Nitrite is a common pollutant that can enter waterways via agricultural runoff or build up in aquaculture ponds when nitrogenous waste is converted to nitrite. Preliminary studies by the Huertas lab ...found that exposure to sublethal concentrations of aquatic nitrite alters the microbiome of goldfish and bioaccumulates in the olfactory epithelia, gills and brain. These studies also showed a negative impact on the olfactory tissue of exposed fish, which could lead to higher susceptibility to nasal pathogens. Our objective is to assess nitrite bioaccumulation in tissues and the alteration of the microbiome in the key aquaculture species channel catfish (Ictalurus punctatus). We hypothesize that the relative abundance and diversity of bacteria in the nose and gut microbiomes of channel catfish will be altered due to elevated nitrite exposure and that nitrite will bioaccumulate in tissues.
Channel catfish were exposed to 0 mM (control), 0.2 mM, and 2 mM concentrations of nitrite. A total of six 500 liter tanks were used in a two‐phase experiment. For phase one, 16 fish per tank were placed into three 0 mM nitrite tanks and three 2 mM nitrite tanks. The 2 mM fish were kept for 12 hours before sampling. For phase two, 24 of the phase one control fish were placed into three 0.2 mM tanks and the remaining 24 control fish were left in the three control tanks for a total of 8 fish per tank. Phase two lasted 30 days with sub‐samplings at day five and 30. All fish were sampled for nose, gut, muscle, gill, brain, blood, liver, and kidney tissues for biochemical, microbial, or histological analysis. Upon dissection, fish from the 2 mM tanks exhibited marked methemoglobinemia due to nitrite‐induced oxidation of hemoglobin. The mortality rates were 0.04%, 0.08%, and 92% for the control, 0.2 mM, and 2 mM treatments respectively. The nose and gut microbiomes will be sequenced using whole genome shotgun sequencing to determine the microbial composition and measure changes in relative abundance. Histological analysis showed oxidative damage in all tissues from individuals exposed to 2 mM and partial damage in tissues of the 0.2 mM treatment.
Because the microbiome is a powerful barrier against pathogens, disruption of the microbiome could lead to higher rates of disease infection and transmission in fish. Alteration of the nasal microbiome may increase mortality from the bacteria that cause septicemia in catfish, Edwardsiella ictaluri, whose common routes of infection are the nose or gut. Changes to the microbiome could be the missing link between nitrite and increased susceptibility to E. ictaluri infections in intensive farming. In the long term, this research aims to provide guidelines for water quality management in order to decrease the rate of bacterial infection and transmission in aquaculture systems.
Diet is an external factor that affects the physiological baseline of research animals. It can shape gut microbiome, which can impact the host. As a result, dietary variation can challenge ...experimental reproducibility and data integration across studies when not appropriately considered. To control for diet‐induced variation, reference diets have been developed for common biomedical models. However, such reference diets have not yet been developed for nontraditional model organisms, such as Xiphophorus species. In this study, we compared two diets designed for zebrafish, a commercial zebrafish diet (Gemma and GEM), and a proposed zebrafish reference diet developed by the Watts laboratory at the University of Alabama at Birmingham (WAT) to the Xiphophorus Genetic Stock Center custom diet (CON) to evaluate the influence of diet on the Xiphophorus gut microbiome. Xiphophorus maculatus were fed the three diets from 2 to 6 months of age. Feces were collected and the gut microbiome was assessed using 16S rRNA sequencing every month. We observed substantial diet‐driven variation in the gut microbiome. Our results indicate that diets developed specifically for zebrafish can affect the gut microbiome composition and may not be optimal for Xiphophorus.
Diet can lead to substantial variation in the fish gut microbiome.
Research Highlights
Zebrafish diets change Xiphophorus gut microbiome;
Species specific standardized diets need to be developed.
The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, ...metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics.
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.
The gut microbiome is important for host health and can be influenced by environmental and hormonal changes. We studied the interactions between anthropogenic land use, glucocorticoid hormones, and ...gut bacterial communities in common toads (Bufo bufo). We sampled tadpoles from ponds of three habitat types (natural, agricultural, and urban ponds), examined gut microbiome composition using amplicon sequencing of the 16S rRNA gene, and measured the associated stress physiology using water-borne hormones. Tadpoles from different habitat types significantly differed in bacterial composition. However, bacterial richness, Shannon diversity, and Firmicutes to Bacteroidota ratio did not vary with habitat type. In contrast with other studies, we found a positive correlation between baseline corticosterone release rate and bacterial diversity. Stress response and negative feedback were not significantly correlated with bacterial diversity. These results suggest that, despite alterations in the composition of intestinal bacterial communities due to land-use change, common toad tadpoles in anthropogenic habitats may maintain their physiological health in terms of the “gut-brain axis”.
Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here ...we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Differences between community composition and functional capacity of the bacteria in the two types of fungus gardens reflect differences in the substrates that the ants incorporated. These results show that different substrate inputs matter for fungus garden bacteria and shed light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.
