Seasonal Depth-Related Gradients in Virioplankton: Standing Stock and Relationships with Microbial Communities in Lake Pavin (France)

This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative of the physico-chemical gradients of the whole water column of the lake, and the seasonal variability as well. In mixolimnic surface waters, all communities were present and viral abundance peaked in summer and autumn. Viral abundance was significantly correlated (p < 0.001) with Pcy, Peu, and ANF, indicating that cyanophages and perhaps other phytoplankton viruses represent a significant pool of viral standing stocks in the mixolimnion of Lake Pavin. Microautotrophs were absent in the deep monimolimnic water masses, where viruses and heterotrophic prokaryotes exhibited highest seasonal abundances in summer and/or autumn and were significantly correlated (p < 0.001) to each other. This indicates that the anoxic monimolimnion of Lake Pavin is an exclusive habitat for viruses and heterotrophic prokaryotes. We conclude that in this habitat, host availability is prevalent over other factors (temperature, oxygen, nutrients, grazers) in favoring viral proliferation.     

Seasonal Depth-Related Gradients in Virioplankton: Lytic Activity and Comparison with Protistan Grazing Potential in Lake Pavin (France)

This study presents an original depth-related survey of virioplankton lytic activity in relation to prokaryotic production and potential protistan bacterivory in the deep (Z(max) = 92 m) meromictic volcanic Lake Pavin (Massif Central, France). The sampling strategy was designed to be representative of the physico-chemical gradients of the water column of the lake, and of the seasonal variability as well, i.e. 12 different depths sampled in triplicates from April to December 2005. In the space, viral lytic activity estimated from the frequency of visibly infected prokaryotic cells and from burst size over the study period generally decreased with depth. This was viewed as a paradox compared to the abundances of viruses and prokaryotes and to the prokaryotic production which increased with depth. The seasonal variability in viral lytic activity was correlated with prokaryotic variables (abundance and production) in the deepest waters, i.e. from the hypolimnion downwards. Compared to previous studies known from the mixolimnion, we conclude that the deep waters in Lake Pavin represent an exclusive environment for heterotrophic prokaryotes whose seasonal activity offers an optimal and unique resource for thriving viral communities, some of which may be typical, endemic to the ambient dark, cold and stable deep water masses. Overall, the main findings in the present study get well around a previous statement that the ecology of the deepest waters of Lake Pavin is essentially driven by the dark viral loop (dissolved organic matter-prokaryotes-viruses) processes, which can sequester organic matters and nutrients for a long-lived turnover time. This is in agreement with recent demonstrations from marine systems that meso- and bathypelagic waters are optimal environments for viral survival and proliferation.     

Virioplankton and microbial communities in aquatic systems: a seasonal study in two lakes of differing trophy

1. The seasonal and vertical distribution of the abundance of virus‐like particles (VLPs), together with the abundances of other microbial organisms (bacteria, unpigmented and pigmented nanoflagellates and ciliates), were determined in an oligomesotrophic lake (Pavin, France) and in a eutrophic lake (Aydat, France) between March and December 2000. 2. The abundance of the viral plankton and those of other microbial taxa were significantly higher in the more productive system. The same was for the virus‐to‐bacteria quotient (VBQ), which averaged seven in Lake Pavin and nine in Lake Aydat. 3. The abundance of viruses increased during the period of thermal stratification in both lakes, with the highest values being recorded at the end of summer/early autumn in the epi‐ and the metalimnion. The seasonal pattern of abundance of viruses in both lakes in the surface layer was similar, indicating that the dynamics of viruses may be controlled by environmental factors such as light conditions. 4. There was no correlation between the abundance of viruses and protists. We found correlations between viruses and heterotrophic bacteria in the whole water column in Lake Pavin, but only in the dark bottom waters in Lake Aydat. 5. Overall, the empirical findings in this study lead us to speculate that the weaker correlation between bacteria and viruses in Lake Aydat than in Lake Pavin, as well as the higher VBQ in the former, is a consequence of the increasing relative abundance of non‐bacteriophage VLPs along the trophic gradient of aquatic systems.     

Phylogenetic diversity of archaea and bacteria in the anoxic zone of a meromictic lake (Lake Pavin, France)

The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.     

Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)

The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.     

Inexpensive Device for the Aerobic and Anaerobic Sampling of Microorganisms in Lake and Shallow Ocean Waters

An inexpensive device suitable for sampling microorganisms in water and easily constructed from readily available laboratory equipment is described. The need to transfer subsamples to culturing flasks after collection is eliminated by partly filling the sampling vessels with growth medium prior to sampling. The device is readily adapted for sampling different volumes, is simple and quick to operate, and is suitable for use with prereduced media. Contamination from layers other than that being sampled is insignificant.     

Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France)

The vertical distribution of OP11, OD1 and SR1 divisions in the oxycline and in the anoxic water column of Lake Pavin, a freshwater permanently stratified mountain lake in France, was determined by temporal temperature gel gradient electrophoresis and 16S rRNA clone libraries. Gradual changes in the community structure were noted in relation to environmental variables along the oxidized/reduced environment. In addition, a separate effort to identify members of these lineages in the oxic mixolimnion identified sequences affiliated to SR1 and OP11 divisions, indicating that they are more widespread than previously expected.     

Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir

The succession in bacterial community composition was studied over two years in the epilimnion and hypolimnion of two freshwater systems: a natural lake (Pavin Lake) and a lake-reservoir (Sep Reservoir). The bacterial community composition was determined by cloning-sequencing of 16S rRNA and by terminal restriction fragment length polymorphism. Despite large hydrogeological differences, in the Sep Reservoir and Pavin Lake the dominant bacteria were from the same taxonomic divisions, particularly Actinobacteria and Betaproteobacteria. In both ecosystems, these major bacterial divisions showed temporal fluctuations that were much less marked than those occurring at a finer phylogenetic scale. Nutrient availability and mortality factors, the nature of which differed from one lake to another, covaried with the temporal variations in the bacterial community composition at all sampling depths, whereas factors related to seasonal forces (temperature and outflow for Sep Reservoir) seemed to account only for the variation of the hypolimnion bacterial community composition. No seasonal reproducibility in temporal evolution of bacterial community from one year to the next was observed.     

大型浅水湖泊鄱阳湖湿地微生物的研究现状

鄱阳湖是我国第一大淡水湖泊,同时也是一个典型的季节性通江浅水湖泊,独特的水文特征和多样的湿地景观类型形成了复杂多样的微生物群落。本文综述了鄱阳湖水文节律、营养盐及重金属含量对湖泊微生物群落组成的影响,以及水位高程和湿地围垦对鄱阳湖湿地土壤微生物分布特征的影响,同时还探讨了未来湖泊湿地微生物的研究方向和鄱阳湖所拥有的独特研究条件,以期为未来湖泊微生物研究提供重要参考。     

Caractéristiques du microphytobenthos d'un lac volcanique. Characterization of the Microphytobenthos in a Volcanic Meromictic Lake (Lake Pavin,France). II. Productivity and Relationships

The collection of microphytobenthos for primary production studies in Lake Pavin was performed with a Jenkin sampler. This corer permits sampling at different levels below the surface of the lake. Five levels (10, 20, 30, 40, and 60 m below the surface) were regularly investigated for more than one year. Each was inhabited by a characteristic population of dominant diatoms. The primary production, which was very large during the summer, decreases with depth. During the winter, the ¹⁴C assimilation occurs at a very low rate in clear incubators, but in dark incubators, the rate is high. Therefore, the ¹⁴C fixation in darkness is greater than the photosynthetic assimilation. This phenomenon together with the very important data recorded for photosynthetic efficiency (especially at the lowest levels, 40 and 60 m deep) suggest that microphytes on the bottom of the lake assimilate organic compounds during much of the year.     

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

Water samples were collected along transects from the shore to the centre of two French lakes: the deep, volcanic, oligomesotrophic and low allochthonic-impacted Lake Pavin, and the productive and higher allochthonic-impacted Lake Aydat. The biodiversity was analysed using two approaches: the classical approach consisting of cloning/sequencing of the 18S, ITS1, 5.8S, ITS2 and partial 28S region using primers designed for fungus sequences, and the pyrosequencing of 18S rRNA hypervariable V2, V3 and V5 regions using two primer sets (one universal for eukaryotes and one for fungi). The classical approach yielded 146 (Lake Pavin) and 143 (Lake Aydat) sequences, corresponding to 46 and 63 operational taxonomic units (OTUs) respectively. Fungi represented half of the OTUs identified in Lake Pavin and 30% in Lake Aydat, and were dominated by sequences from Chytridiomycota found throughout Lake Pavin but mostly in the central pelagic zone of Lake Aydat. The pyrosequencing approach yielded 42,064 (Pavin) and 61,371 (Aydat) reads, of which 12-15% and 9-19% reads were assigned to fungi in Lakes Pavin and Aydat respectively. Chytridiomycota members were also dominant among these reads, with OTUs displaying up to > 33-fold overrepresentation in the centre compared with the riparian areas of Lake Aydat. Besides fungi, both approaches revealed other major eukaryote groups, with the highest diversity in the central areas of lakes. One of the major findings of our study was that the two lakes displayed contrasting spatial distributions, homogenous for Lake Pavin and heterogeneous for Lake Aydat, which may be related to their peculiarities. This study represents the first unveiling of microbial eukaryote and fungus diversity assessed with two complementary molecular methods, and is considered a major milestone towards understanding the dynamics and ecology of fungi in freshwater lake ecosystems, which are directly link to the abundance and distribution of taxa.     

