Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria

Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome

Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.

Ocean acidification alters microeukaryotic and bacterial food web interactions in a eutrophic subtropical mesocosm

Ocean acidification (OA) is known to influence biological and ecological processes, mainly focusing on its impacts on single species, but little has been documented on how OA may alter plankton community interactions. Here, we conducted a mesocosm experiment with ambient (∼410 ppmv) and high (1000 ppmv) CO2 concentrations in a subtropical eutrophic region of the East China Sea and examined the community dynamics of microeukaryotes, bacterioplankton and microeukaryote-attached bacteria in the enclosed coastal seawater. The OA treatment with elevated CO2 affected taxa as the phytoplankton bloom stages progressed, with a 72.89% decrease in relative abundance of the protist Cercozoa on day 10 and a 322% increase in relative abundance of Stramenopile dominated by diatoms, accompanied by a 29.54% decrease in relative abundance of attached Alphaproteobacteria on day 28. Our study revealed that protozoans with different prey preferences had differing sensitivity to high CO2, and attached bacteria were more significantly affected by high CO2 compared to bacterioplankton. Our findings indicate that high CO2 changed the co-occurrence network complexity and stability of microeukaryotes more than those of bacteria. Furthermore, high CO2 was found to alter the proportions of potential interactions between phytoplankton and their predators, as well as microeukaryotes and their attached bacteria in the networks. The changes in the relative abundances and interactions of microeukaryotes between their predators in response to high CO2 revealed in our study suggest that high CO2 may have profound impacts on marine food webs.

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea

In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.

Hierarchical eco-evo dynamics mediated by the gut microbiome

The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.

Gut Microbiota Uniqueness Is Associated with Lake Size, a Proxy for Diet Diversity, in Stickleback Fish

AbstractOrganismal divergence can be driven by differential resource use and adaptation to different trophic niches. Variation in diet is a major factor shaping the gut microbiota, which is crucial for many aspects of their hosts' biology. However, it remains largely unknown how host diet diversity affects the gut microbiota, and it could be hypothesized that trophic niche width is positively associated with gut microbiota diversity. To test this idea, we sequenced the 16S ribosomal RNA gene from intestinal tissue of 14 threespine stickleback populations from lakes of varying size on Vancouver Island, Canada, that have been shown to differ in trophic niche width. Using lake size as a proxy for trophic ecology, we found evidence for higher gut microbiota uniqueness among individuals from populations with broader trophic niches. While these results suggest that diet diversity might promote gut microbiota diversity, additional work investigating diet and gut microbiota variation of the same host organisms will be necessary. Yet our results motivate the question of how host population diversity (e.g., ecological, morphological, genetic) might interact with the gut microbiota during the adaptation to ecological niches.

Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna

The fitness of the host is highly influenced by the interplay between the host and its associated microbiota. The flexible nature of these microbiota enables them to respond swiftly to shifts in the environment, which plays a key role in the host's capacity to withstand environmental stresses. To understand the role of the microbiome in host tolerance to hypoxia, one of the most significant chemical changes occurring in water ecosystems due to climate change, we performed a reciprocal gut transplant experiment with the freshwater crustacean Daphnia magna. In a microbiome transplant experiment, two genotypes of germ-free recipients were inoculated with gut microbiota from Daphnia donors of their own genotype or from the other genotype, that had been either pre-exposed to normoxic or hypoxic conditions. We found that D. magna individuals had a higher survival probability in hypoxia if their microbiome had been pre-exposed to hypoxia. The bacterial communities of the recipients changed over time with a reduction in alpha diversity, which was stronger when donors were pre-exposed to a hypoxic environment. While donor genotype had no influence on the long-term survival probability in hypoxia, donor genotypes was the most influential factor of the microbial community 3 days after the transplantation. Our results indicate that microbiome influencing factors mediate host fitness in a hypoxic environment in a time depending way.

Comparison between the gut bacterial community of laboratory cultured and wild Daphnia

The fitness of an organism is often impacted by the composition and biological activity of its associated bacterial community. Many factors, including host genetics, diet, and temperature can influence the bacterial community composition. Furthermore, these factors can differ strongly between natural and laboratory environments. Consequently, several studies have highlighted results from laboratory experiments investigating host-associated bacterial communities to be conflicting with those obtained under field conditions. Here, we compared the Daphnia magna gut bacterial communities in natural host populations with those of laboratory cultured hosts. We further analyzed changes in the gut bacterial communities after transferring hosts from natural populations to the laboratory on the short- and long-term. Results show that, in general, the gut bacterial communities from natural populations differ from those of laboratory cultures and that their composition and diversity changed one hour after being transferred to the laboratory. Over the following 14 days, the composition and diversity changed gradually. On the longer term (after two years of rearing hosts in the laboratory) the composition and diversity of the gut bacterial communities was strongly altered compared to the initial state. Our findings indicate that the gut bacterial communities of Daphnia magna in laboratory experiments is not representative for natural field conditions, and that caution should be taken when interpreting results from laboratory experiments for natural settings.

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome

Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.

Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes

AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.

Host-bacteriome transplants of the schistosome snail host Biomphalaria glabrata reflect species-specific associations

Microbial symbionts can affect host phenotypes and, thereby, ecosystem functioning. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts, and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here, we report on the first successful snail bacteriome transplants, which indicate that Biomphalaria glabrata can accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness of the donor host significantly affected recipients' survival probability, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance of B. glabrata and might ultimately pave the way for microbiome-mediated control of snail-borne diseases.