The gut microbiome is important for digestion, host fitness, and defense against pathogens, which provides a tool for host health assessment. Amphibians and their microbiomes are highly susceptible ...to pollutants including antibiotics. We explored the role of an unmanipulated gut microbiome on tadpole fitness and phenotype by comparing tadpoles of Rana berlandieri in a control group (1) with tadpoles exposed to: (2) Roundup® (glyphosate active ingredient), (3) antibiotic cocktail (enrofloxacin, sulfamethazine, trimethoprim, streptomycin, and penicillin), and (4) a combination of Roundup and antibiotics. Tadpoles in the antibiotic and combination treatments had the smallest dorsal body area and were the least active compared to control and Roundup-exposed tadpoles, which were less active than control tadpoles. The gut microbial community significantly changed across treatments at the alpha, beta, and core bacterial levels. However, we did not find significant differences between the antibiotic- and combination-exposed tadpoles, suggesting that antibiotic alone was enough to suppress growth, change behavior, and alter the gut microbiome composition. Here, we demonstrate that the gut microbial communities of tadpoles are sensitive to environmental pollutants, namely Roundup and antibiotics, which may have consequences for host phenotype and fitness via altered behavior and growth.
Abstract only
Around 50% of fish consumption comes from aquaculture. An increase in world population and food demands requires fish production to dramatically increase over the next decade. One of ...the major obstacles of increasing aquaculture production is disease. Thus, a key aspect of aquaculture research is understanding immune health and the spread of disease within farmed populations and into wild stocks. A major portal for pathogen entry in fish is the nose; nasal infections tend to be severe and result in damage to the olfactory and nervous systems. Immune health is impacted by numerous systems including the microbiome. The microbiome trains the immune system, provides a barrier for pathogens, and helps maintain homeostasis. Therefore, dysbiosis, a disruption of the microbiome due to changes in diet, exposure to pollutants, antibiotic consumption, and physiological stress, can contribute to disease. One common pollutant in water is agricultural runoff containing nitrates and nitrites, which are known to cause stress in fish and can be deadly in some concentrations. However, it is unknown how nitrites impact the microbiomes of sensitive tissues and how these changes impact immune health. I hypothesize that increased nitrite concentrations will cause dysbiosis of the microbiome resulting in changing abundance and diversity of the microbiome. This work aims to determine the impacts of sublethal levels of nitrite on the nasal microbiome and compare it to the microbiomes of the gills and gut. For 2 months goldfish (10 fish/30L tank) were held under various nitrite concentrations, 0.0mM (control), 0.01mM, 0.1mM, and 1.0mM. The system utilized continuous aerated water flow at 24°C to maintain the desired concentrations of nitrite. Tissue samples were collected from each fish with water collected to serve as a control to determine the host‐specific microbiome. The DNA from the tissues were extracted, amplified, and prepared as a library for sequencing using 16S rRNA gene primers for Illumina MiSeq. The sequences were analyzed using the DADA2 pipeline in R and MaAsLin from Galaxy. The gill microbiome showed no significant changes in abundance compared to the control treatment. The nose microbiome appears to show an increase in diversity compared to the control microbiome; however, these changes were not determined to be significant. Both the gut and water microbiomes showed significant changes in abundance compared to their control levels, with the gut microbiome changing the most. Sublethal levels of nitrite exposure significantly increase the diversity of the microbial communities of the water and the gut microbiomes. There are also some indications that the nose and gill microbiomes are impacted, however, small sample sizes could be obscuring the changes. These impacts imply that sublethal nitrite concentrations can cause dysbiosis of the fish microbiomes and could have negative impacts of fish health.
Abstract
The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due ...to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.
This study analyzed the microbiome composition of endangered riffle beetle Heterelmis comalensis demonstrating that it is significantly affected by captivity.
Elevated concentrations of nitrite are toxic to fish and can cause a myriad of well documented issues. However, the effects of sublethal concentrations of nitrite on fish health, and specifically, ...fish tissue microbiomes have not been studied. To test the effects of nitrite exposure, goldfish were exposed to sublethal concentrations of nitrite, 0.0 mM, 0.1 mM, and 1.0 mM, for 2 months. The bacteria in the nose, skin, gills, and water were then extracted and sequenced to identify changes to the microbial composition. The water microbiome was not significantly changed by the added nitrite; however, each of the tissue microbiomes was changed by at least one of the treatments. The skin and gill microbiomes were significantly different between the control and 1.0 mM treatment and the nose microbiome showed significant changes between the control and both the 0.1 mM and 1.0 mM treatments. Thus, sublethal concentrations of nitrite in the environment caused a shift in the fish tissue microbiomes independently of the water microbiome. These changes could lead to an increased chance of infection, disrupt organ systems, and raise the mortality rate of fish. In systems with high nitrite concentrations, like intensive aquaculture setups or polluted areas, the effects of nitrite on the microbiomes could negatively affect fish populations.
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