John K. Reed

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

Deep-water Oculina coral reefs of Florida: biology, impacts, and management

Deep-water Oculina coral reefs, which are similar in structure and development to deep-water Lophelia reefs, stretch over 167 km (90 nmi) at depths of 70–100 m along the eastern Florida shelf of the United States. These consist of numerous pinnacles and ridges, 3–35 m in height. Coral growth rates average 16.1 mm yr−1 and biodiversity is very rich. Extensive areas of Oculina rubble may be due to human impacts (e.g. fish trawling and dredging, anchoring, bottom longlines) and natural processes such as bioerosion and episodic die-off. Early in the 1970s, the reefs were teeming with fish. By the early 1990s, both commercial and recreational fisheries, including scallop, shrimp, grouper, snapper and amberjack, had taken a toll on the reefs and especially on populations of grouper and snapper. A 315 km2 (92 nmi2) area was designated the Oculina Habitat of Particular Concern (HAPC) in 1984, prohibiting trawling, dredging, bottom longlines and anchoring, and legislation was enacted in 2000 for expansion of the Oculina HAPC to 1029 km2 (300 nmi2). The United States Coast Guard has been charged with surveillance and enforcement of the ban on bottom fishing and trawling. The primary difficulties in protecting these reefs and other deep-water Marine Protected Areas are their remoteness and time required to engage an enforcement vessel. Education regarding the nature and importance of these rich resources is important for better self regulation and surveillance by the fishing community. Only by bringing deep-water reefs to the public, the fishing community, and enforcement agencies, through video, photos, and education will there be better understanding and acceptance for the need of protection for these unseen resources. This paper reviews the current knowledge on the deep-water Oculina reefs, including the biology, geology, human impacts, and history of conservation and management.

Leiodermatolide, a Potent Antimitotic Macrolide from the Marine Sponge Leiodermatium sp.

Leiodermatolide is a structurally unique macrolide, isolated from the deep-water marine sponge Leiodermatium sp., which exhibits potent antiproliferative activity against a range of human cancer cell lines (IC50 <10 nM) and dramatic effects on spindle formation in mitotic cells. Its unprecedented polyketide skeleton and stereochemistry were established using a combination of experimental and computational (DP4) NMR methods, and molecular modelling.

Comparison of deep-water coral reefs and lithoherms off southeastern USA

Two types of deep-water coral bioherms occur off the coast of southeastern United States: Oculina and Lophelia/Enallopsammia. The deep-water Oculina bioherms form an extensive reef system at depths of 70–100 m along the shelf edge off central eastern Florida. These reefs are comprised of numerous pinnacles and ridges, 3–35 m in height. Each pinnacle is a bank of unconsolidated sediment and coral debris that is capped on the slopes and crest with living and dead colonies of Oculina varicosa, the ivory tree coral. In comparison, deep-water reefs of Lophelia pertusa and Enallopsammia profunda corals occur at depths of 500–850 m (maximum 150-m relief) along the base of the Florida-Hatteras slope in the Straits of Florida. On the western edge of the Blake Plateau off South Carolina and Georgia, 54-m high banks of Enallopsammia and Lophelia occur at depths of 490–550 m, whereas on the eastern edge of the plateau the reefs form structures 146 m in height and at depths of 640–869 m. The geomorphology and functional structure of both the Oculina and Lophelia reefs are similar. North of Little Bahama Bank, at depths of 1000–1300 m, a region of bioherms is dominated by the coral Solenosmilia sp.; Lophelia is reportedly absent. This paper summarizes 25 years of submersible studies on the deep-water Oculina reefs, describes submersible reconnaissance of deep-water Lophelia reefs off the southeastern United States, and contrasts these types of bioherms with the deep-water lithoherms in the Straits of Florida west of the Bahamas.

Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida

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.

Gymnochromes E and F, Cytotoxic Phenanthroperylenequinones from a Deep-Water Crinoid, Holopus rangii

Bioactivity-guided fractionation of metabolites from the crinoid Holopus rangii led to the discovery of two new phenanthroperylenequinone derivatives, gymnochromes E (1) and F (2). Gymnochrome E showed cytotoxic activity toward the NCI/ADR-Res with an IC(50) of 3.5 microM. It also inhibited histone deacetylase-1 with an IC(50) of 3.3 microM. Gymnochrome F was a moderate inhibitor of myeloid cell leukemia sequence 1 (MCL-1) binding to Bak. Two anthraquinone metabolites, emodic acid (4) and its new bromo derivative (5), were also isolated from the crinoid and show remarkable similarity to the phenanthroperylenequinone core, suggesting that these metabolites share the same polyketide biosynthetic pathway.

