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The nitrogen (N) cycle is highly dependent on microbial processes. Distribution of these communities is one of the most important factors in the variation of the N cycling in warm‐monomictic lakes. However, the effects of the alternation of water stratification and mixing periods on the ecology of microbial communities involved in these processes are rarely studied in this type of aquatic ecosystem. We explored vertical and seasonal patterns of picoplankton and the genetic potential for ammonium oxidation (amoA gene for bacteria and archaea), denitrification (nirS and nirK), anammox (hzsA), and DNRA (nrfA) and their relationships with the main limnological variables in Lake Alchichica (Central Mexican Plateau) to provide insight into the distribution and importance of these planktonic communities in warm‐monomictic tropical lakes. Ten depths were sampled during late stratification (November 2015) and mixing (February 2016) periods, covering the epilimnion, metalimnion (oxycline), and hypolimnion layers in the first case. We showed that temperature and oxygen stratification shaped the distribution of picoplankton and functional N genes in this lake. These communities also varied in relation to nutrient availability and underwent temporal changes throughout the water column. The amoA genes, along with autotrophic picoplankton, were more abundant during the stratification, indicating that nitrification could be potentially more important during this period, mainly at the oxycline layer. Denitrifying genes showed strong variations during the stratification period, with highest gene copy numbers at the oxycline and hypolimnion layers. Anoxic conditions were characterised by a relative increase in the abundance of the nrfA gene with depth, which was positively correlated with NH₄ ⁺ concentration. On the other hand, the hzsA gene was not detected in any sample. Our findings highlight the importance of thermal stratification as one of the main factors influencing the genetic potential for N transformations within the water column in warm‐monomictic tropical lakes.

The response of planktonic (phytoplankton, ciliates, rotifers and crustaceans) and littoral (Ephemeroptera, Plecoptera, Trichoptera and Heteroptera: Nepomorpha) assemblages to chemical recovery was studied over a twelve-year period (1999–2011) in eight glacial lakes in the Bohemian Forest (central Europe). The region suffered from high atmospheric pollution from the 1950s to the late 1980s, but has since been recovering from acidification due to 86% and 44% decrease in sulphur and nitrogen deposition, respectively, during the 1990s–2000s. Despite the rapid improvement in water chemistry of all the eight studied lakes, only four have partly recovered so far (low-aluminium lakes), while the other four lakes still remain strongly acidic (high-aluminium lakes). Although biotic responses (especially in the low-Al lakes) showed important signs of recovery, such as reappearance of some indigenous or acid-sensitive species, decline in eurytopic acid-tolerant species and colonisation by vagile species, the assemblages of all the lakes still suffer from acid stress. Our results also indicate an increasing role of biotic interactions between colonisers and residents leading to the reconstruction of aquatic food webs in the low-Al lakes.

Summary 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 imov 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 m g 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 S ˇ n ˇ r s ˇ C ˇ e ˇ C ˇ e ˇ R ˇ 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.

Elimination of inoculated Vibrio cholerae (≥10 7 cells ml -1 ) within a brackish water bacteria assemblage (Mecoacan Lagoon, State of Tabasco, Mexico) was studied in laboratory microcosms with filtration-fractionated water. Feeding of a ciliate, Cyclidium glaucoma was evaluated using fluorescently labelled V. cholerae O1. Even though V. cholerae was not exploited as the major food source, ciliates were able to eliminate it efficiently. An addition of chitin directly supported the growth of bacteria, although not so much of V. cholerae, and indirectly the growth of the protistan assemblage. Generally, the changes in a bacterial assemblage structure were the most important in V. cholerae elimination.

In aquatic microbial ecology, it has been considered that most extracellular enzymes except phosphatases are of bacterial origin. We tested this paradigm by evaluating the relationship between bacterial cell number and the activity of three glycolytic enzymes from 17 fresh waters and also from a laboratory experiment. Our large sets of pooled data do not seem to support such a simple explanation, because we found only a weak correlation of bacterial number with activity of α-glucosidase (rs = 0.63), β-glucosidase (rs = 0.45), and β-N-acetylhexosaminidase (rs = 0.44). We also tested relations of the enzymatic activities to potential sources of natural substrates: dissolved organic carbon (DOC) and phytoplankton (as chlorophyll a). Their correlations with the enzymatic activities tested were very weak or insignificant. On the other hand, we found evidence for distinct producers of extracellular enzymes by analysing enzyme kinetics. The kinetics usually did not follow the simple Michaelis-Menten model but a more complex one, indicating a mixture of two enzymes with distinct affinity to a substrate. In combination with size fractionation, we could sometimes even distinguish three or more different enzymes. During diatom blooms, the diatom biomass tightly correlated with β-N-acetylhexosaminidase activity (>4 μm fraction). We also documented very tight relationships between activity of both glucosidases and dry weight of Daphnia longispina (rs = 1.0 and 0.60 for α- and β-glucosidases, respectively) in an alpine clear-water lake. Our data and evidence from other studies indicate that extracellular glycosidic activities in aquatic ecosystems cannot generally be assigned only to bacteria. Also invertebrate animals and other eukaryotes (fungi, diatoms, protozoa etc.) should be considered as potentially very important enzyme producers. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

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.