Microbiomes in the context of developing sustainable intensified aquaculture

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Gut Microbiota of Freshwater Gastropod (Bellamya aeruginosa) Assist the Adaptation of Host to Toxic Cyanobacterial Stress

Gut microbes play a critical role in helping hosts adapt to external environmental changes and are becoming an important phenotype for evaluating the response of aquatic animals to environmental stresses. However, few studies have reported the role that gut microbes play after the exposure of gastropods to bloom-forming cyanobacteria and toxins. In this study, we investigated the response pattern and potential role of intestinal flora in freshwater gastropod Bellamya aeruginosa when exposed to toxic and non-toxic strains of Microcystis aeruginosa, respectively. Results showed that the composition of the intestinal flora of the toxin-producing cyanobacteria group (T group) changed significantly over time. The concentration of microcystins (MCs) in hepatopancreas tissue decreased from 2.41 ± 0.12 on day 7 to 1.43 ± 0.10 μg·g−1 dry weight on day 14 in the T group. The abundance of cellulase-producing bacteria (Acinetobacter) was significantly higher in the non-toxic cyanobacteria group (NT group) than that in the T group on day 14, whereas the relative abundance of MC-degrading bacteria (Pseudomonas and Ralstonia) was significantly higher in the T group than that in the NT group on day 14. In addition, the co-occurrence networks in the T group were more complex than that in the NT group at day 7 and day 14. Some genera identified as key nodes, such as Acinetobacter, Pseudomonas, and Ralstonia, showed different patterns of variation in the co-occurrence network. Network nodes clustered to Acinetobacter increased in the NT group from day 7 to day 14, whereas the interactions between Pseudomonas and Ralstonia and other bacteria almost changed from positive correlations in the D7T group to negative correlations in the D14T group. These results suggested that these bacteria not only have the ability to improve host resistance to toxic cyanobacterial stress by themselves, but they can also further assist host adaptation to environmental stress by regulating the interaction patterns within the community. This study provides useful information for understanding the role of freshwater gastropod gut flora in response to toxic cyanobacteria and reveals the underlying tolerance mechanisms of B. aeruginosa to toxic cyanobacteria.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Experimental Studies on Zooplankton-Toxic Cyanobacteria Interactions: A Review

Cyanobacterial blooms have been recognized as a problem in fresh water for about 150 years. Over the past 50 years, experimental studies on the subject have gained importance considering the increasing need to control toxic cyanobacterial blooms. This article presents information on the different lines of research that have been undertaken on zooplankton-cyanobacteria interactions over the past 50 years. These include information on filtering/ingestion rates and phytoplankton preferences of small and large rotifers, cladocerans, and copepods; growth rates of zooplankton on cyanobacterial diets; feeding rates of other freshwater invertebrates on cyanobacteria; role of zooplankton in top-down biomanipulation efforts; effect of cyanotoxins on zooplankton; bioaccumulation of cyanotoxins; and physical and chemical control of cyanobacterial blooms. We also highlight measures that have led to successful lake management and improvement of water quality in selected waterbodies.

Effect of allelochemicals sustained-release microspheres on the ingestion, incorporation, and digestion abilities of Daphnia magna Straus

Allelochemicals sustained-release microspheres (ACs-SMs) exhibited great inhibition effect on algae, however, few studies have focused on ACs-SMs toxicity on invertebrate. In this study, the effects of single high-concentration ACs (15 mg/L, SH-ACs), repeated low-concentration ACs (3 × 5 mg/L, RL-ACs) and ACs-SMs containing 15 mg/L ACs exposure on the ingestion, incorporation, and digestion of Daphnia magna Straus (DS) were investigated by stable isotope ¹⁵N labeling method. Meanwhile, the diversity and abundance of microflora in DS guts were determined by 16S rRNA genes and cloning methods. The results showed that SH-ACs exposure caused 50% and 33.3% death rates for newborn and adult DS, while RL-ACs exposure caused 10% death rate for newborn DS and no obvious effect on the activity of adult DS. And ACs-SMs exposure did not diminish the motility of both newborn and adult DS, indicating the lower acute toxicity of ACs-SMs. Furthermore, SH-ACs inhibited the ingestion (-6.45%), incorporation (-47.1%) and digestion (-53.8%) abilities of DS and reduced the microbial abundance (-27.7%) in DS guts. Compared with SH-ACs, RL-ACs showed relatively low impact on the ingestion (-3.23%), incorporation (-5.89%) and digestion (-23.9%) abilities of DS. Interestingly, ACs-SMs enhanced the ingestion (+9.68%), incorporation (+52.9%) and digestion (+51.3%) abilities of DS and increased the microbial abundance (+10.7%) in DS guts. Overall ACs and ACs-SMs reduced the diversity of microflora in DS guts. In conclusion, ACs-SMs can release ACs sustainably and prolong the sustained release time, which not only effectively reduce the toxicity of ACs, but also had positive effects on DS.

