrations and combinations of inorganic and organic N (derived from algal exudate, bacterial protein, and humic matter). The results revealed a strong influence of C availability on bacterial utilization of DON and DIN, with preferential uptake of DON under low C concentrations. Bacterial DON uptake was affected by the concentration and by its chemical nature (labile versus recalcitrant). Labile organic N sources (algal exudate and bacterial protein) were utilized equally well as DIN as an N source, but this was not the case for the recalcitrant humic matter DON treatment. Clear differences in bacterial community composition among treatments were observed based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes. C, DIN, and DON treatments likely drove changes in bacterial community composition that in turn affected the rates of DON and DIN utilization under various C concentrations.