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The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes., Competing Interests: The authors have declared that no competing interests exist. In specific relation to the commercial funder MyFloridaSpecialtyPlate, none of the authors have any of the following financial competing interests to declare: ownership of stocks or shares, paid employment or consultancy, board membership, patent applications, or marketed products. None of the funders involved in this research have any policies nor do any of the authors have an involvement with these funders which would alter our adherence to PLOS ONE policies on sharing data and materials.

This study examined the symbiotic microbiota of the hexacoral Cirrhipathes lutkeni using traditional plate culture, fluorescence in situ hybridization (FISH) and 16S rDNA characterization. FISH counts for the whole coral (holobiont) showed a major presence of gamma-Proteobacteria (22%) and Actinobacteria (19%), followed by alpha-Proteobacteria (14%), Firmicutes (9%), Cytophaga-Flavobacterium (7%), beta-Proteobacteria (6%) and Chloroflexi (2%). In contrast to the diversity observed by FISH, plate cultures were found to be selective for gamma-Proteobacteria (22 cultures) with the exception of an Actinobacterium. The methods employed in this study detected 76% of all microbes estimated by DAPI staining of C. lutkeni homogenates. The absence of zooxanthellae in this particular hexacoral was confirmed by PCR and spectrophotometry using fresh tissue isolated from the holobiont. This is the first study describing the microbial associations of shallow-water hexacorallia, which opens further insight into coral microbial ecology and may enhance the search for novel natural products in the near future.

This study examined the microbiota associated with the marine azooxanthellate octocorals Leptogorgia minimata, Swiftia exertia, and Iciligorgia schrammi collected from moderate depths (45 m). Traditional aerobic plate culture, fluorescence in situ hybridization (FISH), and molecular identification of the 16S rDNA region were used for this purpose. In general, cultures were found to be selective for Gammaproteobacteria, Alphaproteobacteria, and Firmicutes. Interestingly, FISH counts for Firmicutes in the whole coral (holobiont) were near the detection limit of this assay, representing less than 6% of the total detectable microbiota in all counts. Proteobacteria, especially Alpha- and Gammaproteobacteria, made up the majority of the total microbiota in the holobionts. In addition, the absence of zooxanthellae in these three corals was confirmed by the use of polymerase chain reaction (PCR) and dinoflagellate-specific primers, and spectrophotometric chlorophyll pigment measurements. No evidence of zooxanthellae could be found in any of the corals by either of these techniques. This is the first study examining the microbiota marine octocorals, which grow at moderate depth (40 to 100 m) in the absence of direct sunlight.

Marine sediments and sponges may show steep variations in redox potential, providing niches for both aerobic and anaerobic microorganisms. Geodia spp. and sediment specimens from the Straits of Florida were fixed using paraformaldehyde and 95% ethanol (v/v) for fluorescence in situ hybridization (FISH). In addition, homogenates of sponge and sediment samples were incubated anaerobically on various cysteine supplemented agars. FISH analysis showed a prominent similarity of microbiota in sediments and Geodia spp. samples. Furthermore, the presence of sulfate-reducing and annamox bacteria as well as other obligate anaerobic microorganisms in both Geodia spp. and sediment samples were also confirmed. Anaerobic cultures obtained from the homogenates allowed the isolation of a variety of facultative anaerobes, primarily Bacillus spp. and Vibrio spp. Obligate anaerobes such as Desulfovibrio spp. and Clostridium spp. were also found. We also provide the first evidence for a culturable marine member of the Chloroflexi, which may enter into symbiotic relationships with deep-water sponges such as Geodia spp. Resuspended sediment particles, may provide a source of microorganisms able to associate or form a symbiotic relationship with sponges. [ABSTRACT FROM AUTHOR]

The Harbor Branch Marine Microbial Database (HBMMD) provides preliminary taxonomic identifications and features of microorganisms maintained in the Harbor Branch Oceanographic Institution Marine Microbial Culture Collection. The microbes are primarily derived from marine invertebrates such as sponges (phylum Porifera) and soft corals (phylum Cnidaria) found in deep water environments [>120 feet (>35 m) seawater]. The microbes isolated from within marine invertebrates represent some unique taxa and phylogenetic signatures. The database provides a user-friendly method to systemically search or sort a desired input. The site allows a powerful search for multiple parameters of any entry. Images of the microbes are contained within the database and can be accessed from the website. The HBMMD homepage is located at. [ABSTRACT FROM AUTHOR]