Adaptation of a Chytrid Parasite to Its Cyanobacterial Host Is Hampered by Host Intraspecific Diversity

Cigarette butts enable toxigenic cyanobacteria growth by inhibiting their lethal fungal infections

Cigarette butts (CBs), of which around 4.5 trillion are discarded annually, are one of the most common types of litter worldwide. CBs contain various chemicals, including metals, nicotine, and polycyclic aromatic hydrocarbons, which can leach into water and pose a threat to aquatic organisms such as cyanobacteria and chytrid fungi. Chytrids, zoosporic fungi that parasitize cyanobacteria lethally, play a crucial role in regulating cyanobacteria blooms by delaying or suppressing bloom formation. Despite the prevalence of CBs in the environment, the impact of their leachates on cyanobacteria-chytrid interactions is not well understood. We assessed the effects of CB leachate on the interaction between the toxigenic cyanobacterium Planktothrix agardhii and its chytrid parasite Rhizophydium megarrhizum. CB leachate inhibited cyanobacterial growth in uninfected cultures. Infection prevalence decreased at 0.2, 2, and 10 CB L-1, with the two highest concentrations completely suppressing infection. Interestingly, at the highest CB concentration, cyanobacterial biomass in infected cultures was comparable to that of uninfected cultures not exposed to CB leachate, suggesting that the presence of chytrids mitigates the impact of the leachate. This study demonstrates that CB leachates are a potential environmental hazard that can enable cyanobacterial growth by inhibiting chytrid infections during epidemics. In addition, our research highlights the importance of assessing the effects of chemical mixtures, such as those leached from CBs, on multi-species interactions, such as host-parasite dynamics. These assessments are crucial to better understand the impact of pollutants on aquatic ecosystems.

Widely used herbicide metolachlor can promote harmful bloom formation by stimulating cyanobacterial growth and driving detrimental effects on their chytrid parasites

Metolachlor (MET) is a widely used herbicide that can adversely affect phytoplanktonic non-target organisms, such as cyanobacteria. Chytrids are zoosporic fungi ubiquitous in aquatic environments that parasitize cyanobacteria and can keep their proliferation in check. However, the influence of organic pollutants on the interaction between species, including parasitism, and the associated ecological processes remain poorly understood. Using the host-parasite system consisting of the toxigenic cyanobacterium Planktothrix agardhii and its chytrid parasite Rhizophydium megarrhizum, we investigated the effects of environmentally relevant concentrations of MET on host-parasite interactions under i) continuous exposure of chytrids and cyanobacteria, and ii) pre-exposure of chytrids. During a continuous exposure, the infection prevalence and intensity were not affected, but chytrid reproductive structures were smaller at the highest tested MET concentration. In the parasite's absence, MET promoted cyanobacteria growth possibly due to a hormesis effect. In the pre-exposure assay, MET caused multi- and transgenerational detrimental effects on parasite fitness. Chytrids pre-exposed to MET showed reduced infectivity, intensity, and prevalence of the infection, and their sporangia size was reduced. Thus, pre-exposure of the parasite to MET resulted in a delayed decline of the cyanobacterial cultures upon infection. After several parasite generations without MET exposure, the parasite recovered its initial fitness, indicating that detrimental effects are transient. This study demonstrates that widely used herbicides, such as MET, could favor cyanobacterial bloom formation both directly, by promoting cyanobacteria growth, and indirectly, by inhibiting their chytrid parasites, which are known to play a key role as top-down regulators of cyanobacteria. In addition, we evidence the relevance of addressing multi-organism systems, such as host-parasite interactions, in toxicity assays. This approach offers a more comprehensive understanding of the effects of pollutants on aquatic ecosystems.