Integration of Transcriptomics and Microbiomics Reveals the Responses of Bellamya aeruginosa to Toxic Cyanobacteria

Frequent outbreaks of harmful cyanobacterial blooms and the cyanotoxins they produce not only seriously jeopardize the health of freshwater ecosystems but also directly affect the survival of aquatic organisms. In this study, the dynamic characteristics and response patterns of transcriptomes and gut microbiomes in gastropod Bellamya aeruginosa were investigated to explore the underlying response mechanisms to toxic cyanobacterial exposure. The results showed that toxic cyanobacteria exposure induced overall hepatopancreatic transcriptome changes. A total of 2128 differentially expressed genes were identified at different exposure stages, which were mainly related to antioxidation, immunity, and metabolism of energy substances. In the early phase (the first 7 days of exposure), the immune system may notably be the primary means of resistance to toxin stress, and it performs apoptosis to kill damaged cells. In the later phase (the last 7 days of exposure), oxidative stress and the degradation activities of exogenous substances play a dominant role, and nutrient substance metabolism provides energy to the body throughout the process. Microbiomic analysis showed that toxic cyanobacteria increased the diversity of gut microbiota, enhanced interactions between gut microbiota, and altered microbiota function. In addition, the changes in gut microbiota were correlated with the expression levels of antioxidant-, immune-, metabolic-related differentially expressed genes. These results provide a comprehensive understanding of gastropods and intestinal microbiota response to toxic cyanobacterial stress.

Population dynamics of Brachionus calyciflorus driven by the associated natural bacterioplankton

Zooplankton provides bacteria with a complex microhabitat richen in organic and inorganic nutrients, and the bacteria community also changes the physiochemical conditions for zooplankton, where the symbiotic relationship between them plays an important role in the nutrient cycle. However, there are few studies on the effect of associated bacteria on the population dynamics of rotifers. In order to make clear their relationships, we reconstructed the associated bacterial community in Brachionus calyciflorus culture, and examined the life history and population growth parameters, and analyzed the diversity and community composition of the associated bacteria at different growth stages of B. calyciflorus. The results showed that the addition of bacteria from natural water can promote the population growth and asexual reproduction of B. calyciflorus, but has no significant effect on sexual reproduction, exhibited by the improvement of its life expectancy at hatching, net reproduction rates and intrinsic growth rate, no significant effects on the generation time and mixis ratio of offspring. It was found that the B. calyciflorus-associated bacterial community was mainly composed of Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria and Firmicutes. Through correlation network analysis, the members of Burkholderiales, Pseudomonadales, Micrococcales, Caulobacterales and Bifidobacteriales were the keystone taxa of B. calyciflorus-associated bacteria. In addition, the relative abundance of some specific bacteria strains increased as the population density of B. calyciflorus increased, such as Hydrogenophaga, Acidovorax, Flavobacterium, Rheinheimera, Novosphingobium and Limnobacter, and their relative abundance increased obviously during the slow and exponential phases of population growth. Meanwhile, the relative abundance of adverse taxa (such as Elizabethkingia and Rickettsiales) decreased significantly with the increase in rotifer population density. In conclusion, the closely associated bacteria are not sufficient for the best growth of B. calyciflorus, and external bacterioplankton is necessary. Furthermore, the function of keystone and rare taxa is necessary for further exploration. The investigation of the symbiotic relationship between zooplankton-associated bacterial and bacterioplankton communities will contribute to monitoring their roles in freshwater ecosystems, and regulate the population dynamics of the micro-food web.

Species-Specific Effects of Planktonic Bacteria on the Predator-Induced Life-History Defense of Daphnia: Based on Hierarchical Cluster Analysis and Structural Equation Model

Planktonic bacteria are an important part of aquatic ecosystems and interact with zooplankton. However, it is still unclear whether different planktonic bacteria differentially interfere with the responses of zooplankton to their predators. Here, we investigated the effects of different planktonic bacteria, which were isolated and purified from natural lakes, on the anti-predation (Rhodeus ocellatus as the predator) defense responses of Daphnia magna. Our results showed that the effects of planktonic bacteria on the induced life-history defenses of Daphnia were species-specific. Bacteria which increased (e.g., Escherichia coli, Citrobacter braakii) Daphnia body size also promoted the induced defense of body size, whereas bacteria which decreased (e.g., Pseudomonas spp.) Daphnia body size also inhibited the induced defense of body size. In addition, the same bacteria had different effects on induced defense traits. Some bacteria (e.g., E. coli) promoted the induced defense of body size but reduced the induced defense of offspring number, whereas other bacteria (e.g., Aeromonas hydrophila, Aeromonas veronas) weakened the induced defense of body size but had no significant effect on the induced defense of offspring number. Moreover, the differential effects of planktonic bacteria on Daphnia's induced defenses were not related to the bacterial degradation of kairomone. This study illustrated, for the first time, the species-specific effects of planktonic bacteria on predator-induced responses of Daphnia. IMPORTANCE This study is the first to reveal the differential effects of different species of planktonic bacteria on fish kairomone-induced defense traits and energy redistribution in Daphnia. Our results not only help deepen the understanding of Daphnia's inducible defenses in environments containing a variety of bacteria but also provide insights into the energy reallocation involved in anti-predator defenses.

