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Abstract Animals must invest some portion of their metabolism to activities related to physiological maintenance and the remainder to processes related to the production of new biomass for growth and reproduction. Animal metabolism is fuelled by food, and the quality and quantity of food, along with the effort invested to obtain it, are fundamental to supporting populations. Biofilms are a primary basal food resource within riverine food webs, and it is thought that their nutritional value for animals decreases with age due to dynamic changes in community composition. We sought to test assumptions of spatiotemporal changes to biofilm nutritional value by assessing variations in biofilm mass and fatty acid composition in three rivers for 73 days. We also used a multi‐prong eDNA approach to characterize changes to biofilm fungal (ITS1–4), bacterial (16S), and algal (23S) community compositions. We anticipated biofilm food value to decrease with biofilm age due to shifts in composition from high‐quality green algae and diatoms to low‐quality cyanobacteria and filamentous algae. Our results partially support this contention; biofilm food value, assessed as a combination of fatty acid mass per unit area (in grams per square meter) and concentration of fatty acids (in milligrams per gram), was dynamic and peaked between 24 and 43 days following submersion. After 43 days, biofilm food value decreased. However, despite significant temporal changes in biofilm community composition and a decrease in overall lipid concentration, the proportions of different fatty acid classes among total lipids did not vary. Instead, the observed increase in the abundance of cyanobacteria and filamentous algae compared with diatoms and green algae, along with higher quantities of lipid‐poor extracellular polymeric substances (EPS), likely contributed to the reduction in overall lipid concentration relative to the biofilm dry mass. Here we present a novel approach to balance consumer energetic costs with food quality within aquatic food webs. Our results have important implications for river management and provide valuable information for the use of environmental water to support lotic ecosystems.

ABSTRACT A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.

ABSTRACT The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth’s most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.

ABSTRACT Fish bacterial communities provide functions critical for their host’s survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host’s genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities’ structure, while pairwise fixation indexes (FST) from the hosts’ genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host’s genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.

Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologically driven genetic divergence between fish present in both water types. With the objective of better understanding the evolutionary forces behind the central Amazonian teleostean diversification, we sampled 240 Mesonauta festivus from 12 sites on a wide area of the Amazonian basin. These sites included three confluences of black and white water environments to seek for repeated evidences of ecological divergence at the junction of these ecotones. Results obtained through our genetic assessment based on 41,268 single nucleotide polymorphism (SNPs) contrast with previous findings and support a low influence of diverging water physicochemical characteristics on the genetic structuration of M. festivus populations. Conversely, we detected patterns of isolation by downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetics, phylogeographic analysis and environmental association models, we decomposed the spatial and environmental genetic variances to assess which evolutionary forces shaped inter-population differences in M. festivus’ genome. Our sampling design, comprising three confluences of black and white water rivers, supports the main role of evolution by allopatry. While an ecologically driven evolution admittedly played a role in Amazonian fish diversification, we argue that neutral evolutionary processes explain most of the divergence between M. festivus populations.

Contamination of freshwaters is increasing globally, with microalgae considered one of the most sensitive taxa to metal pollution. Here, we used 72 h bioassays to explore the biochemical effects of copper (Cu) on the amino acid (AA) profile and proteome of Chlorella sp. and advance our understanding of the molecular changes that occur in algal cells during exposure to environmentally realistic Cu concentrations. The Cu concentrations required to inhibit algal growth rate by 10% (EC10) and 50% (EC50) were 1.0 (0.7–1.2) µg L−1 and 2.0 (1.9–2.4) µg L−1, respectively. The AA profile of Chlorella sp. showed increases in glycine and decreases in isoleucine, leucine, valine, and arginine, with increasing Cu. Proteomic analysis revealed the modulation of several proteins involved in energy production pathways, including: photosynthesis, carbon fixation, glycolysis, and oxidative phosphorylation, which likely assists in meeting increased energy demands under Cu-stressed conditions. Copper exposure also caused up-regulation of cellular processes and signalling proteins, and the down-regulation of proteins related to ribosomal structure and protein translation. These changes in biomolecular pathways have direct effects on the AA profile and total protein content and provide an explanation for the observed changes in amino acid profile, cell growth and morphology. This study shows the complex mode of action of Cu on Chlorella under environmentally realistic Cu concentrations and highlights several potential biomarkers for future investigations.

