Occurrence and Seasonal Dynamics of ALNs in Freshwater Lakes Are Influenced by Their Biological Environment.

Aster-like nanoparticles (ALNs) are femtoentities, recently discovered in different aquatic environments, whose intrinsic nature and ecological features remain to be determined. In this study, we investigate the in situ temporal dynamics of ALNs during 1 year in 3 different lakes, in relation to the physico-chemical and biological environment. ALN abundances in investigated lakes showed a marked seasonal dynamic (from no detectable to 4.28 ± 0.75 × 106 ALNs mL-1), with characteristic peaks in spring. We recorded a correlation between ALNs and some prokaryotic phyla suggesting a broad and non-specific relationship. From their seasonal dynamics and potential link with prokaryotes, we conclude that ALNs represent an important ecological actor in the functioning of aquatic ecosystems.

Taxonomic and functional dynamics during chytrid epidemics in an aquatic ecosystem.

Fungal parasitism is common in plankton communities and plays a crucial role in the ecosystem by balancing nutrient cycling in the food web. Previous studies of aquatic ecosystems revealed that zoosporic chytrid epidemics represent an important driving factor in phytoplankton seasonal successions. In this study, host-parasite dynamics in Lake Pavin (France) were investigated during the spring diatom bloom while following chytrid epidemics using next generation sequencing (NGS). Metabarcoding analyses were applied to study changes in the eukaryotic microbial community throughout diatom bloom-chytrid epidemics. Relative read abundances of metabarcoding data revealed potential "beneficiaries" and "victims" during the studied period. Subsequently, metatranscriptomic analyses on samples before and during the chytrid epidemic unveiled the active part of the community and functional/metabolic dynamics in association with the progress of chytrid infection. Diatom functions involving lipases, transporters, histones, vacuolar systems, the proteasome, proteases and DNA/RNA polymerases were more abundant during the diatom bloom. Chytrid functions related to a parasitic lifestyle including invasion, colonization and stress tolerance were up-regulated during the chytrid epidemic. In addition, functions related to the degradation/metabolism of proteins, lipids and chitin were in higher proportion in the community during the epidemic event. Results of NGS and bioinformatics analyses offered a panorama of dynamic biodiversity and biological functioning of the community.

Evaluation of the health risks linked to two swimming pools regularly frequented from the city of Yaounde in Cameroon (Central Africa).

The study highlights the presence of pathogenic strains of microorganisms in two swimming pools, highly frequented in the city of Yaounde. Thus, the water samples from these swimming pools have undergone physicochemical and biological treatments using conventional techniques. Three groups of microorganisms (Bacteria, Protozoa, and Helminths) were identified and quantified in these swimming pools with weakly acidic waters (6.79 ± 0.35) with an average temperature of 26.63 ± 0.53 °C and suspended matter ranging from 2 to 150 mg.l-1. The total bacterial load varies between 8 × 103 and 6000 × 103 CFU/100 ml. It consists of mesophilic aerobic heterotrophic bacteria, fecal coliforms, total coliforms, fecal streptococci, Staphylococcus aureus, and Pseudomonas aeruginosa. Protozoan cysts and oocysts range from 122 to 505 per liter of water. These values are slightly lower for helminth eggs and larvae (0 to 108 eggs and larvae/l). In both swimming pools, significant correlations were observed between some abiotic and biotic parameters. The waters of the studied swimming pools are subject to fecal pollution. Swimmers would therefore be exposed to biological contaminations, responsible for pathologies. The most common diseases are linked to gastroenteritis (diarrhea), but infections of all kinds may be overgrown (conjunctivitis, ear infections, dermatitis, respiratory infections).

Trophic Conditions Influence Widespread Distribution of Aster-Like Nanoparticles Within Aquatic Environments.

Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r2 = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 106 ALNs mL-1) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.

Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species.

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.

Rediscovering Zygorhizidium affluens Canter: Molecular Taxonomy, Infectious Cycle, and Cryopreservation of a Chytrid Infecting the Bloom-Forming Diatom Asterionella formosa.