The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates

This study aims to investigate the temporal dynamics of the epiphytic protist community on macroalgae, during the summer months, with a specific focus on fungi, and the interactions between zoosporic chytrid parasites and the proliferation of the dinoflagellates. We employed a combination of environmental sequencing techniques, incubation of natural samples, isolation of target organisms and laboratory experiments. Metabarcoding sequencing revealed changes in the dominant members of the epiphytic fungal community. Initially, fungi comprised < 1% of the protist community, mostly accounted for by Basidiomycota and Ascomycota, but with the emergence of Chytridiomycota during the mature phase of the biofilm, the fungal contribution increased to almost 30%. Chytridiomycota became dominant in parallel with an increase in the relative abundance of dinoflagellates in the community. Microscopy observations showed a general presence of chytrids following the peak proliferation of the dinoflagellate Ostreopsis sp., with the parasite, D. arenysensis as the dominant chytrid. The maximum infection prevalence was 2% indicating host-parasite coexistence. To further understand the in-situ prevalence of chytrids, we characterised the dynamics of the host abundance and prevalence of chytrids through co-culture. These laboratory experiments revealed intraspecific variability of D. arenysensis in its interaction with Ostreopsis, exhibiting a range from stable coexistence to the near-extinction of the host population. Moreover, while chytrids preferentially parasitized dinoflagellate cells, one of the strains examined displayed the ability to utilize pollen as a resource to maintain its viability, thus illustrating a facultative parasitic lifestyle. Our findings not only enrich our understanding of the diversity, ecology, and progression of epiphytic microalgal and fungal communities on Mediterranean coastal macroalgae, but they also shed light on the presence of zoosporic parasites in less-explored benthic habitats.

The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity

Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.

Interactions between chytrids cause variable infection strategies on harmful algal bloom forming species

Cyanobacteria have a great diversity of natural enemies, such as herbivores and pathogens, including fungal pathogens within the Chytridiomycota (chytrids). While these pathogens have been previously described on a select number of cyanobacterial hosts and are suspected to play a significant ecological role, little is understood about species interactions and how competition between parasites can affect epidemic development and bloom formation. Here, three Planktothrix agardhii isolates from Sandusky Bay, Lake Erie (OH, USA) were challenged in monoculture and polyculture against infection by three isolates (C1, C2, C10) of their obligate chytrid fungal pathogen, Rhizophydiales sp. The chytrid isolates were inoculated as single isolates or a mixture of up to three different isolates. In monoculture, host isolates were characterized as highly susceptible (P. agardhii 1030), moderately susceptible (P. agardhii 1808) or mostly resistant (P. agardhii 1801). Co-infection of chytrid isolates on the highly susceptible host isolate had an additive effect on chytrid prevalence, leading to a culture crash where 2 or 3 chytrid isolates were present. Co-infection of chytrid isolates on the moderately susceptible and mostly resistant isolates had no effect on chytrid infection outcome or prevalence compared to infection with a single isolate. In polyculture, the effect on host growth was most significant in the single chytrid isolate treatment, which was attenuated with the addition of mixed chytrid treatments. Genetic analysis of the resulting population after the experimental period showed a tendency for the chytrid isolate C1 and P. agardhii 1801 to dominate in mixed population samples. Two different interspecific interactions seem to be in play; varied parasite infection strategies allow for the amplification of infection prevalence due to mixed chytrids in a susceptible monoculture, or competition allows for the dominance of a single chytrid isolate in monoculture and the reduction of infection prevalence in a host polyculture. This work thus highlights how interactions between chytrid infections can change the course of epidemic development and harmful algal bloom formation.

Differential Adaptation Has Resulted in Aggressiveness Variation of Calonectria pseudonaviculata on Hosts Buxus, Pachysandra, and Sarcococca

Calonectria pseudonaviculata (Cps) infects Buxus (boxwood), Pachysandra (pachysandra), and Sarcococca spp. (sweet box); yet, how it adapts to its hosts has been unclear. Here, we performed serial passage experiments with the three hosts and measured Cps changes in three aggressiveness components: infectibility, lesion size, and conidial production. The detached leaves of individual hosts were inoculated with isolates (P0) from the originating host, followed by nine serial inoculations of new leaves of the same host with conidia from the infected leaves of the previous inoculation. All boxwood isolates maintained their capability of infection and lesion expansion through the 10 passages, whereas most non-boxwood isolates lost these abilities during the passages. Isolates from plants of origin (*-P0) and their descendants isolated from passages 5 (*-P5) and 10 (*-P10) were used to evaluate aggressiveness changes on all three hosts with cross-inoculation. While post-passage boxwood isolates gave enlarged lesions on pachysandra, sweet box P5 and pachysandra P10 isolates showed reduced aggressiveness on all hosts. Cps appears to be most adapted to boxwood and less adapted to sweet box and pachysandra. These results suggest speciation of Cps, with its coevolutionary pace with the hosts the fastest with boxwood, intermediate with sweet box, and the slowest with pachysandra.

