An official website of the United States government
The microbiomes of tropical corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, due to the prokaryotic origins of mitochondria, primers targeting bacterial and archaeal 16S rRNA genes may also amplify homologous 12S mitochondrial rRNA genes from the host coral, associated microbial eukaryotes, and encrusting organisms. Standard microbial bioinformatics pipelines attempt to identify and remove these sequences by comparing them to reference taxonomies. However, commonly used tools have severely under-annotated mitochondrial sequences in 1440 coral microbiomes from the Global Coral Microbiome Project, preventing annotation of over 95% of reads in some samples. This issue persists when using Greengenes or SILVA prokaryotic reference taxonomies, and in other hosts, including 16S studies of vertebrates, and of marine sponges. Worse, mitochondrial under-annotation varies between coral families and across coral compartments, biasing comparisons of - and -diversity. By supplementing existing reference taxonomies with over 3000 animal mitochondrial rRNA gene sequences, we resolved roughly 97% of unique unclassified sequences as mitochondrial. These additional sequences did not cause a false elevation in mitochondrial annotations in mock communities with known compositions. We recommend using these extended taxonomies for coral microbiome analysis and whenever eukaryotic contamination may be a concern.
more »
« less
The respiratory microbiota of three cohabiting beluga whales (Delphinapterus leucas) under human care
We sampled the respiratory mucus from voluntary blowhole exhalations (“blow”) of three healthy beluga whales (Delphinapterus leucas) under professional human care. Blow samples were collected from three resident belugas, one adult male (M1) and two adult females (F1, F2), with voluntary behaviors via non-invasive methods over three days in July 2021 (four days for M1). Samples were weighed and examined microscopically for the enumeration of eukaryotic and prokaryotic microbes, and then were used to evaluate carbon substrate use and taxonomic diversity of prokaryotic communities in the host respiratory sytem. Microscopical observations and 18S rRNA gene sequencing indicated the presence of eukaryotic microbiota, the ciliate generaPlanilaminaandKyaroikeusin all three individuals. Exposure of samples to different metabolic carbon substrates indicated significant differences in the number of carbon sources usable by the prokaryotic communities of different whales (range: 11-25 sources), as well as a signficantly decreased diversity of carbon sources used by the community in the habitat water (5 sources). Sequencing of the hypervariable V4 region of the 16S rRNA gene revealed 19 amplicon sequence variants (ASVs) that were present in all whale samples. The oldest femaleD. leucas(F2) had the lowest overall diversity, and was significantly different from M1 and F1 in taxon composition, including an anomalously low ratio of Baccillota: Bacteroidota (0.01) compared to the other whales. In comparisons of microbial community composition, M1 had a significantly higher diversity than F1 and F2. These results suggest that attention should be given to regular microbiome sampling, and indicate a need for the pairing of microbiome and clinical data for animals in aquaria. Overall, these data contribute to the growing database on the core respiratory microbiota in cohabiting cetaceans under professional human care, indicate the utility of non-invasive sampling, and help characterize a baseline for healthyD. leucas.
more »
« less
- Award ID(s):
- 1950480
- PAR ID:
- 10488503
- Publisher / Repository:
- creative commons attribution license
- Date Published:
- Journal Name:
- Frontiers in Marine Science
- Volume:
- 10
- ISSN:
- 2296-7745
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associatedOreomunnea mexicana(Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of theITS2(fungi) and16SrRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.more » « less
-
Arctic systems are warming at four times the global average, causing permafrost—permanently frozen soil, ice, organic matter, and bedrock—to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition—a process mediated by microbes—which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the familiesBeijerinckiaceae,Burkholderiaceae,Clostridiaceae,Oxalobacteraceae,Pseudomonadaceae, andSporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost–climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.more » « less
-
Abstract BackgroundAs coral diseases become more prevalent and frequent, the need for new intervention strategies also increases to counteract the rapid spread of disease. Recent advances in coral disease mitigation have resulted in increased use of antibiotics on reefs, as their application may halt disease lesion progression. Although efficacious, consequences of deliberate microbiome manipulation resulting from antibiotic administration are less well-understood– especially in non-diseased corals that appear visually healthy. Therefore, to understand how apparently healthy corals are affected by antibiotics, we investigated how three individual antibiotics, and a mixture of the three, impact the microbiome structure and diversity of a disease-resistant Caribbean staghorn coral (Acropora cervicornis) genotype. Over a 96-hour, aquarium-based antibiotic exposure experiment, we collected and processed coral tissue and water samples for 16S rRNA gene analysis. ResultsWe found that antibiotic type and dose distinctively impact microbiome alpha diversity, beta diversity, and community composition. In experimental controls, microbiome composition was dominated by an unclassified bacterial taxon from the orderCampylobacterales, while each antibiotic treatment significantly reduced the relative abundance of this taxon. Those taxa that persisted following antibiotic treatment largely differed by antibiotic type and dose, thereby indicating that antibiotic treatment may result in varying potential for opportunist establishment. ConclusionTogether, these data suggest that antibiotics induce microbiome dysbiosis– hallmarked by the loss of a dominant bacterium and the increase in taxa associated with coral stress responses. Understanding the off-target consequences of antibiotic administration is critical not only for informed, long-term coral restoration practices, but also for highlighting the importance of responsible antibiotic dissemination into natural environments.more » « less
-
Blow flies (Lucilia sericataandPhormia regina) are necrophagous insects that interact with dense microbial reservoirs and are opportunistic vectors of human and animal pathogens. Despite constant exposure to diverse environmental microbes, it is unclear whether their bacterial communities are primarily acquired stochastically or shaped by host factors that could influence pathogen carriage. We conducted a systematic comparison of wildL. sericataandP. reginacollected from seven cities across an urban-rural gradient to determine whether microbiome composition is structured by host species identity or environmental variables. Using 16S rRNA gene sequencing of individual flies, we profiled bacterial communities and applied alpha- and beta-diversity analyses, PERMANOVA, and Random Forest classification to quantify species-level microbiome differentiation. Species identity was the strongest predictor of microbiome composition (PERMANOVA,p = 0.001), while location, land cover type, sampling month, and sex had no significant effects. Random Forest modeling identified multiple bacterial taxa that consistently distinguished the two species, includingIgnatzschineriaandDysgonomonas, which were enriched inP. regina, andVagococcusandEscherichia-Shigella, which were enriched inL. sericata. These taxa are of clinical relevance, withIgnatzschineriain particular increasingly reported from human myiasis and soft-tissue infections, sometimes exhibiting antimicrobial resistance. Our findings demonstrate that wild blow flies maintain species-specific microbiomes despite shared environments, suggesting that host identity strongly filters microbial communities. The presence of opportunistic pathogens within these structured microbiomes underscores the need to understand how blow fly–microbe associations contribute to pathogen persistence and dissemination. By revealing predictable, species-dependent microbiome patterns, this study highlights potential targets for microbiome-based strategies aimed at mitigating blow fly–associated disease risks.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.3389/fmars.2023.1168623
