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1. Fecal and cloacal microbiomes of cold-stunned loggerhead Caretta caretta, Kemp’s ridley Lepidochelys kempii, and green sea turtles Chelonia mydas

   https://doi.org/10.3354/esr01220  

   Forbes, ZR; Scro, AK; Patel, SH; Dourdeville, KM; Prescott, RL; Smolowitz, RM (February 2023, Endangered Species Research)

   Investigating animal gut microbiomes can lead to a better understanding of their foraging preferences and their overall health. In this study, the fecal and cloacal microbiomes of 4 cold-stunned, frozen loggerhead Caretta caretta, 9 Kemp’s ridley Lepidochelys kempi , and 5 green sea turtles Chelonia mydas that stranded on beaches in Massachusetts, USA, were surveyed. Cloacal swabs and in situ fecal samples were collected from each turtle. From the extracted DNA, the hypervariable V1-V3 regions of the 16S rRNA gene were amplified with PCR, then sequenced using next generation Illumina MiSeq technology. Fecal and cloacal microbiomes were primarily composed of the phyla Proteobacteria , Bacteroidetes , and Firmicutes . Microbial communities varied significantly based on location of the gut sampled. Cloacal samples were largely dominated by Proteobacteria , while fecal samples appeared to have a greater distribution of taxa and higher alpha diversity. Green turtles had a higher abundance of Firmicutes and Bacteroidetes than Kemp’s ridley and loggerhead turtles, but a lower abundance of Proteobacteria . The information gained from this study contributes to knowledge of cold-stunned sea turtle gut microbiomes and may eventually be applied to rehabilitation efforts. 

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2. Nitrogen driven niche differentiation in bacterioplankton communities of northeast coastal Bay of Bengal

   https://doi.org/10.1088/2515-7620/ac5a69  

   Ghosh, Anwesha; Woodward, E Malcolm; Saha, Ratul; Nelson, Craig E; Bhadury, Punyasloke (March 2022, Environmental Research Communications)

   Abstract The Bay of Bengal receives nitrogen inputs from multiple sources and the potential role of nitrogen-metabolizing microbial communities in the surface water is not well understood. The nitrogen budget estimate shows a deficit of 4.7 ± 2.4 Tg N yr -1 , suggesting a significant role of dissolved organic nitrogen remineralization in fuelling ecosystem processes. Unravelling the process of remineralization leading to increasing concentrations of dissolved inorganic nitrogen (DIN) in coastal ecosystems such as in mangroves require a better understanding of the composition of functional resident bacterioplankton communities. Bacterioplankton communities were elucidated from eight stations along different estuaries spanning west to east of northeast coastal Bay of Bengal to understand the influence of DIN on shaping these communities. The eight stations were differentiated into ‘low’ and ‘high’ DIN stations based on DIN concentration, with five stations with High DIN concentration (>45 μ M) and three stations with Low DIN concentration (<40 μ M). The V3–V4 region of 16S rRNA was amplified and sequenced to elucidate resident bacterioplankton community structure from environmental DNA. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant bacterioplankton phyla across all stations. Nitrogen-fixing groups such as Nitrospirae, Lentisphaerae, Chloroflexi, and Planctomycetes make up about 1% of the bacterioplankton communities. Abundances of Spirochaetes and Tenericutes showed a positive correlation with DIN. Pseudomonadales, Alteromonadales, and Desulfovibrionales were found to distinctly vary in abundance between Low and High DIN stations. Predicted metagenomic profiles from taxonomically derived community structures indicated bacterial nitrate-nitrite reductase to be negatively correlated with prevalent DIN concentration in High DIN stations but positively correlated in Low DIN stations. This trend was also consistent for genes encoding for nitrate/nitrite response regulators and transporter proteins. This indicates the need to delineate functional bacterioplankton community structures to better understand their role in influencing rates and fluxes of nitrogen within mangroves. 

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3. Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities

   https://doi.org/10.1111/jpy.13424  

   Cissell, Ethan C; McCoy, Sophie J (April 2024, Journal of Phycology)

   Abstract As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built byOkeaniasp., were co‐dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample‐specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer‐resource dynamics on future reefs and trajectories of reef functional ecology. 

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4. Trait-Based Comparison of Coral and Sponge Microbiomes

   https://doi.org/10.1038/s41598-020-59320-9  

   Fiore, Cara L.; Jarett, Jessica K.; Steinert, Georg; Lesser, Michael P. (February 2020, Scientific Reports)

   Abstract Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral,Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge,Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed inM. cavernosa, while inX. mutathere was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host. 

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5. Harnessing machine learning and synthetic microbial communities to control harmful algal blooms

   https://doi.org/10.1016/j.teengi.2025.100030  

   Imam_ul_Khabir, Md; Alam, Nur E; Jhumur, JF; Rehman, Tanzeel U; Jain, Sapna; Rahman, MA; Zhao, Yongpo; Saleem, Muhammad (September 2025, Total Environment Engineering)

   Freshwater with high quality is crucial for both public health and aquatic biodiversity. However, freshwater resources face numerous challenges, including the proliferation of harmful algal blooms (HABs) caused by various cyanobacterial species that are generally triggered by human activities like agricultural runoff and wastewater. Native algicidal microbiomes may offer potential solutions, although challenges remain in utilizing microbial resources to mitigate HABs in freshwater environments. The combination of synthetic microbial community and probiotic development approaches with robust machine learning tools could allow us to harness native microbiomes to address water quality issues caused by HABs in large water bodies. A meta-analysis of around 100 research studies regarding algicidal bacteria-algae interactions was conducted to quantitatively assess the potential of taxonomically diverse microbial species in controlling HABs in freshwater ecosystems. Meta-analysis findings revealed that diverse species from common freshwater bacterial phyla such as Actinobacteria, Bacteroidota, Firmicutes, and Proteobacteria exhibited 50100 % algicidal activity against different algal species depending on interacting species and environmental conditions. Algicidal taxa (mainly against Microcystis aeruginosa) from both Actinobacteria and Firmicutes primarily included Actinomycetes and Bacillus species. However, Bacteroidota and alpha/beta Proteobacteria exhibited algicidal activity against a broader range of algal species, thus highlighting their potential for controlling multi-species HABs in freshwater environments. Based on this quantitative analysis, the current review puts forward synthetic microbial communities and machine-learning based frameworks to develop microbial solutions for protecting freshwater resources from HABs invasions. 

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