A road map for in vivo evolution experiments with blood-borne parasitic microbes

Laboratory experiments in which blood-borne parasitic microbes evolve in their animal hosts offer an opportunity to study parasite evolution and adaptation in real time and under natural settings. The main challenge of these experiments is to establish a protocol that is both practical over multiple passages and accurately reflects natural transmission scenarios and mechanisms. We provide a guide to the steps that should be considered when designing such a protocol, and we demonstrate its use via a case study. We highlight the importance of choosing suitable ancestral genotypes, treatments, number of replicates per treatment, types of negative controls, dependent variables, covariates, and the timing of checkpoints for the experimental design. We also recommend specific preliminary experiments to determine effective methods for parasite quantification, transmission, and preservation. Although these methodological considerations are technical, they also often have conceptual implications. To this end, we encourage other researchers to design and conduct in vivo evolution experiments with blood-borne parasitic microbes, despite the challenges that the work entails.

Linking pathogen-microbiome-host interactions to explain amphibian population dynamics

Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome-wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity-fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases.

Fate of hepatotoxin microcystin during infection of cyanobacteria by fungal chytrid parasites

Chytrid parasites are increasingly recognized as ubiquitous and potent control agents of phytoplankton, including bloom-forming toxigenic cyanobacteria. In order to explore the fate of the cyanobacterial toxin microcystins (MCs) and assess potential upregulation of their production under parasite attack, a laboratory experiment was conducted to evaluate short- and long-term variation in extracellular and intracellular MC in the cyanobacteria Planktothrix agardhii and P. rubescens, both under chytrid infection and in the presence of lysates of previously infected cyanobacteria. MCs release under parasite infection was limited and not different to uninfected cyanobacteria, with extracellular toxin shares never exceeding 10%, substantially below those caused by mechanical lysis induced by a cold-shock. Intracellular MC contents in P. rubescens under infection were not significantly different from uninfected controls, whereas infected P. agardhii showed a 1.5-fold increase in intracellular MC concentrations, but this was detected within the first 48 hours after parasite inoculation and not later, indicating no substantial MC upregulation in cells being infected. The presence of lysates of previously infected cyanobacteria did not elicit higher intracellular MC contents in exposed cyanobacteria, speaking against a putative upregulation of toxin production induced via quorum sensing in response to parasite attack. These results indicate that chytrid epidemics can constitute a bloom decay mechanism that is not accompanied by massive release of toxins into the medium.

Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

Parasites do not adapt to elevated temperature, as evidenced from experimental evolution of a phytoplankton-fungus system

Global warming is predicted to impact the prevalence and severity of infectious diseases. However, empirical data supporting this statement usually stem from experiments in which parasite fitness and disease outcome are measured directly after temperature increase. This might exclude the possibility of parasite adaptation. To incorporate the adaptive response of parasites into predictions of disease severity in a warmer world, we undertook an experimental evolution assay in which a fungal parasite of phytoplankton was maintained at elevated or control temperatures for six months, corresponding to 100–200 parasite generations. Host cultures were maintained at the respective temperatures and provided as substrate, but were not under parasite pressure. A reciprocal infection experiment conducted after six-month serial passages revealed no evidence of parasite adaptation. In fact, parasite fitness at elevated temperatures was inferior in parasite populations reared at elevated temperatures compared with those maintained under control temperature. However, this effect was reversed after parasites were returned to control temperatures for a few (approx. 10) generations. The absence of parasite adaptation to elevated temperatures suggests that, in phytoplankton–fungus systems, disease outcome under global warming will be largely determined by both host and parasite thermal ecology.

Anabaenopeptins: What We Know So Far

Cyanobacteria are microorganisms with photosynthetic mechanisms capable of colonizing several distinct environments worldwide. They can produce a vast spectrum of bioactive compounds with different properties, resulting in an improved adaptative capacity. Their richness in secondary metabolites is related to their unique and diverse metabolic apparatus, such as Non-Ribosomal Peptide Synthetases (NRPSs). One important class of peptides produced by the non-ribosomal pathway is anabaenopeptins. These cyclic hexapeptides demonstrated inhibitory activity towards phosphatases and proteases, which could be related to their toxicity and adaptiveness against zooplankters and crustaceans. Thus, this review aims to identify key features related to anabaenopeptins, including the diversity of their structure, occurrence, the biosynthetic steps for their production, ecological roles, and biotechnological applications.