Gut microbiota and holobiont metabolome composition of the medaka fish (Oryzias latipes) are affected by a short exposure to the cyanobacterium Microcystis aeruginosa

Blooms of toxic cyanobacteria are a common stress encountered by aquatic fauna. Evidence indicates that long-lasting blooms affect fauna-associated microbiota. Because of their multiple roles, host-associated microbes are nowadays considered relevant to ecotoxicology, yet the respective timing of microbiota versus functional changes in holobionts response needs to be clarified. The response of gut microbiota and holobiont's metabolome to exposure to a dense culture of Microcystis aeruginosa was investigated as a microcosm-simulated bloom in the model fish species Oryzias latipes (medaka). Both gut microbiota and gut metabolome displayed significant composition changes after only 2 days of exposure. A dominant symbiont, member of the Firmicutes, plummeted whereas various genera of Proteobacteria and Actinobacteriota increased in relative abundance. Changes in microbiota composition occurred earlier and faster compared to metabolome composition. Liver and muscle metabolome were much less affected than guts, supporting that the gut and associated microbiota are in the front row upon exposure. This study highlights that even short cyanobacterial blooms, that are increasingly frequent, trigger changes in microbiota composition and holobiont metabolome. It emphasizes the relevance of multi-omics approaches to explore organism's response to an ecotoxicological stress.

Incorporating Microbial Species Interaction in Management of Freshwater Toxic Cyanobacteria: A Systems Science Challenge

Water resources are critically important, but also pose risks of exposure to toxic and pathogenic microbes. Increasingly, a concern is toxic cyanobacteria, which have been linked to the death and disease of humans, domesticated animals, and wildlife in freshwater systems worldwide. Management approaches successful at reducing cyanobacterial abundance and toxin production have tended to be short-term solutions applied on small scales (e.g., algaecide application) or solutions that entail difficult multifaceted investments (e.g., modification of landscape and land use to reduce nutrient inputs). However, implementation of these approaches can be undermined by microbial species interactions that (a) provide toxic cyanobacteria with protection against the method of control or (b) permit toxic cyanobacteria to be replaced by other significant microbial threats. Understanding these interactions is necessary to avoid such scenarios and can provide a framework for novel strategies to enhance freshwater resource management via systems science (e.g., pairing existing physical and chemical approaches against cyanobacteria with ecological strategies such as manipulation of natural enemies, targeting of facilitators, and reduction of benthic occupancy and recruitment). Here, we review pertinent examples of the interactions and highlight potential applications of what is known.

Negative Effects of Cyanotoxins and Adaptative Responses of Daphnia

The plethora of cyanobacterial toxins are an enormous threat to whole ecosystems and humans. Due to eutrophication and increases in lake temperatures from global warming, changes in the distribution of cyanobacterial toxins and selection of few highly toxic species/ strains are likely. Globally, one of the most important grazers that controls cyanobacterial blooms is Daphnia, a freshwater model organism in ecology and (eco)toxicology. Daphnia-cyanobacteria interactions have been studied extensively, often focusing on the interference of filamentous cyanobacteria with Daphnia's filtering apparatus, or on different nutritional constraints (the lack of essential amino acids or lipids) and grazer toxicity. For a long time, this toxicity only referred to microcystins. Currently, the focus shifts toward other deleterious cyanotoxins. Still, less than 10% of the total scientific output deals with cyanotoxins that are not microcystins; although these other cyanotoxins can occur just as frequently and at similar concentrations as microcystins in surface water. This review discusses the effects of different cyanobacterial toxins (hepatotoxins, digestive inhibitors, neurotoxins, and cytotoxins) on Daphnia and provides an elaborate and up-to-date overview of specific responses and adaptations of Daphnia. Furthermore, scenarios of what we can expect for the future of Daphnia-cyanobacteria interactions are described by comprising anthropogenic threats that might further increase toxin stress in Daphnia.

Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome

Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.

Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community

Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.

Gut Bacterial Diversity and Community Structure of Spodoptera exigua (Lepidoptera: Noctuidae) in the Welsh Onion-producing Areas of North China

Gut microbiota play an important role in digestion, development, nutritional metabolism, and detoxification in insects. However, scant information exists on the gut bacterial variation, composition, and community structure of the beet armyworm, Spodoptera exigua (Hübner), and how its gut microbiota has adapted to different geographical environments. Using 16S rRNA high-throughput sequencing technology, we detected 3,837,408 high-quality reads and 1,457 operational taxonomic units (OTUs) in 47 gut samples of S. exigua collected from ten sites in northern China. Overall, we identified 697 bacterial genera from 30 phyla, among which Proteobacteria and Firmicutes were the most dominant phyla. Gut bacterial alpha-diversity metrics revealed significant differences among these populations. We detected the highest alpha bacterial diversity in Xinming, northern Liaoning Province, and the lowest bacterial diversity in Zhangwu, western Liaoning Province. Beta diversity indicated that the gut microbial community structure of S. exigua in Liaoning Province was significantly different from that of other populations. There was a similar microbial community structure among populations in the adjacent province, suggesting that the environment influences bacterial succession in this pest. Finally, PICRUSt analysis demonstrated that microbial functions closely associated with the gut microbiomes mainly included membrane transport, carbohydrate metabolism and replication, and amino acid metabolism.

Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species

Chronic antibiotic exposure impacts host health through changes to the microbiome. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied, but less is understood about multigenerational effects of antibiotic exposure and subsequent recovery. In this study, we examined microbiome composition and host fitness across five generations of exposure to antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we examined recovery and resilience of the microbiome. Unexpectedly, we discovered that isolation of single host individuals across generations exerted a strong effect on microbiome composition, with microbiome diversity decreasing over generations regardless of treatment while host body size and cumulative reproduction increased across generations. Though antibiotics did cause substantial changes to microbiome composition within a generation, recovery generally occurred in one generation regardless of the number of prior generations spent in antibiotics. Our results demonstrate that isolation of individual hosts leads to stochastic extinction of less abundant taxa in the microbiome, suggesting that these taxa are likely maintained via transmission in host populations.