Parasitic Chytridiomycota (chytrids) are ecologically significant in various aquatic ecosystems, notably through their roles in controlling bloom-forming phytoplankton populations and in facilitating the transfer of nutrients from inedible algae to higher trophic levels. The diversity and study of these obligate parasites, while critical to understand the interactions between pathogens and their hosts in the environment, have been hindered by challenges inherent to their isolation and stable long-term maintenance under laboratory conditions. Here, we isolated an obligate chytrid parasite (CCAP 4086/1) on the freshwater bloom-forming diatom Asterionella formosa and characterized its infectious cycle under controlled conditions. Phylogenetic analyses based on 18S, 5.8S, and 28S ribosomal DNAs (rDNAs) revealed that this strain belongs to the recently described clade SW-I within the Lobulomycetales. All morphological features observed agree with the description of the known Asterionella parasite Zygorhizidium affluens Canter. We thus provide a phylogenetic placement for this chytrid and present a robust and simple assay that assesses both the infection success and the viability of the host. We also validate a cryopreservation method for stable and cost-effective long-term storage and demonstrate its recovery after thawing. All the above-mentioned tools establish a new gold standard for the isolation and long-term preservation of parasitic aquatic chytrids, thus opening new perspectives to investigate the diversity of these organisms and their physiology in a controlled laboratory environment.IMPORTANCE Despite their ecological relevance, parasitic aquatic chytrids are understudied, especially due to the challenges associated with their isolation and maintenance in culture. Here we isolated and established a culture of a chytrid parasite infecting the bloom-forming freshwater diatom Asterionella formosa The chytrid morphology suggests that it corresponds to the Asterionella parasite known as Zygorhizidium affluens The phylogenetic reconstruction in the present study supports the hypothesis that our Z. affluens isolate belongs to the order Lobulomycetales and clusters within the novel clade SW-I. We also validate a cryopreservation method for stable and cost-effective long-term storage of parasitic chytrids of phytoplankton. The establishment of a monoclonal pathosystem in culture and its successful cryopreservation opens the way to further investigate this ecologically relevant parasitic interaction.

Integrating chytrid fungal parasites into plankton ecology: research gaps and needs.

Chytridiomycota, often referred to as chytrids, can be virulent parasites with the potential to inflict mass mortalities on hosts, causing e.g. changes in phytoplankton size distributions and succession, and the delay or suppression of bloom events. Molecular environmental surveys have revealed an unexpectedly large diversity of chytrids across a wide range of aquatic ecosystems worldwide. As a result, scientific interest towards fungal parasites of phytoplankton has been gaining momentum in the past few years. Yet, we still know little about the ecology of chytrids, their life cycles, phylogeny, host specificity and range. Information on the contribution of chytrids to trophic interactions, as well as co-evolutionary feedbacks of fungal parasitism on host populations is also limited. This paper synthesizes ideas stressing the multifaceted biological relevance of phytoplankton chytridiomycosis, resulting from discussions among an international team of chytrid researchers. It presents our view on the most pressing research needs for promoting the integration of chytrid fungi into aquatic ecology.

Genotypic, size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake (Lac Pavin, France).

We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April-December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphoviridae or were untailed, with capsid sizes ranging from 30 to 60nm, and exhibited genome sizes ranging from 15 to 45kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer (mean=14 bands per PFGE fingerprint) and in the epilimnion (mean=13 bands per PFGE fingerprint). Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.

Analysis of metagenomic data reveals common features of halophilic viral communities across continents.

Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.

Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism.

