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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. Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales

   https://doi.org/10.3354/ame01944  

   Becker, CC ; Weber, L ; Suca, JJ ; Llopiz, JK ; Mooney, TA ; Apprill, A ( October 2020 , Aquatic Microbial Ecology)

   In coral reefs and adjacent seagrass meadow and mangrove environments, short temporal scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and community structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial ( Bacteria and Archaea ) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, capturing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes exhibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dynamics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental parameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms revealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sediment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles contributing to a highly dynamic microbial environment in mangroves, and time of day likely contributing to microbial dynamics in seagrass and reef biomes. 

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3. Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition

   https://doi.org/10.1111/1462-2920.15279  

   Sallinger, Eleni ; Robeson, Michael S. ; Haselkorn, Tamara S. ( November 2020 , Environmental Microbiology)

   As predators of bacteria, amoebae select for traits that allow bacteria to become symbionts by surviving phagocytosis and exploiting the eukaryotic intracellular environment. Soil‐dwelling social amoebae can help us answer questions about the natural ecology of these amoeba‐bacteria symbioses along the pathogen‐mutualist spectrum. Our objective was to characterize the natural bacterial microbiome of phylogenetically and morphologically diverse social amoeba species using next‐generation sequencing of 16S rRNA amplicons directly from amoeba fruiting bodies. We found six phyla of amoeba‐associated bacteria: Proteobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, Firmicutes, and Acidobacteria. The most common associates of amoebae were classified to order Chlamydiales and genusBurkholderia‐Caballeronia‐Paraburkholderia. These bacteria were present in multiple amoeba species across multiple locations. While there was substantial intraspecific variation, there was some evidence for host specificity and differentially abundant taxa between different amoeba hosts. Amoebae microbiomes were distinct from the microbiomes of their soil habitat, and soil pH affected amoeba microbiome diversity. Alpha‐diversity was unsurprisingly lower in amoebae samples compared with soil, but beta‐diversity between amoebae samples was higher than between soil samples. Further exploration of social amoebae microbiomes may help us understand the roles of bacteria, host, and environment on symbiotic interactions and microbiome formation in basal eukaryotic organisms.

    

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4. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

   https://doi.org/10.1186/s40793-023-00499-5  

   Wainwright, Benjamin J. ; Millar, Trevor ; Bowen, Lacee ; Semon, Lauren ; Hickman, K. J. ; Lee, Jen Nie ; Yeo, Zhi Yi ; Zahn, Geoffrey ( December 2023 , Environmental Microbiome)

   Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs

   Here we examine the microbiome ofAvicenia albaandSonneratia albaand identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa,Tunicatimonas,Halomonas,Marinomonas,Rubrivirga,Altererythrobacte,Lewinella,andErythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.

   The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.

    

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5. Morphological evolution of a macrotidal back‐barrier environment: The Amazon Coast

   https://doi.org/10.1111/sed.12752  

   McLachlan, Robin_L ; Ogston, Andrea_S ; Asp, Nils_E ; Fricke, Aaron_T ; Nittrouer, Charles_A ; Schettini, Carlos_A_F ; Fielding, ed., Christopher ( June 2020 , Sedimentology)

   Coastal barriers provide sheltered, low‐energy settings for fine‐grained sediment deposition and retention, although the process of back‐barrier infilling and how tidal‐channel connectivity impacts this process is not well‐understood. Understanding how back‐barrier environments infill and evolve is necessary to predict how they will respond to future changes in sea‐level and sediment supply. With this motivation,in situobservations and sedimentary signatures from an Amazonian tidal‐channel system are interpreted to create a conceptual model of morphological evolution in a macrotidal back‐barrier environment that is rich in fine‐grained sediment, vegetated by mangroves and incised by tidal channels with multiple outlets. Results indicate that within a high‐connectivity back‐barrier channel, tidal processes dominate sedimentation and morphological development. Sediment cores (<60 cm) exhibited millimetre‐scale tidalites composed of sand and mud. High‐connectivity channels allow tidal propagation from multiple inlets, and in this case, the converging flood waves promote delivery of sediment fluxing through the system to the mangrove flats in the convergence zone. Sediment preferentially deposits in regions with adequate accommodation space and dense vegetation, and in these zones, sediment grain size is slightly finer than that transiting through the system. The greatest sediment‐accumulation rates (3 to 4 cm yr⁻¹), calculated from steady‐state²¹⁰Pb profiles, were found in the convergence zone near the mangrove‐channel edge. As tidal flats aggrade vertically and prograde into the channels, accommodation space diminishes. In effect, the channel’s narrowest stretch is expected to migrate along the path of net‐sediment flux towards regions with more accommodation space until it reaches the tidal‐convergence zone. The location of recent preferential infilling is evidenced by relatively rapid sediment‐accumulation rates, finer sediment and significant clustering of small secondary tidal channels. These findings shed light on how sediment transported through vegetated back‐barrier environments is ultimately preserved and how evidence preserved in surface morphology and the geological record can be interpreted.

    

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