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The toxic cyanobacterium Microcystis causes worldwide health concerns, being frequently found in freshwater and estuarine ecosystems. Under natural conditions, Microcystis spp. show a colonial lifestyle involving a phycosphere populated by a highly diverse associated microbiome. In a previous study, we have proposed that colony formation and growth may be achieved through mechanisms of multispecies bacterial biofilm formation. Starting with single-cells, specific bacteria would be recruited from the environment to attach and create a buoyant biofilm or colony. This progression from a few single cells to large colonies would encompass the growth of the Microcystis community and bloom formation. In order to test this, we applied 16S rDNA metabarcoding to evaluate the changes in bacterial community structure (gDNA) and its active portion (cDNA) between different sample sizes obtained from a Microcystis bloom. Bloom sample was sieved by size, from one or a few cells (U fraction) to large colonies (maximum linear dimension ≥ 150 µm; L fraction), including small (20–60 µm, S fraction) and medium size (60–150 µm, M fraction) colonies. We found that gDNA- and cDNA-based bacterial assemblages significantly differed mostly due to the presence of different taxa that became active among the different sizes. The compositional variations in the communities between the assessed sample sizes were mainly attributed to turnover. From U to M fractions the turnover was a result of selection processes, while between M and L fractions stochastic processes were likely responsible for the changes. The results suggest that colony formation and growth are a consequence of mechanisms accounting for recruitment and selection of specific bacterial groups, which activate or stop growing through the different phases of the biofilm formation. When the final phase (L fraction colonies) is reached the colonies start to disaggregate (bloom decay), few cells or single cells are released and they can start new biofilms when conditions are suitable (bloom development).

In this paper we attempt to explain observed niche differences among species (i.e. differences in their distribution along environmental gradients) by differences in trait values (e.g. volume) in phytoplankton communities. For this, we propose the trait-modulated Gaussian logistic model in which the niche parameters (optimum, tolerance and maximum) are made linearly dependent on species traits. The model is fitted to data in the Bayesian framework using OpenBUGS (Bayesian inference Using Gibbs Sampling) to identify according to which environmental variables there is niche differentiation among species and traits. We illustrate the method with phytoplankton community data of 203 lakes located within four climate zones and associated measurements on 11 environmental variables and six morphological species traits of 60 species. Temperature and chlorophyll-a (with opposite signs) described well the niche structure of all species. Results showed that about 25% of the variance in the niche centres with respect to chlorophyll-a were accounted for by traits, whereas niche width and maximum could not be predicted by traits. Volume, mucilage, flagella and siliceous exoskeleton are found to be the most important traits to explain the niche centres. Species were clustered in two groups with different niches structures, group 1 high temperature-low chlorophyll-a species and group 2 low temperature-high chlorophyll-a species. Compared to group 2, species in group 1 had larger volume but lower surface area, had more often flagella but neither mucilage nor siliceous exoskeleton. These results might help in understanding the effect of environmental changes on phytoplankton community. The proposed method, therefore, can also apply to other aquatic or terrestrial communities for which individual traits and environmental conditioning factors are available.

This paper analyses 6 years of temporal and spatial dynamics of submerged aquatic vegetation (SAV) in a subtropical choked coastal lagoon in Uruguay. In this lagoon, macrophyte proliferation is frequently observed. Nutrient inputs and a highly dynamic salinity regime may be promoting the observed changes in SAV. We explored the main potential factors causing plants proliferation. We took seasonal samples of SAV biomass and physicochemical variables in vegetated areas of the entire lagoon and analysed the spatial distribution with correspondence analysis. Generalised linear models were used to quantify the contribution of physicochemical variables to SAV species biomass, total biomass and richness. Salinity was the most important factor determining SAV structure, causing a decrease of richness and biomass at salinity values higher than ca. 10. The SAV temporal and spatial dynamics were also determined by the species life strategies. Freshwater and slightly brackish conditions allowed competitive species to develop high biomass and cover, while marine water declined biomass and richness promoting stunted species dominance. The wide variation of salinity resulted in a highly dynamic SAV community, and the artificial opening of this coastal lagoon sand bar could therefore have strong effects on SAV. Further eutrophication due to land use intensification might enhance SAV variability and the alternating dominance of submerged angiosperms, macroalgae and phytoplankton.

The identification of the main factors driving phytoplankton community structure is essential to understand and adequately manage freshwater ecosystems. We hypothesize that differences in morphological traits reflect phytoplankton functional properties that will be selected under particular environmental conditions, namely their habitat template . We apply a morphology-based functional groups (MBFG) approach to classify phytoplankton organisms and define each group template. We use machine learning techniques to classify a large number of phytoplankton communities and environmental variables from different climate zones and continents. Random forest analysis explained well the distribution of most groups’ biovolume and the selected variables reflected ecological preferences according to morphology. By means of a classification tree it was also possible to identify thresholds of the environmental variables promoting groups dominance in different lakes. For example group III (filaments with aerotopes and high surface/volume including potentially toxic species) was dominant when light attenuation coefficient was >3.9 m −1 and total nitrogen was >2,800 μg l −1 . We demonstrate that morphology captures ecological preferences of phytoplankton groups and provides empirical values to describe their habitat template.

Assessing zooplankton grazing on phytoplankton is crucial to understand, model, and predict the structure and dynamics of pelagic communities. Our hypothesis is that phytoplankton consumption by zooplankton in freshwater lakes can be well represented by clustering phytoplankton species into morphology-based functional groups (MBFG) and zooplankton species into broad taxonomic units: cladocerans, calanoid copepods, and rotifers. We characterized zooplankton potential grazing on MBFG based on an extensive literature review of experimental data including clearance and ingestion rates. Rotifers show greater potential grazing upon small- and medium-sized species (MBFG I and IV) and presented a Type III trait-based functional response. Cladocerans also show greater potential impact upon MBFG IV but a Type II response. Both groups maintained their respective feeding response regardless of the type of food available, indicating poor food selectivity. Copepods consumed different MBFGs, but a clear Type II pattern was observed when feeding on MBFGs V and VI. Prediction intervals indicated a greater variability in cladocerans’ and copepods’ response. This approach is a step to summarize and characterize grazing to the future quantification of ecosystem models. Further efforts should be done to include information about different larval stages and phytoplankton traits not directly related to morphology.

Reynolds Functional Groups (RFG) were designed to represent the diversity of phytoplankton assemblages of freshwater ecosystems and are among the most enduring legacies of C. S. Reynolds to freshwater phytoplankton ecologists. The RFG concept summarises a rich base of knowledge, clustering species according to functional criteria. RFG allow researchers to organise information, understand community and ecosystem functioning, and identify future outcomes, also contributing to construct hypotheses and define community assembly. This approach represents the environmental requirements, tolerances and sensitivities of species, organizing them into diagnostic environmental axes representing the habitat template of phytoplankton communities. In this contribution, we highlight the importance of this trait-based approach for phytoplankton ecology, and summarise its history and usage for phytoplankton species classifications and prediction based on environmental gradients. We present some of the applications of the approach, to describe patterns, explain mechanisms and predict new situations. We hope that this review will contribute both to describe the trajectory and practice of RFG and to encourage its use in addressing new ecological questions and in generating new avenues of research.

Issue Title: Shallow Lakes 2002 Submerged plants are thought to negatively affect phytoplankton crops in the temperate zone by a number of mechanisms, including nutrient and light limitation, and enhancement of top-down control by offering diurnal refuge for zooplankton against visual predation, and by favouring piscivores. In 1997-1998, Lake Blanca (34° 54' S, 54° 50' W), a yellow-brownish shallow lake in Uruguay, suffered a severe water level reduction (associated with El Niño events between 1995-1997) that resulted in a massive fish kill and an extensive colonisation by Egeria densa. A clear water phase is established nowadays in the system (Secchi depth > 1 m), despite a fish community restricted to two small omnivorous-planktivorous fish: Jenynsia multidentata and Cnesterodon decemmaculatus. We studied the effects of E. densa on bottom-up and top-down controls on phytoplankton by comparing physical, chemical, and biological characteristics between submerged plant beds and sites without plants, from autumn 2000 to autumn 2001. The water column had low to intermediate nutrient concentrations, and phytoplankton community was highly diverse with a low to moderate biomass (mean Chl-a = 10.6 μg l^sup -1^). The water level, recovered during the study, promoted a dilution process that explained the temporal pattern of many chemical variables. Macrophyte PVI represented 28-39% of the lake volume (annual mean biomass = 174 g DW m^sup -2^). The zooplankton community was generally dominated by copepods in terms of biomass. Fish and zooplankton were significantly associated with submerged plant beds. In spite of the high biomass and density of omnivorous-planktivorous fish (115 kg ha^sup -1^, 13 ind m^sup -2^), zooplankton strongly affected phytoplankton spatial and temporal variation. The most important differences of algal biomass between zones coincided with a high herbivorous zooplankton biomass and/or with plants occupying the entire water column during the low level period. Medium-sized zooplankton declined with fish reproduction. The consequent stronger predation of juvenile fish seemed to decrease macrophyte efficiency as a zooplankton refuge in summer. E. densa bottom-up mechanisms would also be present, contributing to maintaining clear water. Besides the usually described nutrient and light limitation, the internal production of humic substances could enhance the observed top-down effect.[PUBLICATION ABSTRACT]

Trait-based approaches are increasingly being used in aquatic ecology to elucidate how environmental conditions affect community assembly. However, studies of zooplankton from tropical regions are relatively rare. Our objective was to construct zooplankton trait-based functional groups (ZFG) to study tropical reservoirs that differ with respect to precipitation, eutrophication and hydrological operations. We selected and analysed zooplankton and associated environmental variables from four tropical reservoirs that were sampled during dry and rainy seasons for three years. Eight traits were evaluated to construct ZFGs using hierarchical clusters and classification trees. Six ZFGs were identified based on three non-redundant functional traits: habitat type, feeding and predatory escape response. Significant differences in the density and biomass of ZFGs were observed as indicated by regression models showing reservoir morphometry, hydrology, rainfall, and phytoplankton biomass as main environmental drivers. Our results highlight the usefulness of ZFG to monitoring programmes and for predicting zooplankton community changes in tropical reservoirs, allowing a greater understanding of plankton dynamics and ecosystems functioning.

Abstract Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms. Microcystis is a unicellular genus of Cyanobacteria provoking dense blooms formed by colonies of different sizes, which result from specific interactions between the cyanobacterium and its microbiome through a biofilm-like mechanism.

The mean body size of limnetic cladocerans decreases from cold temperate to tropical regions, in both the northern and the southern hemisphere. This size shift has been attributed to both direct (e.g. physiological) or indirect (especially increased predation) impacts. To provide further information on the role of predation, we compiled results from several studies of subtropical Uruguayan lakes using three different approaches: (i) field observations from two lakes with contrasting fish abundance, Lakes Rivera and Rodó, (ii) fish exclusion experiments conducted in in-lake mesocosms in three lakes, and (iii) analyses of the Daphnia egg bank in the surface sediment of eighteen lakes. When fish predation pressure was low due to fish kills in Lake Rivera, large-bodied Daphnia appeared. In contrast, small-sized cladocerans were abundant in Lake Rodó, which exhibited a typical high abundance of fish. Likewise, relatively large cladocerans (e.g. Daphnia and Simocephalus ) appeared in fishless mesocosms after only 2 weeks, most likely hatched from resting egg banks stored in the surface sediment, but their abundance declined again after fish stocking. Moreover, field studies showed that 9 out of 18 Uruguayan shallow lakes had resting eggs of Daphnia in their surface sediment despite that this genus was only recorded in three of the lakes in summer water samples, indicating that Daphnia might be able to build up populations at low risk of predation. Our results show that medium and large-sized zooplankton can occur in subtropical lakes when fish predation is removed. The evidence provided here collectively confirms the hypothesis that predation, rather than high-temperature induced physiological constraints, is the key factor determining the dominance of small-sized zooplankton in warm lakes.