Evolution of pesticide tolerance and associated changes in the microbiome in the water flea Daphnia magna

Exposure to pesticides can have detrimental effects on aquatic communities of non-target species. Populations can evolve tolerance to pesticides which may rescue them from extinction. However, the evolution of tolerance does not always occur and insights in the underlying mechanisms are scarce. One understudied mechanism to obtain pesticide tolerance in hosts are shifts toward pesticide-degrading bacteria in their microbiome. We carried out experimental evolution trials where replicated experimental populations of the water flea Daphnia magna were exposed to the pesticide chlorpyrifos or a solvent control, after which we performed acute toxicity assays to evaluate the evolution of chlorpyrifos tolerance. Additionally, we quantified changes in the microbiota community composition of whole body and gut samples to assess which sample type best reflected the pesticide tolerance of the Daphnia host. As expected, chlorpyrifos-selected clones became more tolerant to chlorpyrifos as shown by the higher EC_5048 h (36% higher) compared with the control clones. This was associated with shifts in the microbiome composition whereby the abundance of known organophosphate-degrading bacterial genera increased on average ~4 times in the chlorpyrifos-selected clones. Moreover, the abundances of several genera, including the organophosphate-degrading bacteria Pseudomonas, Flavobacterium and Bacillus, were positively correlated with the EC_5048 h of the host populations. These shifts in bacterial genera were similar in magnitude in whole body and gut samples, yet the total abundance of organophosphate-degrading bacteria was ~6 times higher in the whole body samples, suggesting that the gut is not the only body part where pesticide degradation by the microbiome occurs. Our results indicate that the microbiome is an important mediator of the development of tolerance to pesticides in Daphnia.

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms

BACKGROUND

Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host-microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host-microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1 µm microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed.

RESULTS

Exposure to microplastics and deltamethrin had a direct effect on the microbiome of the species exposed to these pollutants. An indirect effect was also found since exposure to the pollutants at lower trophic levels showed carry over effects on the diversity and abundance of the microbiome on higher trophic levels, even though the organisms at these levels where not directly exposed to the pollutants. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies fed with daphnids that had been exposed to microplastics.

CONCLUSIONS

Our study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.

Responses of Gut Microbial Community Composition and Function of the Freshwater Gastropod Bellamya aeruginosa to Cyanobacterial Bloom

Freshwater gastropods are widely distributed and play an important role in aquatic ecosystems. Symbiotic microorganisms represented by gut microbes can affect the physiological and biochemical activities of their hosts. However, few studies have investigated the response of the gut microbial community of snails to environmental stress. In this study, the dynamics of the gut microbiota of the gastropod Bellamya aeruginosa were tracked to explore their responses in terms of their composition and function to cyanobacterial bloom. Differences in gut microbial community structures during periods of non-cyanobacterial bloom and cyanobacterial bloom were determined. Results showed that the alpha diversity of the gut microbiota exposed to cyanobacterial bloom was lower than that of the gut microbiota exposed to non-cyanobacterial bloom. The main genera differentiating the two periods were Faecalibacterium, Subdoligranulum, Ralstonia, and Pelomonas. Microcystins (MCs) and water temperature (WT) were the primary factors influencing the gut microbial community of B. aeruginosa; between them, the influence of MCs was greater than that of WT. Fourteen pathways (level 2) were notably different between the two periods. The pathways of carbohydrate metabolism, immune system, environmental adaptation, and xenobiotics biodegradation and metabolism in these differential pathways exhibited a strong linear regression relationship with MCs and WT. Changes in the functions of the gut microbiota may help B. aeruginosa meet its immunity and energy needs during cyanobacterial bloom stress. These results provide key information for understanding the response pattern of freshwater snail intestinal flora to cyanobacterial blooms and reveal the underlying environmental adaptation mechanism of gastropods from the perspective of intestinal flora.

Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism

Microbes perform a variety of vital functions that are essential for healthy ecosystems, ranging from nutrient recycling, antibiotic production and waste decomposition. In many animals, microbes become an integral part by establishing diverse communities collectively termed as "microbiome/s". Microbiomes defend their hosts against pathogens and provide essential nutrients necessary for their growth and reproduction. The microbiome is a polygenic trait that is dependent on host genotype and environmental variables. However, the alteration of microbiomes by stressful condition and their recovery is still poorly understood. Despite rapid growth in host-associated microbiome studies, very little is known about how they can shape ecological processes. Here, we review current knowledge on the microbiome of Daphnia, its role in fitness, alteration by different stressors, and the ecological and evolutionary aspects of host microbiome interactions. We further discuss how variation in Daphnia physiology, life history traits, and microbiome interactive responses to biotic and abiotic factors could impact patterns of microbial diversity in the total environment, which drives ecosystem function in many freshwater environments. Our literature review provides evidence that microbiome is essential for Daphnia growth, reproduction and tolerance against stressors. Though the core and flexible microbiome of Daphnia is still debatable, it is clear that the Daphnia microbiome is highly dependent on interactions among host genotype, diet and the environment. Different environmental factors alter the microbiome composition and diversity of Daphnia and reduce their fitness. These interactions could have important implications in shaping microbial patterns and their recycling as Daphnia are keystone species in freshwater ecosystem. This review provides a framework for studying these complex relationships to gain a better understanding of the ecological and evolutionary roles of the microbiome.