Viral activity in two contrasting lake ecosystems

For aquatic systems, especially freshwaters, there is little data on the long-term (i.e., >6-month period) and depth-related variability of viruses. In this study, we examined virus-induced mortality of heterotrophic bacteria over a 10-month period and throughout the water column in two lakes of the French Massif Central, the oligomesotrophic Lake Pavin and the eutrophic Lake Aydat. Concurrently, we estimated nonviral mortality through heterotrophic nanoflagellate and ciliate bacterivory. Overall, viral infection parameters were much less variable than bacterial production. We found that the frequency of visibly infected cells (FVIC), estimated using transmission electron microscopy, peaked in both lakes at the end of spring (May to June) and in early autumn (September to October). FVIC values were significantly higher in Lake Pavin (mean [M] = 1.6%) than in Lake Aydat (M = 1.1%), whereas the opposite trend was observed for burst sizes, which averaged 25.7 and 30.2 virus particles bacterium(-1), respectively. We detected no significant depth-related differences in FVIC or burst size. We found that in both lakes the removal of bacterial production by flagellate grazing (M(Pavin) = 37.7%, M(Aydat) = 18.5%) was nearly always more than the production removed by viral lysis (M(Pavin) = 16.2%, M(Aydat) = 19%) or ciliate grazing (M(Pavin) = 2.7%, M(Aydat) = 8.8%). However, at specific times and locations, viral lysis prevailed over protistan grazing, for example, in the anoxic hypolimnion of Lake Aydat. In addition, viral mortality represented a relatively constant mortality source in a bacterial community showing large variations in growth rate and subject to large variations in loss rates from grazers. Finally, although viruses did not represent the main agent of bacterial mortality, our data seem to show that their relative importance was higher in the less productive system.     

Genetic diversity of small eukaryotes in lakes differing by their trophic status

Small eukaryotes, cells with a diameter of less than 5 mum, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.     

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.     

Ecology of purple sulfur bacteria in the highly stratified meromictic Lake Shunet (Siberia, Khakassia) in 2002–2009

Phototrophic sulfur bacteria form dense accumulations in the chemocline zones of stratified lakes where light reaches the sulfide-containing layers of water. Many works are dedicated to the ecophysiology of these microorganisms in meromictic lakes. However, the role of these microorganisms in the trophic network of these ecosystems, the ways of biomass utilization, and the contribution to the turnover of biogenic elements have so far been insufficiently understood. This work deals with the analysis of many years?? seasonal dynamics of the biomass of purple sulfur bacteria and the physicochemical conditions of their environment in Lake Shunet (Siberia, Khakassia, Russia), unraveling the causes of their anomalous development in the chemocline of this lake, as well as the comparative analysis of such type of ecosystems. Lake Shunet is characterized by markedly pronounced stratification and the high density of purple sulfur bacteria (PSB) in the chemocline, which is comparable to that of Lake Mahoney (Canada) where the number of PSB is the greatest among those known in the world. It was shown that, in the period 2002?C2009, the total amount of bacterio-chlorophyll a in the water column of Lake Shunet increased and did not correlate with the seasonal variations in temperature and illumination in the chemocline. It was established that PSB cells in the purple layer experienced the effect of self-shading. The sedimentation rate of purple sulfur bacteria in Lake Shunet was low due to the pronounced density gradient in the chemocline zone. Thus, the high number of PSB in the chemocline was due to the combination of strong illumination, a high sulfide concentration, and a high water density gradient, which was responsible for stable stratification and contributed to the accumulation of the cells in a narrow layer. The data obtained could be useful for the paleoreconstruction of climatically deter-mined changes in the level of the lake and its periods of meromixis by the presence of carotenoids and bacte-riochlorophylls in the bottom sediments.     