In the forthcoming decades, it is widely believed that the dominance of colonial and filamentous bloom-forming cyanobacteria (e.g. Microcystis, Planktothrix, Anabaena and Cylindrospermopsis) will increase in freshwater systems as a combined result of anthropogenic nutrient input into freshwater bodies and climate change. While the physicochemical parameters controlling bloom dynamics are well known, the role of biotic factors remains comparatively poorly studied. Morphology and toxicity often - but not always - limit the availability of cyanobacteria to filter feeding zooplankton (e.g. cladocerans). Filamentous and colonial cyanobacteria are widely regarded as trophic dead-ends mostly inedible for zooplankton, but substantial evidence shows that some grazers (e.g. copepods) can bypass this size constraint by breaking down filaments, making the bloom biomass available to other zooplankton species. A wide range of algicidal bacteria (mostly from the Alcaligenes, Flavobacterium/Cytophaga group and Pseudomonas) and viruses (Podoviridae, Siphoviridae and Myoviridae) may also contribute to bloom control, via their lytic activity underpinned by a diverse array of mechanisms. Fungal parasitism by the Chytridiomycota remains the least studied. While each of these biotic factors has traditionally been studied in isolation, emerging research consistently point to complex interwoven interactions between biotic and environmental factors.

Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system.

The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.

A double staining method using SYTOX green and calcofluor white for studying fungal parasites of phytoplankton.

We propose a double staining method based on the combination of two fluorochromes, calcofluor white (CFW; specific chitinous fluorochrome) and SYTOX green (nucleic acid stain), coupled to epifluorescence microscopy for counting, identifying, and investigating the fecundity of parasitic fungi of phytoplankton and the putative relationships established between hosts and their chytrid parasites. The method was applied to freshwater samples collected over two successive years during the terminal period of autumnal cyanobacterial blooms in a eutrophic lake. The study focused on the uncultured host-parasite couple Anabaena macrospora (cyanobacterium) and Rhizosiphon akinetum (Chytridiomycota). Our results showed that up to 36.6% of cyanobacterial akinetes could be parasitized by fungi. Simultaneously, we directly investigated the zoosporic content inside the sporangia and found that both the host size and intensity of infection conditioned the final size and hence fecundity of the chytrids. We found that relationships linking host size, final parasite size, and chytrid fecundity were conserved from year to year and seemed to be host-chytrid couple specific. We concluded that our double staining method was a valid procedure for improving our knowledge of uncultured freshwater phytoplankton-chytrid couples and so of the quantitative ecology of chytrids in freshwater ecosystems.

Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes.

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.

A practical guide to separate and concentrate ALNs and femtoplankton entities.

The development of new technologies of microscopy, flow cytometry and genomics has allowed a profound reconsideration of the diversity and ecological role of femtoplankton entities (i.e., viruses, vesicles, aster like nanoparticles -ALNs-). Among these, the discovery of ALNs, raise serious questions about their exact nature and their biological and environmental roles. The elaboration of a practical guide for the concentration and separation of femtoplankton entities, including ALNs, is necessary for a better understanding of their diversity, ontogeny, and ecology. Here, we propose a step-by-step procedure for the enrichment and isolation of femtoplankton entities and prokaryotes. The established protocol couples tangential flow filtration to differential centrifugation, leading to differentiate enriched samples (with different target entity contents), usable as a matrix for sorting by flow cytometry. All entities were identified, characterized and counted by transmission electron microscopy and flow cytometry. The procedure allows an efficient detection, concentration and separation of femtoplankton entities (up to purity rate of 92, 67, 81 and 85% for virus like particles, vesicles, prokaryotes and ALNs, respectively), and different morphotypes of ALNs into different fractions (up to 51, 72, 52, 40 and 79% of total ALNs for 20-, 11-, budding 11-, 5-10- and 4-armed ALNs, respectively).

Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages.

Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses-amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.

Phytoplankton chytridiomycosis: community structure and infectivity of fungal parasites in aquatic ecosystems.