More Light Please: Daphnia Benefit From Light Pollution by Increased Tolerance Toward Cyanobacterial Chymotrypsin Inhibitors

Cryptochromes are evolutionary ancient blue-light photoreceptors that are part of the circadian clock in the nervous system of many organisms. Cryptochromes transfer information of the predominant light regime to the clock which results in the fast adjustment to photoperiod. Therefore, the clock is sensitive to light changes and can be affected by anthropogenic Artificial Light At Night (ALAN). This in turn has consequences for clock associated behavioral processes, e.g., diel vertical migration (DVM) of zooplankton. In freshwater ecosystems, the zooplankton genus Daphnia performs DVM in order to escape optically hunting predators and to avoid UV light. Concomitantly, Daphnia experience circadian changes in food-supply during DVM. Daphnia play the keystone role in the carbon-transfer to the next trophic level. Therefore, the whole ecosystem is affected during the occurrence of cyanobacteria blooms as cyanobacteria reduce food quality due to their production of digestive inhibitors (e.g., protease inhibitors). In other organisms, digestion is linked to the circadian clock. If this is also the case for Daphnia, the expression of protease genes should show a rhythmic expression following circadian expression of clock genes (e.g., cryptochrome 2). We tested this hypothesis and demonstrated that gene expression of the clock and of proteases was affected by ALAN. Contrary to our expectations, the activity of one type of proteases (chymotrypsins) was increased by ALAN. This indicates that higher protease activity might improve the diet utilization. Therefore, we treated D. magna with a chymotrypsin-inhibitor producing cyanobacterium and found that ALAN actually led to an increase in Daphnia’s growth rate in comparison to growth on the same cyanobacterium in control light conditions. We conclude that this increased tolerance to protease inhibitors putatively enables Daphnia populations to better control cyanobacterial blooms that produce chymotrypsin inhibitors in the Anthropocene, which is defined by light pollution and by an increase of cyanobacterial blooms due to eutrophication.

Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer

Gut microbiota forms a unique microecosystem and performs various irreplaceable metabolic functions for ruminants. The gut microbiota is important for host health and provides new insight into endangered species conservation. Forest musk deer (FMD) and alpine musk deer (AMD) are typical small ruminants, globally endangered due to excessive hunting and habitat loss. Although nearly 60 years of captive musk deer breeding has reduced the hunting pressure in the wild, fatal gastrointestinal diseases restrict the growth of captive populations. In this study, 16S rRNA high-throughput sequencing revealed the differences in gut microbiota between FMD and AMD based on 166 fecal samples. The alpha diversity was higher in FMD than in AMD, probably helping FMD adapt to different and wider habitats. The ß-diversity was higher between adult FMD and AMD than juveniles and in winter than late spring. The phylum Firmicutes and the genera Christensenellaceae R7 group, Ruminococcus, Prevotellaceae UCG-004, and Monoglobus were significantly higher in abundance in FMD than in AMD. However, the phylum Bacteroidetes and genera Bacteroides, UCG-005, Rikenellaceae RC9 gut group, and Alistipes were significantly higher in AMD than FMD. The expression of metabolic functions was higher in AMD than in FMD, a beneficial pattern for AMD to maintain higher energy and substance metabolism. Captive AMD may be at higher risk of intestinal diseases than FMD, with higher relative abundances of most opportunistic pathogens and the expression of disease-related functions. These results provide valuable data for breeding healthy captive musk deer and assessing their adaptability in the wild. KEY POINTS: • Alpha diversity of gut microbiota was higher in FMD than that in AMD • Expression of metabolic and disease-related functions was higher in AMD than in FMD.

Specialised digestive adaptations within the hindgut of a colobine monkey

In mammal herbivores, fiber digestion usually occurs predominantly in either the foregut or the hindgut. Reports of mechanisms showing synergistic function in both gut regions for the digestion of fiber and other nutrients in wild mammals are rare because it requires integrative study of anatomy, physiology, and gut microbiome. Colobine monkeys (Colobinae) are folivorous, with high-fiber foods fermented primarily in their foreguts. A few colobine species live in temperate regions, so obtaining energy from fiber during the winter is essential. However, the mechanisms enabling this remain largely unknown. We hypothesized that such species possess specialized mechanisms to enhance fiber digestion in the hindgut and studied microbial and morphological digestive adaptations of golden snub-nosed monkeys (GSMs), Rhinopithecus roxellana. which is a temperate forest colobine from central China that experiences high-thermal-energy demands while restricted to a fibrous, low-energy winter diet. We tested for synergistic foregut and hindgut fiber digestion using comparisons of morphology, microbiome composition and function, and digestive efficiency. We found that the GSM colon has a significantly greater volume than that of other foregut-fermenting colobines. The microbiomes of the foregut and hindgut differed significantly in composition and abundance. However, while digestive efficiency and the expression of microbial gene functions for fiber digestion were higher in the foregut than in the hindgut, both gut regions were dominated by microbial taxa producing enzymes to enable active digestion of complex carbohydrates. Our data suggest that both the GSM foregut and hindgut facilitate fiber digestion and that an enlarged colon is likely an adaptation to accommodate high throughput of fiber-rich food during winter.