Caracteristiques du microphytobenthos d'un lac volcanique meromictique (Lac Pavin,France). I. Biomasse chlorophyllienne et déterminisme du cycle annuel

Characterization of the Microphytobenthos in a Volcanic Meromictic Lake (Lake Pavin, France). I. Chorophyll Biomass and Determination of the Annual Cycle The sediments in Lake Pavin are almost exclusively biogen. The fine fraction (≤ 40 μm). comprises 99% of these sediments, making them appear as very fine and fluid silt. Up to 85% of the microphytobenthos is composed of epipelic Bacillariophyceae. The benthos at the different depths studied (10 m, 20 m, 30 m, 40 m, 50 m, and 60 m). are colonized by characteristic populations of diatoms. Analyses of the sediments revealed high concentrations of pigments ( ≥ 1 mg/g dried sediment). Such high concentrations usually result from phytoplankton sedimentation. The deepest area of the lake, as expected, contains the highest concentation of accumulated pigment, while shallower locations are richer in active pigments.     

Yeasts from an oligotrophic lake in Patagonia (Argentina): diversity, distribution and synthesis of photoprotective compounds and extracellular enzymes

Nahuel Huapi (NH) Lake is an oligotrophic temperate lake of glacial origin with high transparency, surrounded by well-developed forests and located at San Carlos de Bariloche, Nahuel Huapi National Park, in Patagonia, Argentina. In this lake, we characterized yeast distribution and diversity along a south-to-north transect and established a relationship between the ability to produce photoprotective compounds (PPCs) (carotenoid pigments and mycosporines) and the occurrence of yeast at different collection points. Subsurface water samples were filtered for yeast isolation. Total yeast counts ranged between 22 and 141?CFU?L(-1) , and the highest values corresponded to the most impacted sites. Littoral sites had a low proportion of yeast-producing PPCs and this group prevailed in pelagic sites. This is probably a result of the high transparency of the water and the increased UV exposure. The yeast community from NH Lake showed a high species richness and a uniform distribution of taxa between pelagic and border collection points. Yeasts were identified as belonging to 14 genera and 34 species. Rhodotorula mucilaginosa and Cryptococcus victoriae were the most frequently found species, representing 14.4% and 13.6% of the total yeast isolates, respectively. Most of the yeast isolates demonstrated at least one extracellular enzymatic activity (mainly cellulase and lipase activities), which suggested that these microorganisms are metabolically active in the lake.     

The toxic effects of rubber contaminants on microbial food webs and zooplankton of two lakes of different trophic status

Rubber is commonly used in recreational equipment and devicesforsampling in lakes, but there have been few studies of theeffectsof rubber on planktonic organisms. We investigated the toxiceffects of rubber on the microbial food webs of a mesotrophiclakeand a eutrophic lake. Lake water was collected by pumping via,(i) a polyvinylchloride hose and, (ii) a rubber hose. Samplesoflake water collected by each method were incubated insitu in4.25 l enclosures for four days. The lake water was sampledbeforeand after incubation to determine the concentrations ofinorganicnutrients, chlorophyll a, microorganisms (bacteria,picophytoplankton, flagellates, ciliates) and zooplankton.In the mesotrophic lake, momentary exposure (ten seconds) oflakewater to the rubber hose significantly lowered theconcentrationsof chlorophyll a, bacteria, picophytoplankton and somespecies of zooplankton (Boeckella hamata, Bosmina,androtifers), relative to those in water exposed to the plastichose;flagellates, ciliates and Ceriodaphnia dubia were notsignificantly affected. In the eutrophic lake, the effects oftherubber hose on components of the microbial food web were muchlesssevere, and were consistent with the lake's high levels ofdissolved organic carbon (DOC), which is known to chelatetoxicmetals in water.     

Limnology of Botos Lake, a tropical crater lake in Costa Rica

Botos Lake, located at the Poas Volcano complex (Costa Rica) was sampled eight times from 1994 to 1996 for physicochemical conditions of the water column and phytoplanktonic community composition. Depth was measured at fixed intervals in several transects across the lake to determine its main morphometric characteristics. The lake has an outlet to the north. It is located 2580 m above sea level and is shallow, with a mean depth of 1.8 m and a relative depth of 2.42 (surface area 10.33 ha, estimated volume 47.3 hm3). The lake showed an isothermal water column in all occasions, but it heats and cools completely according to weather fluctuations. Water transparency reached the bottom on most occasions (> 9 m). The results support the idea that the lake is polymictic and oligotrophic. The lake has at least 23 species of planktonic algae, but it was always dominated by dinoflagellates, especially Peridinium inconspicuum. The shore line is populated by a sparse population of Isoetes sp. and Eleocharis sp. mainly in the northern shore where the bottom has a gentle slope and the forest does not reach the shore.