Isolation and Characterization of Rhizophydiales sp. (Chytridiomycota), Obligate Parasite of Planktothrix agardhii in a Laurentian Great Lakes Embayment

Planktothrix agardhii dominates the cyanobacterial harmful algal bloom community in Sandusky Bay, Lake Erie (USA) from May through September. This filamentous cyanobacterium is host to a known obligate parasite; the chytrid Rhizophydium sp. During the 2018 bloom season, by utilizing dilution and single filament isolation techniques, 7 chytrid and 12 P. agardhii strains were isolated from Sandusky Bay. These 7 chytrids and a selection of P. agardhii hosts were then characterized with respect to infection rates. Infections by the isolated chytrids were specific to Planktothrix planktonic species and were not found on other filamentous cyanobacterial taxa present in the bay (Aphanizomenon sp. and Cuspidothrix sp.). Even among the potential P. agardhii host strains, individual chytrid isolates had different degrees of infectivity and showed preference for different host isolates, suggesting possible ecological partitioning even within the same sample population. Examining mechanisms of chytrid pathogenesis, the zoospores displayed a swarming pattern to attack and fracture the host filament and create new infection sites at the trichome termini. Infections by these parasitic chytrids also led to a release of intracellular microcystin toxins from the hosts. Additionally, infections were dependent on media type, highlighting the importance of media choice on experimental outcomes. Media in which chytrid swarming was observed closely matched the ionic strength of the natural environment. Understanding pathogenesis by fungal parasites will assist future efforts aimed at determining environmental factors favoring loss mechanisms for Planktothrix agardhii-dominated blooms.IMPORTANCE Whereas many studies have focused on the factors contributing to the establishment and persistence of cyanobacterial harmful algal blooms (cHABs), few studies have examined bloom pathogenesis. Chytrid fungi infect cyanobacteria and stimulate food web interactions through manipulation of previously hard to digest filaments and the release of nutrients to support heterotrophic microbes. Specifically, chytrids infective on filamentous Planktothrix agardhii exhibit a species-specific infection that fragments trichomes into shorter units that can be consumed more easily by grazers. Chytrid zoospores also serve as a high-quality food source for the lower food web. Understanding host-pathogen relationships and mechanisms of pathogenesis on cyanobacteria will be necessary to effectively model the ecology of cHABs.

Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems

If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value—notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and noncrop hosts and between experimental and natural host populations. Here, we used a meta‐analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested. We synthesized the results of 102 studies, comprising 2004 effect sizes representing a diversity of approaches and host‐parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ∼20% for noncrop hosts and by ∼50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.

Shared PKS Module in Biosynthesis of Synergistic Laxaphycins

Cyanobacteria produce a wide range of lipopeptides that exhibit potent membrane-disrupting activities. Laxaphycins consist of two families of structurally distinct macrocyclic lipopeptides that act in a synergistic manner to produce antifungal and antiproliferative activities. Laxaphycins are produced by range of cyanobacteria but their biosynthetic origins remain unclear. Here, we identified the biosynthetic pathways responsible for the biosynthesis of the laxaphycins produced by Scytonema hofmannii PCC 7110. We show that these laxaphycins, called scytocyclamides, are produced by this cyanobacterium and are encoded in a single biosynthetic gene cluster with shared polyketide synthase enzymes initiating two distinct non-ribosomal peptide synthetase pathways. The unusual mechanism of shared enzymes synthesizing two distinct types of products may aid future research in identifying and expressing natural product biosynthetic pathways and in expanding the known biosynthetic logic of this important family of natural products.

Genomic and fossil windows into the secret lives of the most ancient fungi

Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.