•

How folivores extract adequate nutrition from their ultra-high-fiber diets remains unclear

•

We studied the morphology, microbiome and digestive efficiency of gut for R. roxellana (GSM)

•

Both fore- and hind-gut regions of GSM play important function of digesting complex carbohydrates

•

An enlarged colon of GSM likely accommodates a high throughput of fiber-rich food during winter

Microbiota-Dependent and -Independent Production of l-Dopa in the Gut of Daphnia magna

Host-microbiome interactions are essential for the physiological and ecological performance of the host, yet these interactions are challenging to identify. Neurotransmitters are commonly implicated in these interactions, but we know very little about the mechanisms of their involvement, especially in invertebrates. Here, we report a peripheral catecholamine (CA) pathway involving the gut microbiome of the model species Daphnia magna. We demonstrate the following: (i) tyrosine hydroxylase and Dopa (3,4-dihydroxyphenylalanine) decarboxylase enzymes are present in the gut wall; (ii) Dopa decarboxylase gene is expressed in the gut by the host, and its expression follows the molt cycle peaking after ecdysis; (iii) biologically active l-Dopa, but not dopamine, is present in the gut lumen; (iv) gut bacteria produce l-Dopa in a concentration-dependent manner when provided l-tyrosine as a substrate. Impinging on gut bacteria involvement in host physiology and ecologically relevant traits, we suggest l-Dopa as a communication agent in the host-microbiome interactions in daphnids and, possibly, other crustaceans.

IMPORTANCE Neurotransmitters are commonly implicated in host-microbiome communication, yet the molecular mechanisms of this communication remain largely elusive. We present novel evidence linking the gut microbiome to host development and growth via neurotransmitter l-Dopa in Daphnia, the established model species in ecology and evolution. We found that both Daphnia and its gut microbiome contribute to the synthesis of the l-Dopa in the gut. We also identified a peripheral pathway in the gut wall, with a molt stage-dependent dopamine synthesis, linking the gut microbiome to the daphnid development and growth. These findings suggest a central role of l-Dopa in the bidirectional communication between the animal host and its gut bacteria and translating into the ecologically important host traits suitable for subsequent testing of causality by experimental studies.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Host Dependence of Zooplankton-Associated Microbes and Their Ecological Implications in Freshwater Lakes

Zooplankton is colonized by quite different microbes compared with free-living and particle-associated bacteria, serving as a non-negligible niche of bacteria in aquatic ecosystems. Yet detailed analysis of these bacterial groups is still less known, especially in freshwater lakes. To widen our knowledge of host-microbe interaction and bacterial ecosystem functions, we chose two specific populations of zooplankton, i.e., cladoceran Moina and copepod Calanoids, as hosts from five natural lakes, and illustrated detailed features of their associated bacteria. Through 16S rRNA gene sequencing, we found microbes colonized on Calanoids presented significantly higher α-diversity, stronger bacterial interaction and metabolic function potentials than for Moina. It was also notable that zooplankton-associated bacteria showed a high potential of fatty acid metabolism, which is beneficial for host’s development. Moreover, we found that zooplankton-associated microbes may exert profound effects on biogeochemical cycles in freshwater lakes, since several bacterial members able to participate in carbon and nitrogen cycles were found abundant. Overall, our study expands current understanding of the host-microbe interaction and underlying ecological dynamics in freshwater ecosystem.

Daphnia populations are similar but not identical in tolerance to different protease inhibitors

Cyanobacterial blooms often produce different classes and chemical variants of toxins such as dietary protease inhibitors (PIs) that affect the keystone grazer Daphnia. However, it has been shown that Daphnia populations are able to locally adapt to frequently occurring dietary PIs by modulating their digestive proteases. Up until now, local adaptation has exclusively been tested by making use of single cyanobacterial strains and by measuring average population tolerance. In contrast, we measured juvenile somatic growth rates and egg numbers of several individual clones per each of three different D. magna populations that have previously been found to be either tolerant or sensitive to the Microcystis strain BM25. Clones from the three D. magna populations were either treated with BM25 that produces three different protease inhibitor variants of the class of Ahp-cyclodepsipeptides or another Microcystis strain that produces two other Ahp-cyclodepsipeptide variants. Subsequently, the population growth was calculated as mean of the single-clone growth rates. Both tolerant populations (which originate from ponds with a cyanobacterial history) proved to be similarly tolerant to both Microcystis strains. However, single genotypes of the populations differed in their response to the different strains. Both the tolerant and the sensitive populations contained both sensitive and tolerant genotypes but in different proportions. Furthermore, the genotypes from the sensitive population showed a higher variance in response to one or both strains. Trade-offs between somatic growth rate and clutch size were found in one of the tolerant populations that originated from a pond where cyanobacteria were frequent in the past but completely absent since the pond's restoration. Because of those intra-population difference, we conclude that the tolerant populations were putatively selected by different Ahp-cyclodepsipeptide variants in the past and that all populations still possess the potential to adapt to other environmental conditions by genotype frequency shifts.

Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar)

Understanding the effects of environmental disturbances on insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts are known to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. In this study, subterranean termites [Reticulitermes flavipes (Kollar)] were exposed to three different temperature treatments characterized as low (15°C), medium (27°C), and high (35°C). Results suggested that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites also showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termite's physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.

Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially

Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness.

IMPORTANCE Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments.

Locally adapted gut microbiomes mediate host stress tolerance

While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.

A review: Application of allelochemicals in water ecological restoration--algal inhibition

Problems caused by harmful algal blooms have attracted worldwide attention due to their severe harm to aquatic ecosystems, prompting researchers to study applicable measures to inhibit the growth of algae. Allelochemicals, as secondary metabolites secreted by plants, have excellent biocompatibility, biodegradability, obvious algal inhibiting effect and little ecological harm, and have promising application prospect in the field of water ecological restoration. This review summarized the research progress of allelochemicals, including (i) definition, development, and classification, (ii) influencing factors and mechanism of algal inhibition, (iii) the preparation methods of algal inhibitors based on allelochemicals. The future research directions of allelochemicals sustained-released microspheres (SRMs) were also prospected. In the future, it is urgent to explore more efficient allelochemicals, to study the regulation mechanism of allelochemicals in natural water bodies, and to improve the preparation method of allelopathic algal suppressant. This paper proposed a feasible direction for the development of allelochemicals SRMs which exhibited certain guiding significance for their application in water ecological restoration.

Invasive freshwater snails form novel microbial relationships

Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact on microbiota and the host-microbiome relationship (e.g., how rapidly new microbial associations are formed, whether microbes influence invasion success). We used high-throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, their microbial community is largely distinct. This finding highlights that invasions can result in the formation of novel host-microbiome relationships. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to a narrower set of core members. Furthermore, native snails exhibit relatively low alpha diversity but high inter-individual variation, whereas invasive snails have higher alpha diversity but are relatively similar to each other. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.

Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment

The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co-evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species-specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of "core" microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co-evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host-microbiome association to originate and persist.

Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)

Simple Summary

Copepods are important components of marine coastal food chains, supporting fishery resources by providing prey items mainly for fish. Copepods interact with small microorganisms via feeding on phytoplankton. DNA methods can determine the gut contents of copepods and provide important information regarding how copepods interact with phytoplankton and bacteria. In the present study, we designed a method for extracting the gut content DNA from small-sized copepods that are important in coastal and brackish areas. Based on DNA analyses, Rhodobacteraceae, which is common in marine waters and sediments, was most abundant in the gut contents of the three copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus). However, the detailed composition of bacteria was different among species and locations. The results suggested that environmental variables and species-specific feeding behaviour can affect the gut bacterial community. The bacteria play an important role in digestion and in the overall degradation and release of metabolites to the outside water. Further analyses with advanced methods regarding DNA isolation from small microorganisms and identification skills using a DNA library for better understanding of biological interactions and matter cycling in marine food webs are required.

Abstract

The gut bacterial communities of copepods can affect metabolic processes, and consequently, their activity can be related to the release of organic substances to the environment. Hence, they are important for organic matter cycling in marine coast food webs. However, information regarding the variation in gut bacterial communities based on copepod species and environmental variations is limited. We analysed the differences in gut bacterial communities from dominant copepod species, i.e., Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus, in a brackish reservoir. The core bacteria among the copepod species and locations consisted of the following main operational taxonomic units (OTUs): Novosphingobium capsulatum and the family Rhodobacteraceae belonging to Alphaproteobacteria, which is abundant in seawater and freshwater aquatic ecosystems as a zooplankton-associated bacterial community. The bacterial community composition of each copepod (except the core species) showed high variability. The bacterial community diversity differed depending on the copepod species and the sites’ environmental conditions, especially salinity, e.g., compositional variations in the bacterial community of P. inopinus were high at sites with low salinity. Therefore, the gut bacterial community of each copepod species responds differently to the environment.

Elevated temperature and toxic Microcystis reduce Daphnia fitness and modulate gut microbiota

The gut microbiota has been increasingly recognized to regulate host fitness, which in turn is dependent on stability of community structure and composition. Many biotic and abiotic factors have been demonstrated to shape gut microbiota of cladocerans. However, the interactive effects of these variables on cladocerans fitness due to alteration of gut microbiota and their linkage with life history parameters are poorly understood. Here, we investigated the responses of Daphnia magna gut microbiota to the combined effects of toxic Microcystis aeruginosa and high temperature and its associations with fitness. We found that under good food regime, the temperature has no effect on the composition of the gut microbiota, whereas under high proportion of toxic M. aeruginosa and high temperature conditions, D. magna lost their symbionts. High proportion of toxic M. aeruginosa and high temperature had synergistically negative effects on D. magna performance due to altered gut microbiota. The high abundance of symbiotic Comamonadaceae and good food increased D. magna fitness. The present study illustrates that understanding life history strategies in response to multiple stressors related to changes in the gut microbiota diversity and composition requires integrated approaches that incorporate multiple linked traits and tether them to one another.

How Copepods Can Eat Toxins Without Getting Sick: Gut Bacteria Help Zooplankton to Feed in Cyanobacteria Blooms

Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of mlrA genes in the gut of the Baltic copepods Acartia bifilosa and Eurytemora affinis during cyanobacteria bloom season (August) and outside it (February). The mlrA genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The mlrA genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in Eurytemora than Acartia. To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the mlrA abundance in the microbiota affect: (1) uptake of toxic Nodularia spumigena, (2) uptake of a non-toxic algal food offered in mixtures with N. spumigena, and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of mlrA genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.