Production and off-bank transport of carbonate sediment, Black Rock, southwest Little Bahama Bank

Abstract Surficial sediments between the intertidal zone and 600 m were studied with the objectives of characterizing their source, dispersal pathways and sites of accumulation. Bioerosion is a major source of sediment in the intertidal and shallow subtidal environments. In-situ enclosure experiments showed that the urchin Echinometra lucunter produced 667 mg sediment cm−2 yr−1, and an associated diverse rock infauna produced an additional 183 mg cm−2 yr−1. Microborers caused erosion of 25 mg cm−2 yr−1, and feeding activity by the chiton Acanthopleura granulata caused additional erosion of 10 mg cm−2 yr−1. Sequential weighing of tethered limestone plates showed an abrasion rate of 5.5 mg cm−2 yr−1, due chiefly to impacts on the plate edges. Surficial sediments between the intertidal zone and the top of the bank-margin wall at 30 m are gravel-sand mixtures containing 0–2% mud. Molluscs and Halimeda plates are the main constituents of gravel fractions. Sand fractions are composed of bioerosion-produced carbonate rock fragments (1–70%), skeletal material from Halimeda (3–63%), forams (1–33%), molluscs (6–15%) and coral (0–6%). Gravel and sand are transported as bedload in chutes across the narrow, rocky shelf. Chutes end at 45 m, and sediment traps indicate an average flux of 5.4 kg chute−1 yr−1, equivalent to 945 kg km−1 yr−1, moving to deep water. A dense population of Halimeda living on the wall, between 30–70 m, contributes gravel and sand to sediment on wall ledges. At the base of the steep wall (65°), a ramp slopes into the Northwest Providence Channel. Between 120–300 m, the ramp (30° slope) is a zone by-passed by coarse and fine sediment. At 300 m, the slope decreases to an average of 13°, and an apron-shaped body of mud is accumulating. The apron extends parallel to the bank margin and wall, and reaches depths > 600 m. Traps showed that sediment flux to the ramp is 0.12 kg m−2 yr−1, which is 2% of the particle flux overtopping the bank margin. Surficial sediment of the ramp is mostly mud (> 70%) which is primarily of shallow-water origin. Some form of bottom current transporting gravel and sand (mostly Halimeda and abraded coral heads) has cut gullies into the ramp. This bottom flow is probably episodic, and turbulent enough to suspend and supply Halimeda sand to sediment traps on the ramp at 463 m.

Isolation, synthesis, and biological activity of aphrocallistin, an adenine-substituted bromotyramine metabolite from the Hexactinellida sponge Aphrocallistes beatrix.

A new adenine-substituted bromotyrosine-derived metabolite designated as aphrocallistin (1) has been isolated from the deep-water Hexactinellida sponge Aphrocallistes beatrix. Its structure was elucidated on the basis of spectral data and confirmed through a convergent, modular total synthetic route that is amenable toward future analogue preparation. Aphrocallistin inhibits the growth of a panel of human tumor cell lines with IC(50) values ranging from 7.5 to >100 microM and has been shown to induce G1 cell cycle arrest in the PANC-1 pancreatic carcinoma cell line. Aphrocallistin has been fully characterized in the NCI cancer cell line panel and has undergone in vitro ADME pharmacological profiling.

Neopetrosiquinones A and B, sesquiterpene benzoquinones isolated from the deep-water sponge Neopetrosia cf. proxima.

Two new marine-derived sesquiterpene benzoquinones which we designate as neopetrosiquinones A (1) and B (2), have been isolated from a deep-water sponge of the family Petrosiidae. The structures were elucidated on the basis of their spectroscopic data. Compounds 1 and 2 inhibit the in vitro proliferation of the DLD-1 human colorectal adenocarcinoma cell line with IC(50) values of 3.7 and 9.8 μM, respectively, and the PANC-1 human pancreatic carcinoma cell line with IC(50) values of 6.1 and 13.8 μM, respectively. Neopetrosiquinone A (1) also inhibited the in vitro proliferation of the AsPC-1 human pancreatic carcinoma cell line with an IC(50) value of 6.1 μM. The compounds are structurally related to alisiaquinone A, cyclozonarone, and xestoquinone.

Habitat Characterization, Distribution, and Areal Extent of Deep-sea Coral Ecosystems off Florida, Southeastern U.S.A.

Abstract. The deep-sea (200–1000 m) seafloor off the southeastern U.S. has a variety of extensive deep-sea coral ecosystem (DSCE) habitats including: deep-water coral mounds; various hard-bottom habitats off Florida including the Miami Terrace, Pourtalès Terrace, and deep-water canyons (Agassiz and Tortugas Valleys); and deep island slopes off western Bahamas and northern Cuba. The dominant structure-forming scleractinian corals are Lophelia pertusa and Enallopsammia profunda; other structure-forming taxa include stylasterid corals, gorgonians, black corals, and sponges. This biota is associated with hard-bottom seafloor of variable high-relief topography which can be remotely identified from bathymetric data. NOAA bathymetric contour maps and digital elevation models were used to identify and delineate the areal extent of potential DSCE habitat in the region from northeastern Florida through the Straits of Florida. These were ground-truthed with 241 dives with submersibles and remotely operated vehicles which confirmed deep-sea coral habitat. We estimate a total of 39,910 km2 of DSCE habitat in this region. By comparison, the estimated areal extent of shallow-water coral habitat for all U.S. waters is 36,813 km2. Bottom trawling remains the greatest threat to DSCEs worldwide, and as a result NOAA has established five deep-water Coral Habitat Areas of Particular Concern (CHAPCs), encompassing 62,714 km2 from North Carolina to south Florida, which will protect much of the known deep-sea coral habitat in this region. High-resolution surveys are not only critical to define DSCE habitats but also to define areas devoid of coral and sponge habitats that may allow for potential bottom fisheries and energy development.