Extracellular hydrolysis of 4-methylumbelliferyl β-N-acetylglucosaminide was measured in the oligomesotrophic Piburger See and the eutrophic Rimov reservoir during spring and summer phytoplankton blooms, respectively. Total enzymatic activity (TEA) ranged between 0.2 and 19.1 nmol 1 -1 h -1 in the reservoir and between 0.8 and 12.4 nmol 1 -1 h -1 in the lake. High-affinity (K m 100 μmol 1 -1 ) enzymes were kinetically identifiable in most samples from both localities. The low-affinity enzyme activity (LEA) usually accounted for >60% (mean: 80%) of TEA. LEA and diatom biomass significantly correlated over time in the reservoir epilimnion (r s = 0.578) and in the lake metalimnion (r s = 0.862). As diatoms possess chitin and take up its monomer, N-acetylglucosamine, two explanations of the observed relationships are suggested: extracellular β-N-acetylglucosaminidase activity partly originates either from ectoenzymes of chitinolytic bacteria attached to diatom cells or from ectoenzymes of diatoms, enabling them to take up N-acetylglucosamine from ambient amino sugars instead of synthesizing it de novo. A significant positive correlation of LEA with crustacean abundance was found in the lake epilimnion (r s = 0.850), apparently reflecting the growing spring populations of frequently moulting juvenile crustaceans. A possible contribution of chitinolytic bacteria, accompanying the crustacean populations, to LEA is discussed.

In late summer 1993 an intensive study was carried out on protozoan grazing in the epilimnion and metalimnion of the eutrophic Rimov Reservoir in south Bohemia. On average, - 70% of bacterial production was consumed by heterotrophic flagellates and -20% by ciliates. Ciliate numbers increased from 5 to 70 cells ml l over the 5-week study period. Ciliates ~30 pm in size were numerically dominant in both layers and included Halteria grandinella and Strobilidium hexakinetum (Oligotrichida), Cyrtolophosis mucicola (Cyrtolophosida), Cinetochilum margaritaceum (Scuticociliatida), Urotricha spp., and Coleps sp. (Prostomatida). Ciliate species-specific grazing rates on bacteria and picocyanobacteria were determined. The highest individual cell grazing rates, 4,200 bacteria and 560 picocyanobacteria cell-’ h-l, were observed in Vorticella aquadulcis-complex. Oligotrichs ingested on average 360-2,130 bacteria and 76-2 10 picocyanobacteria cell ’ h - I, with H. grandinella (1,560 bacteria cell I h-l), due to its high abundance, as the most important ciliate bacterivore within the system. C. mucicola ingested on average 173 bacteria and 27 cyanobacteria cell- ’ h- l; C. margaritaceum, 57 bacteria and 7 picocyanobacteria cell-’ h--l; and prostomatids, 23-100 bacteria and 2-14 picocyanobacteria cell-’ h- I. Although there was a tight relationship between grazing rates on bacteria and picocyanobacteria (rs = 0.89, n = 12, P < 0.00 I), most of the ciliate species preferred larger picoplankton (i.e. picocyanobacteria), as indicated by their clearance rates. According to our data, several oligotrichous ciliate species and Cyclidium sp. can grow in pelagic conditions and exclusively on picoplankton food at rates of one doubling every 24-75 h.

Participation of nitrilotriacetic acid degrading bacterial strain NTA-1 in the continuous-cultivated mixed culture was studied under different conditions including predation pressure of the ciliate Dexiostoma campyla (STOKES, 1886). From the viewpoint of dispersed/flocculated biomass distribution, significant relationships between NTA-1 and total bacteria ratio, and dispersed and total biomass ratio were proved in the systems without high concentrations of ciliates. The ciliate concentrations reaching 104 ml−1 stabilized flocculated biomass growth without directly affecting NTA-1 portion. Using fluorescently labelled NTA-1 bacteria, filter feeding rates of ciliates were evaluated (maximum individual uptake rate upon NTA-1 bacteria as a number of bacteria per ciliate per hour being 120 h−1 and 260 h−1 under ciliate division rate of 0.3 day−1 and 1 day−1, respectively). Biomass balance showed that dispersed NTA-1 bacteria should not serve as the sole feeding source for these free-swimming ciliates. The role of diversity of mixed bacterial diet in ciliate growth and the role of ciliate predation in stabilizing bacterial assemblage structure was proved.

Ingestion of fluorescent particles by natural protozoan assemblage was studied in the Řimov Reservoir (Southern Bohemia) from April to October, 1987. Attached and free-living bacterial abundance, proportion of active bacteria, density of suspended particles and biomass of cladocerans were also monitored. Heterotrophic nanoflagellates (HNF; 5–12.8 102ml−1) were the dominant bacterial micrograzers during the spring period and consumed 3 to 9% of the total bacteria per day. After the spring phytoplankton bloom maximum densities of suspended particles and attached bacteria (up to 28% of the total counts) were found. Development of cladocerans in May sharply decreased the proportion of attached bacteria and kept them below 5% of the total counts. All the studied components of plankton except Cladocera decreased during the clearwater phase. The most significant drop was observed in the numbers of protozoans, and they were negligible for bacterial elimination. Bacterial losses during that time apparently were due to cladoceran grazing. During the summer period, ciliates (15–142 ml−1) were mostly dominant micrograzers, and protozoan community grazing increased up to 21% of bacterial standing stock per day. The proportion of active bacteria was strongly correlated with protozoan grazing (r=0.83).

Relationship between bacteria and ciliates was investigated in continuous cultures with and without the recycling of flocculated biomass. Monocultures of ciliates of various ecological types were used together with mixed cultures of bacteria or bacteria and flagellates. The effect of ciliates on the distribution of flocculated and dispersed, biomass was tested with respect to characterizing an optimum mixed culture for activated-sludge treatment. Monoprotozoal populations were not successful in stabilizing the morphology of a bacterial community in a system with recycling of flocculated biomass. Stabilization was observed (with particular ecological types of ciliates) in the system with a high residence time without recycling and/or in the system with the recycling inoculated by both flagellates and ciliates.