Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water

Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins

Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.

IMPORTANCE

Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.

From Sea to Freshwater: Shared and Unique Microbial Traits in Sponge Associated Prokaryotic Communities

Despite their ecological significance and biotechnological potential, freshwater sponges remain relatively understudied compared to their marine counterparts. In special, the prokaryotic communities of species from isolated yet highly diverse ecosystems, such as the Amazon Rainforest, remain unknown, leaving an important part of the Porifera microbiome underexplored. Using high-throughput sequencing of the 16S rRNA gene, we unraveled the structure of the microbiota associated to the freshwater sponges Heteromeyenia cristalina and Metania reticulata for the first time. Their microbiome was compared with that of the haplosclerid marine sponges Amphimedon viridis and Haliclona melana; and the tetractinellid Cinachyrella alloclada. Our findings reveal not only a shared core microbiome between the freshwater and marine environments but also indicate functional redundancy in their communities, suggesting that certain microbial metabolic functions are conserved across diverse habitats. Comparisons between ecosystems also revealed that microbiomes of freshwater sponges can be richer and more diverse than those of marine species. Moreover, we compared the microbiome of adults and asexual reproduction structures (buds and gemmules) of sponges from both habitats, revealing a remarkable similarity between adults and their respective offsprings, indicating an important role of vertical transmission in this mode of reproduction. Our observations emphasize the dynamic interactions and the adaptability of the sponge-associated microbiota, providing insights into how these symbiotic associations were affected during the colonization of freshwater environments and shedding light into how symbiotic relationships are maintained throughout generations.

Low Genetic Diversity and Complex Population Structure in Black Piranha (Serrasalmus rhombeus), a Key Amazonian Predator

The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white, and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

Response processes to water quality changes driven by the dynamic regeneration of the surface microlayer film in slow-flowing freshwater bodies

The freshwater surface microlayer film (SMF) is a dynamically evolving micro-ecosystem closely related to water quality and microbial growth in water. However, the mechanisms of dynamic regeneration of SMF after their destruction and their impacts on the aquatic environment are still largely unknown. Herein, we modeled the dynamic processes of SMF destruction and recovery in the natural environment by constructing a water-SMF ecosystem. Chemical and biological changes in the dynamic regeneration of SMF were investigated. The results showed that the dynamic regeneration of SMF was very fast, with a regeneration thickness of up to 300 ± 50 μm in two days, and at the same time, it would rapidly enrich organic matter and Fe ions. In addition, the cyclic dynamic regeneration process of SMF is significantly correlated with the surge metabolic growth of microorganisms associated with organic matter metabolism (e.g., Methylophilus, Nevskia) and iron-redox-associated (e.g., Curvibacter). The experimental results suggest that the microbial-mediated process of iron-organic matter coupled oxidation-reduction in SMF may be another important mechanism driving water quality changes. Overall, our study provides valuable theoretical guidance for predicting changes in water quality in slow-flowing water bodies.

Chlormequat inhibits Vallisneria natans growth and shapes the epiphytic biofilm microbial community

Submerged macrophytes can overgrow and negatively affect freshwater ecosystems. This study aimed to investigate the use of chlormequat (CQ) to regulate submerged Vallisneria natans growth as well as its impact on the microbial community of epiphytic biofilms. V. natans height under CQ dosages of 20, 100, and 200 mg/L decreased within 21 days by 12.57%, 30.07%, and 44.62%, respectively, while chlorophyll content increased by 1.94%, 20.39%, and 38.83%. At 100 mg/L, CQ reduced the diversity of bacteria in the biofilm attached to V. natans leaves but increased the diversity of the eukaryotic microbial community. CQ strongly inhibited Cyanobacteria; compared with the control group, the treatment group experienced a significant reduction from 36.54% to 2.61%. Treatment significantly inhibited Gastrotricha and Rotifera, two dominant phyla of eukaryotes in the leaf biofilm, reducing their relative abundances by 17.41% and 6.48%, respectively. CQ significantly changed the leaf biofilm microbial community correlation network. The treatment group exhibited lower modularity (2.012) compared with the control group (2.249); however, the central network of the treated group contained a higher number of microbial genera (13) than the control group (4), highlighting the significance of eukaryotic genera in the network. The results obtained from this study provide invaluable scientific context and technical understanding pertinent to the restoration of submerged macrophytes within aquatic ecosystems. PRACTITIONER POINTS: Chlormequat reduced the plant height but increased leaf chlorophyll content. Chlormequat reduced biofilm bacterial diversity but increased eukaryotic diversity. Chlormequat affected the bacterial-fungal association networks in biofilms.

Characterizing the regional distribution, interaction with microorganisms, and sources of dissolved organic matter for summer rainfall: Insights from spectroscopy, community structure, and back-trajectory analyses

Dissolved organic matter (DOM) in rainfall participates in many biogeochemical cycles in aquatic environments and affects biological activities in water bodies. Revealing the characteristics of rainfall DOM could broaden our understanding of the carbon cycle. Therefore, the distribution characteristics and response mechanisms of DOM to microorganisms were investigated in different regions of Hebei. The results indicated that the water quality of the northern region was worse than that of the middle and southern regions. The two protein like components (C1, C2) and one humic like component (C3) were obtained; at high molecular weight (MW), the fluorescence intensity is high in the northern region (0.03 ± 0.02 R.U.), while at low MW, the fluorescence intensity is highest in the southern region (0.50 ± 0.18 R.U.). Furthermore, C2 is significantly positively correlated with C1 (P < 0.01), while C2 is significantly negatively correlated with C3 (P < 0.05) was observed. The spectral index results indicated that rainfall DOM exhibited low humification and highly autochthonous characteristics. The southern region obtained higher richness and diversity of microbial species than northern region (P < 0.05). The community exhibits significant spatiotemporal differences, and the Acinetobacter, Enterobacter, and Massilia, were dominant genus. Redundancy and network analyses showed that the effects of C1, C2, and nitrate on microorganisms increased with decreasing MW, while low MW exhibited a more complex network between DOM and microorganisms than high MW. Meanwhile, C1, C2 had a large total effect on β-diversity and function through structural equation modeling. The backward trajectory model indicates that the sources of air masses are from the northwest, local area, and sea in the northern, middle, and southern regions, respectively. This study broadened the understanding of the composition of summer rainfall DOM and its interactions with microorganisms during rainfall.

Interwoven processes in fish development: microbial community succession and immune maturation

Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.

Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems

Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.

Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters

Amazonian blackwaters are extremely biodiverse systems containing some of Earth's most naturally acidic, dissolved organic carbon -rich and ion-poor waters. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16 S rRNA of gill samples. We find that host transcriptional responses to blackwaters are species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish survive poorly when exposed to sterile/inverted blackwater. Overall, our results suggest a critical role for endogenous symbionts in blackwater fish physiology.