Cladocerans are important filter-feeders transferring energy up the food web to different invertebrate and vertebrate predators. Along the flood period, cladocerans are one of the primary food sources for juvenile fish in floodplain. Resting egg banks allow cladoceran populations to overcome the environmental stress, related to several limnological changes, including complete drying of temporary wetlands. After drought, resting egg banks influence cladoceran community attributes during the cyclic and successional processes driven by episodic flood events. In this study we compared the taxonomic richness of active (from the water column) and dormant (from the sediment) Cladocera assemblages and analyzed the structure of resting egg banks, comparing the diversity, abundance and apparent viability/unviability of the eggs, between six temporary and six permanent wetlands, located along the Ovens River Floodplain, Victoria, Australia. The qualitative analysis shows higher taxonomic richness in active assemblages from temporary (24 taxa) than permanent (13 taxa) wetlands compared to dormant assemblages present in resting egg banks (9 taxa) from temporary and permanent wetlands. However, richness was influenced by taxonomic level of identification, with the majority of resting eggs only being identified to the taxonomic level of family (i.e. Chydoridae). Total taxa richness within egg banks was similar between wetland types, however, on average higher Shannon’s diversity of resting eggs was found within permanent (1.53) than temporary (0.82) wetlands. This is likely to be due to more stable wetlands not providing appropriate cues to trigger dormancy induction or breakage for specific populations, leading to higher values of evenness in permanent than temporary wetlands. Comparing permanent and temporary wetlands, higher abundance of resting eggs (more than four times) consisting of higher abundance of unviable eggs and similar viable egg abundance to permanent wetlands, was found within temporary wetlands, suggesting that the increased resting egg abundance in temporary wetlands is balanced by the losses due to factors such as predation, parasitism or other physical damage, during the terrestrial phase. Despite resistant outer shell structure, this study highlights that the damage to egg integrity is intensified in wetlands that undergo dry phases. Cladoceran resting egg banks represent the potential assemblage to recover after disturbance events such as drying, and information about these is important to ensure appropriate management and conservation of floodplain biodiversity.

To date, most research on freshwater cyanotoxin(s) has focused on understanding the dynamics of toxin production and decomposition, as well as evaluating the environmental conditions that trigger toxin production, all with the objective of informing management strategies and options for risk reduction. Comparatively few research studies have considered how this information can be used to understand the broader ecological role of cyanotoxin(s), and the possible applications of this knowledge to the management of toxic blooms. This paper explores the ecological, toxicological, and genetic evidence for cyanotoxin production in natural environments. The possible evolutionary advantages of toxin production are grouped into two main themes: That of “competitive advantage” or “physiological aide”. The first grouping illustrates how compounds produced by cyanobacteria may have originated from the need for a cellular defence mechanism, in response to grazing pressure and/or resource competition. The second grouping considers the contribution that secondary metabolites make to improved cellular physiology, through benefits to homeostasis, photosynthetic efficiencies, and accelerated growth rates. The discussion also includes other factors in the debate about possible evolutionary roles for toxins, such as different modes of exposures and effects on non-target (i.e., non-competitive) species. The paper demonstrates that complex and multiple factors are at play in driving evolutionary processes in aquatic environments. This information may provide a fresh perspective on managing toxic blooms, including the need to use a “systems approach” to understand how physico-chemical conditions, as well biological stressors, interact to trigger toxin production.

Adverse impacts of acidification on aquatic biota have been observed worldwide; however, most reports are based on fresh waters acidified by anthropogenic means. By contrast, naturally low pH values may not affect biota within naturally acidic fresh waters. This field study provides information on the water quality, macroinvertebrate and fish communities in little-studied, naturally acidic wallum streams in Central Queensland, Australia. Mid-range pH sites (pH 5-6) were compared with low pH sites (pH 5-3.8) to investigate the effect of pH and other key water quality variables on these communities. Field data indicated that pH had less of an effect in these systems in terms of biotic changes compared with other water quality variables, with dissolved oxygen (% saturation) identified as the key driver for changes in macroinvertebrate composition. Fish were present at all sites, including those with pH <4. Several possible explanations for this lack of pH effect are discussed. These results provide support for the reduced importance of acidity, relative to other water quality parameters, in naturally acidic waters. The work also provides baseline data on the biota of little-studied wallum streams. Adverse impacts of acidification on aquatic biota have been observed worldwide; however, most reports are based on anthropogenically acidified fresh waters rather than naturally acidic systems. This study aimed to investigate the effect of decreased pH on macroinvertebrate and fish communities within naturally acidic (wallum) streams. The results provide support for the reduced importance of acidity in naturally acidic waters. [ABSTRACT FROM AUTHOR]