Light intensity and spectral distribution affect chytrid infection of cyanobacteria via modulation of host fitness

Light gradients are an inherent feature in aquatic ecosystems and play a key role in shaping the biology of phytoplankton. Parasitism by chytrid fungi is gaining increasing attention as a major control agent of phytoplankton due to its previously overlooked ubiquity, and profound ecological and evolutionary consequences. Despite this interest, if and how light conditions modulate phytoplankton chytridiomycosis remains poorly studied. We investigated life-history traits of a chytrid parasite, Rhizophydium megarrhizum, under different light intensities and spectral compositions when infecting two closely related planktonic cyanobacteria with different light-harvesting strategies: Planktothrix rubescens and P. agardhii. In general, parasite transmission was highest under light conditions (both intensity and quality) that maximized growth rates for uninfected cyanobacteria. Chytrid encystment on hosts was significantly affected by light intensity and host strain identity. This likely resulted from higher irradiances stimulating the increased discharge of photosynthetic by-products, which drive parasite chemotaxis, and from strain-specific differences at the cell-surface. Comparisons of parasite transmission and host growth rates under different light conditions suggest the potential for epidemic development at higher irradiances, whereas host and parasite could coexist without epidemic outbreaks at lower light levels. These results illustrate the close relationship between parasite transmission and host fitness, which is ultimately modulated by the external environment.

Fungicides at environmentally relevant concentrations can promote the proliferation of toxic bloom-forming cyanobacteria by inhibiting natural fungal parasite epidemics

Fungal parasites of the phylum Chytridiomycota (chytrids) are increasingly recognized as potent control agents of phytoplankton, including toxic bloom-forming cyanobacteria. We experimentally tested whether agricultural fungicides can interfere with natural epidemics caused by parasitic chytrid fungi and thereby favor cyanobacterial bloom formation. Specifically, we exposed the toxic bloom-forming cyanobacterium Planktothrix and its chytrid parasite Rhizophydium megarrhizum to different concentrations of the widely used agricultural fungicides tebuconazole and azoxystrobin, as well as the medical fungicide itraconazole (the latter was included to test its potential to suppress infection in vitro). Environmentally relevant concentrations of tebuconazole (20-200 μg/L) and azoxystrobin (1-30 μg/L) significantly decreased infection prevalence over a timespan of seven days, while not affecting the growth of uninfected cyanobacteria. Itraconazole suppressed infection completely. Our findings demonstrate that agricultural fungicide run-off has the potential to inhibit natural chytrid epidemics and, thereby, to promote the proliferation of toxic cyanobacteria.

Biological Concepts for the Control of Aquatic Zoosporic Diseases

Aquatic zoosporic diseases are threatening global biodiversity and ecosystem services, as well as economic activities. Current means of controlling zoosporic diseases are restricted primarily to chemical treatments, which are usually harmful or likely to be ineffective in the long term. Furthermore, some of these chemicals have been banned due to adverse effects. As a result, there is a need for alternative methods with minimal side-effects on the ecosystem or environment. Here, we integrate existing knowledge of three poorly interconnected areas of disease research - amphibian conservation, aquaculture, and plankton ecology - and arrange it into seven biological concepts to control zoosporic diseases. These strategies may be less harmful and more sustainable than chemical approaches. However, more research is needed before safe application is possible.

Spatial-temporal survey of Microcystis oligopeptide chemotypes in reservoirs with dissimilar waterbody features and their relation to genetic variation

The ability of cyanobacteria to produce toxins and other secondary metabolites is patchily distributed in natural populations, enabling the use of cellular oligopeptide compositions as markers to classify strains into ecologically-relevant chemotypical subpopulations. The composition and spatiotemporal distribution of Microcystis chemotypes within and among waterbodies was studied at different time scales by analyzing (i) Microcystis strains isolated between 1998 and 2007 from different Spanish reservoirs and (ii) individual Microcystis aeruginosa colonies collected from pelagic and littoral habitats in Valmayor reservoir (Spain) during a bloom. No agreement between chemotypes and both morphotypes and genotypes (based on cpcBA-IGS, 16S-23S rRNA ITS and mcyB genes) was found, suggesting that oligopeptide profiles in individual strains evolve independently across morphospecies and phylogenetic genotypes, and that the diversity of microcystin variants produced cannot be explained by mcyB gene variations alone. The presence of identical chemotypes in spatially-distant reservoirs with dissimilar trophic state, lithology or depth indicate that waterbody characteristics and geographical boundaries weakly affect chemotype composition and distribution. At smaller spatiotemporal scales (i.e. during bloom), M. aeruginosa populations showed high number of chemotypes, as well as marked differences in chemotype composition and relative abundance among the littoral and pelagic habitats. This indicates that the factors influencing chemotype composition, relative abundance and dynamics operate at short spatial and temporal scales, and supports emerging hypotheses about interactions with antagonistic microorganisms as possible drivers for widespread chemical polymorphisms in cyanobacteria.