Fungal parasitism is recurrent in plankton communities, especially in the form of parasitic chytrids. However, few attempts have been made to study the community structure and activity of parasites at the natural community level. To analyse the dynamics of zoosporic fungal parasites (i.e. chytrids) of phytoplankton, samples were collected from February to December 2007 in two freshwater lakes. Infective chytrids were omnipresent in lakes, with higher diversity of parasites and infected phytoplankton than in previous studies. The abundance and biomass of parasites were significantly higher in the productive Lake Aydat than in the oligomesotrophic Lake Pavin, while the infection prevalence in both lakes were similar and averaged about 20%. The host species composition and their size appeared as critical for chytrid infectivity, the larger hosts being more vulnerable, including pennate diatoms and desmids in both lakes. The highest prevalence (98%) was noted for the autumn bloom of the cyanobacterium Anabaena flosaquae facing the parasite Rhizosiphon crassum in Lake Aydat. Because parasites killed their hosts, this implies that cyanobacterial blooms, and other large size inedible phytoplankton blooms as well, may not totally represent trophic bottlenecks because their zoosporic parasites can release dissolved substrates for microbial processes through host destruction, and provide energetic particles as zoospores for grazers. Overall, we conclude that the parasitism by zoosporic fungi represents an important ecological driving force in the food web dynamics of aquatic ecosystems, and infer general empirical models on chytrid seasonality and trophodynamics in lakes.

Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes.

This study presents an original rDNA PCR and microscopic survey of pelagic freshwater fungal communities, and was designed to unveil the diversity of true Fungi (i.e. the kingdom Eumycota) in three contrasting lake ecosystems (Lakes Pavin, Aydat and Vassivière) located in the French Massif Central. Three clone libraries were constructed from samples collected in the euphotic layers of the lakes during spring 2007. Phylogenetic analysis of the combined data from the three lakes clustered our sequences into thee divisions: Chytridiomycota (50% of total sequences), Ascomycota (40%) and Basidiomycota (10% in Pavin and Aydat only). Several sequences were assigned to a novel Chytridiomycota clade first recovered in Lake Pavin in 2005. Most of the sequences retrieved in the investigated lakes were affiliated with known fungal species, most of which were apparently well adapted to thrive in the pelagic realm. Their main functions (i.e. parasitism and saprophytism), putatively inferred from the closest relatives of the retrieved molecular sequences, were confirmed by microscopic approaches and by enrichment experiments with pollen grains. The occurrence of three fungal forms (zoosporic, yeast and mycelial) was associated with different trophic modes, establishing fungi as strong potential competitors for various niches in pelagic ecosystems, primarily in relation to the processing of particulate organic matter and the production of propagule food sources for grazers. For the first time, this study provides insight into the diversity and the associated functions of all members of the Kingdom Eumycota investigated in the whole plankton fraction of aquatic ecosystems.

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.

Top-Down Controls of Bacterial Metabolism: A Case Study from a Temperate Freshwater Lake Ecosystem.

In freshwater environments, limited data exist on the impact of mortality forces (viruses and heterotrophic nanoflagellates) on bacterial growth efficiency (BGE, index of bacterial carbon metabolism) compared to resource availability. An investigation to determine the relative influence of viral lysis and flagellate predation (top-down forces) on BGE was conducted in a mesotrophic freshwater system (Lake Goule, France) with time and space. Viral abundance was significantly (p < 0.001) related to bacterial abundance by a power law function with an exponent less than 1, emphasizing that the increases in host population (bacteria) together with viruses were not proportionate. A lytic viral strategy was evident throughout the study period, with high lysis of the bacterial population (up to 60%) supported by viral production rates. Viral processes (lysis and production) that were influenced by bacterial production and heterotrophic nanoflagellate abundance had a positive impact on BGE. Estimates of BGE were variable (9.9−45.5%) due to uncoupling between two metabolic parameters­namely bacterial production and respiration. The existence of a synergistic relationship between viruses and flagellates with bacteria in Lake Goule highlighted the decisive impact of top-down agents in sustaining the bacterial carbon metabolism of non-infected population through the nature of vital resources released via mortality processes.

Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria.

Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes, and CPR bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage "Candidatus Peribacter" was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ∼30% and ∼1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a >300-kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem.