Molecular mechanisms of tolerance to cyanobacterial protease inhibitors revealed by clonal differences in Daphnia magna

Protease inhibitors of primary producers are a major food quality constraint for herbivores. In nutrient‐rich freshwater ecosystems, the interaction between primary producers and herbivores is mainly represented by Daphnia and cyanobacteria. Protease inhibitors have been found in many cyanobacterial blooms. These inhibitors have been shown (both in vitro and in situ) to inhibit the most important group of digestive proteases in the daphnid's gut, that is, trypsins and chymotrypsins. In this study, we fed four different Daphnia magna genotypes with the trypsin‐inhibitor‐containing cyanobacterial strain Microcystis aeruginosa PCC 7806 Mut. Upon exposure to dietary trypsin inhibitors, all D. magna genotypes showed increased gene expression of digestive trypsins and chymotrypsins. Exposure to dietary trypsin inhibitors resulted in increased activity of chymotrypsins and reduced activity of trypsin. Strong intraspecific differences in tolerance of the four D. magna genotypes to the dietary trypsin inhibitors were found. The degree of tolerance depended on the D. magna genotype. The genotypes' tolerance was positively correlated with the residual trypsin activity and the different IC₅₀ values of the trypsins. On the genetic level, the different trypsin loci varied between the D. magna genotypes. The two tolerant Daphnia genotypes that both originate from the same lake, which frequently produces cyanobacterial blooms, clustered in a neighbour‐joining phylogenetic tree based on the three trypsin loci. This suggests that the genetic variability of trypsin loci was an important cause for the observed intraspecific variability in tolerance to cyanobacterial trypsin inhibitors. Based on these findings, it is reasonable to assume that such genetic variability can also be found in natural populations and thus constitutes the basis for local adaptation of natural populations to dietary protease inhibitors.     

High‐resolution melting analysis: a genotyping tool for population studies on Daphnia

Determining genetic variation at the DNA level within and between natural populations is important for understanding the role of natural selection on phenotypic traits, but many techniques of screening for genetic variation are either cost intensive, not sensitive enough or too labour‐ and time‐consuming. Here, we demonstrate high‐resolution melting analysis (HRMA) as a cost‐effective and powerful tool for screening variable target genes in natural populations. HRMA is based on monitoring the melting of PCR amplicons. Owing to saturating concentrations of a dye that binds at high concentrations to double‐stranded DNA, it is possible to genotype high numbers of samples rapidly and accurately. We analysed digestive trypsins of two Daphnia magna populations as an application example for HRMA. One population originated from a pond containing toxic cyanobacteria that possibly produce protease inhibitors and the other from a pond without such cyanobacteria. The hypothesis was that D. magna clones from ponds with cyanobacteria have undergone selection by these inhibitors, which has led to different trypsin alleles. We first sequenced pooled genomic PCR products of trypsins from both populations to identify variable DNA sequences of active trypsins. Second, we screened variable DNA sequences of each D. magna clone from both populations for single nucleotide polymorphisms via HRMA. The HRMA results revealed that both populations exhibited phenotypic differences in the analysed trypsins. Our results indicate that HRMA is a powerful genotyping tool for studying the variation of target genes in response to selection within and between natural Daphnia populations.     

Gene expression and activity of digestive proteases in <Emphasis Type="Italic">Daphnia</Emphasis>: effects of cyanobacterial protease inhibitors

Background  

The frequency of cyanobacterial blooms has increased worldwide, and these blooms have been claimed to be a major factor leading to the decline of the most important freshwater herbivores, i.e. representatives of the genus Daphnia. This suppression of Daphnia is partly attributed to the presence of biologically active secondary metabolites in cyanobacteria. Among these metabolites, protease inhibitors are found in almost every natural cyanobacterial bloom and have been shown to specifically inhibit Daphnia 's digestive proteases in vitro, but to date no physiological responses of these serine proteases to cyanobacterial protease inhibitors in Daphnia have been reported in situ at the protein and genetic levels.     

Context dependency of infectious disease: the cyanobacterium Microcystis aeruginosa decreases white bacterial disease in Daphnia magna

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Cyanobacterial protease inhibitors lead to maternal transfer of increased protease gene expression in Daphnia

Protease inhibitors (PIs) have frequently been found in cyanobacterial blooms and have been shown to affect the major herbivore Daphnia by decreasing growth and inhibiting gut protease activity. However, it has been shown that a clone of Daphnia is able to respond to dietary PIs by increasing its protease gene expression. Such an inducible response might be maternally transferred to the next generation. Therefore, we tested a tolerant clone for maternal transfer of protease gene expression. When exposed to the trypsin inhibitor-producing cyanobacterium Microcystis aeruginosa PCC7806 Mut, Daphnia mothers and their untreated newborns showed an increase in trypsin gene expression compared to naïve mothers grown on control food and their offspring. The maternally transferred increase in gene expression was accompanied by a higher somatic growth rate of the offspring generation from exposed mothers compared to offspring from naïve mothers. This higher growth rate compensated for the lower dry mass of newborns from exposed mothers and led to the same fitness as observed in the offspring of naïve mothers. In nature, clones that can maternally transfer increased protease gene expression should have an advantage over clones that cannot. The selection for such more tolerant clones by naturally occurring PIs might lead to microevolution of natural Daphnia populations, and to local adaptation in the long term. This is the first study to show an adaptive maternal transfer of increased target gene expression in an ecological context.     

Eutrophication mediates rapid clonal evolution in Daphnia pulicaria

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Maternal consumption of non‐toxic Microcystis by Daphnia magna induces tolerance to toxic Microcystis in offspring

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Linking biotic interactions and climate change to the success of exotic Daphnia lumholtzi

1. Warmer temperatures may increase cyanobacterial blooms in freshwater ecosystems, yet few ecological studies examine how increases in temperature and cyanobacterial blooms will alter the performance of non‐native species. We evaluated how competitive interactions and interactions between these two drivers of ecological change influence the performance of non‐native species using the native zooplankton Daphnia pulex and the non‐native zooplankton Daphnia lumholtzi as a model system. Based on the literature, we hypothesised that D. lumholtzi would perform best in warmer temperatures and in the presence of cyanobacteria. 2. Laboratory competition experiments showed that in the absence of competitors, growth rates of D. pulex (but not D. lumholtzi) were reduced at higher temperatures and with the cyanobacterial foods Anabaena flos‐aquae and Microcystis aeruginosa. In the presence of competitors, however, D. pulex emerged as the superior resource competitor at both temperatures with cyanobacterial food. We therefore predicted that, if competitive interactions are important to its establishment, D. lumholtzi would perform best in the absence of cyanobacteria in heated environments. 3. As predicted, when both species were introduced at low densities in field mesocosms, D. lumholtzi performed best at high temperatures without added cyanobacteria and worst at ambient temperatures with added cyanobacteria, indicating that competitive interactions are likely to be important for its establishment. 4. Taken together, these studies indicate that, while D. lumholtzi may benefit from increases in temperature, associated increased cyanobacterial blooms may hinder its performance. Thus, our findings underscore the importance of considering biotic interactions such as competition when predicting the future establishment of non‐native species in response to climate warming.     

Contemporary evolution of a Lepidopteran species,Heliothis virescens,in response to modern agricultural practices

Adaptation to human‐induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton‐feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt‐cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD‐seq‐enabled genome scan to identify loci with significant allele frequency changes over the 15‐year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.     

Adaptation dynamics and evolutionary rescue under sulfide selection in cyanobacteria: a comparative study between Microcystis aeruginosa and Oscillatoria sp. (cyanobacteria)

Experimental evolution studies using cyanobacteria as model organisms are scarce despite the role of cyanobacteria in the evolution of photosynthesis. Three different experimental evolution approaches have been applied to shed light on the sulfide adaptation process, which played a key role in the evolution of this group. We used a Microcystis aeruginosa sulfide‐sensitive strain, unable to grow above ~0.1 mM, and an Oscillatoria sp. strain, isolated from a sulfureous spa (~0.2 mM total sulfide). First, performing a fluctuation analysis design using the spa waters as selective agent, we proved that M. aeruginosa was able to adapt to this sulfide level by rare spontaneous mutations. Second, applying a ratchet protocol, we tested if the limit of adaptation to sulfide of the two taxa was dependent on their initial sulfide tolerance, finding that M. aeruginosa adapted to 0.4 mM sulfide, and Oscillatoria sp. to ~2 mM sulfide, twice it highest tolerance level. Third, using an evolutionary rescue approach, we observed that both speed of exposure to increasing sulfide concentrations (deterioration rate) and populations’ genetic variation determined the survival of M. aeruginosa at lethal sulfide levels, with a higher dependence on genetic diversity. In conclusion, sulfide adaptation of sensitive cyanobacterial strains is possible by rare spontaneous mutations and the adaptation limits depend on the sulfide level present in strain’s original habitat. The high genetic diversity of a sulfide‐sensitive strain, even at fast environmental deterioration rates, could increase its possibility of survival even to a severe sulfide stress.     

Local adaptation of sex induction in a facultative sexual crustacean: insights from QTL mapping and natural populations of Daphnia magna

Dormancy is a common adaptation in invertebrates to survive harsh conditions. Triggered by environmental cues, populations produce resting eggs that allow them to survive temporally unsuitable conditions. Daphnia magna is a crustacean that reproduces by cyclical parthenogenesis, alternating between the production of asexual offspring and the sexual reproduction of diapausing eggs (ephippia). Prior to ephippia production, males (necessary to ensure ephippia fertilization) are produced parthenogenetically. Both the production of ephippia and the parthenogenetic production of males are induced by environmental factors. Here, we test the hypothesis that the induction of D. magna resting egg production shows a signature of local adaptation. We postulated that Daphnia from permanent ponds would produce fewer ephippia and males than Daphnia from intermittent ponds and that the frequency and season of habitat deterioration would correlate with the timing and amount of male and ephippia production. To test this, we quantified the production of males and ephippia in clonal D. magna populations in several different controlled environments. We found that the production of both ephippia and males varies strongly among populations in a way that suggests local adaptation. By performing quantitative trait locus mapping with parent clones from contrasting pond environments, we identified nonoverlapping genomic regions associated with male and ephippia production. As the traits are influenced by two different genomic regions, and both are necessary for successful resting egg production, we suggest that the genes for their induction co‐evolve.     

Structuring of the cyanobacterial community by pelagic fish in subtropical reservoirs: experimental evidence from Australia

1. Subtropical reservoirs of Australia are commonly subject to summer blooms of cyanobacteria. The potential for food web manipulation to control cyanobacterial blooms was investigated in Lake Maroon, south east Queensland using enclosures in which the density of the Australian gudgeon Hypseleotris spp. was manipulated. 2. Zooplankton biomass and community structure were strongly affected by fish density. A size dependent predation effect of Hypseleotris on zooplankton was observed at ambient fish densities, and the community shifted towards a dominance of copepod juveniles and nauplii. Substantial increases in the populations of Ceriodaphnia and calanoid copepods were observed at low fish densities and in the absence of fish. 3. At ambient fish densities total phytoplankton and the proportion of cyanobacteria were maintained at levels similar to those prevailing at day 0. Total phytoplankton and the proportion of cyanobacteria decreased substantially at low fish densities and in the absence of fish. Chlorophytes became dominant in the ‘no fish’ treatment and the grazing‐resistant species Oocystis and Dictyosphaerium were significantly higher than at ambient fish densities. 4. The experiment demonstrated a strong positive relationship between Hypseleotris density and cyanobacteria, and the results suggest that subtropical reservoirs may be suited to food web manipulation as a means of controlling summer cyanobacterial blooms.     

Mesozooplankton and microzooplankton grazing during cyanobacterial blooms in the western basin of Lake Erie

Lake Erie is the most socioeconomically important and productive of the Laurentian (North American) Great Lakes. Since the mid-1990s cyanobacterial blooms dominated primarily by Microcystis have emerged to become annual, late summer events in the western basin of Lake Erie yet the effects of these blooms on food web dynamics and zooplankton grazing are unclear. From 2005 to 2007, grazing rates of cultured (Daphnia pulex) and natural assemblages of mesozooplankton and microzooplankton on five autotrophic populations were quantified during cyanobacterial blooms in western Lake Erie. While all groups of zooplankton grazed on all prey groups investigated, the grazing rates of natural and cultured mesozooplankton were inversely correlated with abundances of potentially toxic cyanobacteria (Microcystis, Anabaena, and Cylindrospermopsis; p < 0.05) while those of the in situ microzooplankton community were not. Microzooplankton grazed more rapidly and consistently on all groups of phytoplankton, including cyanobacteria, compared to both groups of mesozooplankton. Cyanobacteria displayed more rapid intrinsic cellular growth rates than other phytoplankton groups under enhanced nutrient concentrations suggesting that future nutrient loading to Lake Erie could exacerbate cyanobacterial blooms. In sum, while grazing rates of mesozooplankton are slowed by cyanobacterial blooms in the western basin of Lake Erie, microzooplankton are likely to play an important role in the top-down control of these blooms; this control could be weakened by any future increases in nutrient loads to Lake Erie.     

Ecological genetics of sediment browsing behaviour in a planktonic crustacean

Zooplankton can display complex habitat selection behaviours that influence the way they interact with their environments. Some species, although primarily pelagic, can exploit sediment‐borne particles as a food source or use sediments as a refuge from pelagic predation. However, this strategy may increase the exposure to other risks such as benthic predation and infection from sediment‐borne parasite transmission stages. The evolution of habitat selection behaviour in these species is thus expected to be influenced by multiple and possibly contrasting selective forces. Here, we study the browsing behaviour of the water flea Daphnia magna on bottom sediments. First, we demonstrated genetic variation for sediment browsing among D. magna genotypes from natural populations sampled across a broad geographic range. Next, we used an F2 recombinant panel to perform a QTL analysis and identified three regions in the D. magna genome contributing to variation in browsing behaviour. We also analysed the correlation between our data and previously published data on the phototactic behaviour of genotypes from the same F2 panel. Clonal means of the two behavioral traits were not correlated, suggesting that they may evolve independently. Browsing behaviour is likely to be a relevant component of habitat selection in D. magna, and its study may help to incorporate the interactions with the sediment into eco‐evolutionary models of this key freshwater species.     

Understanding cyanobacteria‐zooplankton interactions in a more eutrophic world

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Modelling lake cyanobacterial blooms: Disentangling the climate‐driven impacts of changing mixed depth and water temperature

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Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin,USA

Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine‐scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (F_ST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine‐scale adaptation.     

Thermal tolerance in the keystone species Daphnia magna—a candidate gene and an outlier analysis approach

Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long‐term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm‐ and cold‐adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST‐linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna.     

Risk evaluation of cyanobacteria-dominated algal blooms in a North Louisiana reservoir

Cyanobacteria blooms may produce toxins thatare harmful to invertebrates and fishinhabiting aquatic systems. The objectives ofthis risk evaluation were: (1) to investigatethe potential toxicity (i.e., adverse effectsof cyanobacteria on the survival, reproduction,and behavior) of Lyngbya-dominated algalblooms from a North Louisiana reservoir to Daphnia magna and Pimephales promelas;and (2) to develop mitigation strategies forthis cyanobacteria infestation using physicaland chemical methods. Survival and reproductionof D. magna populations significantlydecreased after exposure to reservoircyanobacteria collected in spring in comparisonwith populations of test organisms exposed toeither Chlorophyta species or a combination ofreservoir cyanobacteria and Chlorophytaspecies. In April 1998, reservoir cyanobacteriaalso elicited a significant avoidance reactionby juvenile P. promelas (20–30 d).However, cyanobacteria collected in August andDecember (1997) did not cause adverse effectsfor either D. magna or P. promelasin terms of survival, reproduction, orbehavior. A physical control method, loweringthe water level of the reservoir (i.e.,drawdown), was simulated in the laboratory for8, 20, and 35 d. After re-saturation of algalpopulations with nutrient enriched medium, theyrecovered to 132.9, 129.4, and 23.7% oforiginal chlorophyll a concentrations,respectively. Herbicide application resulted in>78% decrease in chlorophyll aconcentration of reservoir cyanobacteria by7-d after initial herbicide application. Todecrease risk(s) of Lyngbya-dominatedcyanobacteria and maintain seasonal control inthis reservoir, drawdown in conjunction withherbicide application or recurrent herbicideapplication is recommended prior to onset ofcyanobacteria proliferation.     

To bloom or not to bloom: contrasting responses of cyanobacteria to recent heat waves explained by critical thresholds of abiotic drivers

Past heat waves are considered harbingers of future climate change. In this study, we have evaluated the effects of two recent Central European summer heat waves (2003 and 2006) on cyanobacterial blooms in a eutrophic, shallow lake. While a bloom of cyanobacteria developed in 2006, consistent with our expectations, cyanobacterial biomass surprisingly remained at a record-low during the entire summer of 2003. Critical thresholds of abiotic drivers extracted from the long-term (1993–2007) data set of the studied lake using classification tree analysis (CTA) proved suitable to explain these observations. We found that cyanobacterial blooms were especially favoured in 2006 because thermal stratification was critically intense (Schmidt stability >44 g cm cm⁻²) and long-lasting (>3 weeks). Our results also suggest that some cyanobacterial species (Anabaena sp.) benefitted directly from the stable water column, whereas other species (Planktothrix sp.) took advantage of stratification-induced internal nutrient loading. In 2003, conditions were less favourable for cyanobacteria due to a spell of lower temperatures and stronger winds in mid-summer; as a result, the identified thresholds of thermal stratification were hardly ever reached. Overall, our study shows that extracting critical thresholds of environmental drivers from long-term records is a promising avenue for predicting ecosystem responses to future climate warming. Specifically, our results emphasize that not average temperature increase but changes in short-term meteorological variability will determine whether cyanobacteria will bloom more often in a warmer world.