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1. Microbial Biofilms Along a Geochemical Gradient at the Shallow-Water Hydrothermal System of Vulcano Island, Mediterranean Sea

   https://doi.org/10.3389/fmicb.2022.840205  

   Sciutteri, Valentina; Smedile, Francesco; Vizzini, Salvatrice; Mazzola, Antonio; Vetriani, Costantino (February 2022, Frontiers in Microbiology)

   Shallow water hydrothermal vents represent highly dynamic environments where strong geochemical gradients can shape microbial communities. Recently, these systems are being widely used for investigating the effects of ocean acidification on biota as vent emissions can release high CO 2 concentrations causing local pH reduction. However, other gas species, as well as trace elements and metals, are often released in association with CO 2 and can potentially act as confounding factors. In this study, we evaluated the composition, diversity and inferred functional profiles of microbial biofilms in Levante Bay (Vulcano Island, Italy, Mediterranean Sea), a well-studied shallow-water hydrothermal vent system. We analyzed 16S rRNA transcripts from biofilms exposed to different intensity of hydrothermal activity, following a redox and pH gradient across the bay. We found that elevated CO 2 concentrations causing low pH can affect the response of bacterial groups and taxa by either increasing or decreasing their relative abundance. H 2 S proved to be a highly selective factor shaping the composition and affecting the diversity of the community by selecting for sulfide-dependent, chemolithoautotrophic bacteria. The analysis of the 16S rRNA transcripts, along with the inferred functional profile of the communities, revealed a strong influence of H 2 S in the southern portion of the study area, and temporal succession affected the inferred abundance of genes for key metabolic pathways. Our results revealed that the composition of the microbial assemblages vary at very small spatial scales, mirroring the highly variable geochemical signature of vent emissions and cautioning for the use of these environments as models to investigate the effects of ocean acidification on microbial diversity. 

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2. Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments

   https://doi.org/10.1093/ismejo/wraf088  

   Maritan, Andrew J; Clements, Cody S; Pratte, Zoe A; Hay, Mark E; Stewart, Frank J (May 2025, The ISME Journal)

   Abstract Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites. 

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3. Removal of detritivore sea cucumbers from reefs increases coral disease

   https://doi.org/10.1038/s41467-024-45730-0  

   Clements, Cody S.; Pratte, Zoe A.; Stewart, Frank J.; Hay, Mark E. (February 2024, Nature Communications)

   Abstract Coral reefs are in global decline with coral diseases playing a significant role. This is especially true for Acroporid corals that represent ~25% of all Pacific coral species and generate much of the topographic complexity supporting reef biodiversity. Coral diseases are commonly sediment-associated and could be exacerbated by overharvest of sea cucumber detritivores that clean reef sediments and may suppress microbial pathogens as they feed. Here we show, via field manipulations in both French Polynesia and Palmyra Atoll, that historically overharvested sea cucumbers strongly suppress disease among corals in contact with benthic sediments. Sea cucumber removal increased tissue mortality ofAcropora pulchraby ~370% and colony mortality by ~1500%. Additionally, farmerfish that killAcropora pulchrabases to culture their algal gardens further suppress disease by separating corals from contact with the disease-causing sediment—functioning as mutualists rather than parasites despite killing coral bases. Historic overharvesting of sea cucumbers increases coral disease and threatens the persistence of tropical reefs. Enhancing sea cucumbers may enhance reef resilience by suppressing disease. 

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4. Ticks without borders: microbiome of immature neotropical tick species parasitizing migratory songbirds along northern Gulf of Mexico

   https://doi.org/10.3389/fcimb.2024.1472598  

   Karim, Shahid; Zenzal, Theodore J; Beati, Lorenza; Sen, Raima; Adegoke, Abdulsalam; Kumar, Deepak; Downs, Latoyia P; Keko, Mario; Nussbaum, Ashly; Becker, Daniel J; et al (November 2024, Frontiers in Cellular and Infection Microbiology)

   IntroductionThe long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can cause the emergence of novel tick-borne pathogens. This study examined the prevalence of exotic tick species parasitizing migratory songbirds at stopover sites along the northern Gulf of Mexico using the mitochondrial 12S rRNA gene. MethodsOverall, 421 individual ticks in the generaAmblyomma,Haemaphysalis, andIxodeswere recorded from 28 songbird species, of whichAmblyommaandAmblyomma longirostrewere the most abundant tick genera and species, respectively. A high throughput 16S ribosomal RNA sequencing approach characterized the microbial communities and identified pathogenic microbes in all tick samples. Results and discussionMicrobial profiles showed that Proteobacteria was the most abundant phylum. The most abundant pathogens wereRickettsiaand endosymbiontFrancisella,Candidatus Midichloria, andSpiroplasma. Permutation multivariate analysis of variance revealed that the relative abundance ofFrancisellaandRickettsiadrives microbial patterns across the tick genera. We also noted a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a)FrancisellaandRickettsiaand, b)FrancisellaandCutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing mean dispersal distances from 421–5003 kilometers. These findings spotlight the potential role of migratory birds in the epidemiology of tick-borne pathogens. 

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5. An urban diet differentially alters the gut microbiome and metabolomic profiles compared with a seed diet in mourning doves

   https://doi.org/10.1152/ajpregu.00323.2021  

   Mohr, Alex E.; Basile, Anthony J.; Sweazea, Karen L. (October 2022, American Journal of Physiology-Regulatory, Integrative and Comparative Physiology)

   Urbanization influences food quality and availability for many avian species, with increased access to human refuse and food subsidies in built environments. In relation to such nutritional intakes and their presumed impact on microbes harbored in the intestinal tract and metabolic profiles of host physiological systems, our overall knowledge of the role of gut microbiome (GM) and metabolomic expression in the avian host lags far behind our understanding of mammals. Therefore, the objective of this investigation was to examine the potential differential effect of an urban modeled versus control (i.e., bird seed) diet on the GM, the metabolic profiles of plasma, liver, adipose, kidney, and muscle tissues, and circulating endotoxin and inflammatory factors in urban-caught mourning doves ( Zenaida macroura). We hypothesized that the urban diet would differently impact the profiles of the GM and tissue metabolomes and increase plasma lipopolysaccharide (LPS) and proinflammatory factors compared with animals fed a seed diet. After a 4-wk-diet period, contents of the large intestine were sequenced to profile the microbiome, metabolomic analyses were performed on plasma and tissue homogenates, and circulating LPS and inflammatory markers were assessed. The composition of the GM was significantly dissimilar between diets, with greater abundance of Erysipelatoclostridiaceae, Sanguibacteraceae, Oribacterium, and Sanguibacter and decreased circulating LPS in the urban-fed birds. These differences were largely not reflected in the surveyed metabolomes and plasma inflammatory markers. This research supports the notion that the microbial composition in urban doves is impacted by diet, though may only weakly associate with host physiology. 

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