Non-coral Habitats Research Articles

Population differentiation of Rhodobacteraceae along with coral compartments.

Coral mucus, tissue, and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we sampled bacteria inhabiting a prevalent coral species Platygyra acuta and sequenced genomes of 234 isolates comprising two populations in Rhodobacteraceae, an alphaproteobacterial lineage representing a significant but variable proportion (5-50%) of the coral microbiota. The Ruegeria population (20 genomes) contains three clades represented by eight, six, and six isolates predominantly sampled from the skeleton (outgroup), mucus (clade-M), and skeleton (clade-S), respectively. The clade-M possesses functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine, and L-proline), whereas the clade-S uniquely harbors traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including genomes of 24 related isolates (including seven new genomes) from other marine environments suggest that clade-M and clade-S may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The unassigned Rhodobacteraceae population (214 genomes) varies only at a few dozen nucleotide sites across the whole genomes, but the number of between-compartment migration events predicted by the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism diversifying microbial populations. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.

Long-term ecological changes in fishes and macro-invertebrates in the world's warmest coral reefs

The Arabian Gulf is a natural laboratory for examining the consequences of large-scale disturbances due to global warming on coral reef ecosystems because of its extreme temperature regime. Using a coral reef monitoring time series extending from 1985 to 2015, we examined the long-term ecological changes in fish and macro-invertebrate communities as these habitats suffered heat shocks. We used a GLMM modelling framework to obtain clean annual signals in community indicators from noisy data. We also visualized temporal change in the taxonomic composition of fishes and macro-invertebrates. A phase shift from predominantly reef-building corals to barren grounds occurred between 1996 and 2000. Macro-invertebrates responded rapidly, and most of associated indicators recovered to pre-shift levels in 15 years. Fishes generally had lagged responses to the phase shift and had shifted to a new state with lower abundance, as well as different species composition. Increased levels of herbivory first by macro-invertebrates, mostly sea urchins, and then fishes, could have suppressed macro-algae expansion and consequently led to the dominance of barren ground. When the phase shift occurred, most of the 14 fish families declined in abundance while macro-invertebrate groups increased. Fish families able to utilize non-coral habitats appeared more resilient to the disturbances and subsequent coral degradation. Unlike other regions, we observed high resilience of the coral-dependent butterflyfishes to coral loss, possibly due to local migration from other less-impacted coral reefs. We hypothesized a top-down control mechanism mediated by predation by fishes has contributed to shaping the temporal and spatial patterns of the macro-invertebrates. Our results also revealed differences in spatial preferences among fishes and macro-invertebrate groups, which could be used to set priorities and develop effective conservation and management strategies.

Habitat maps to enhance monitoring and management of the Great Barrier Reef

The Great Barrier Reef (GBR) is of immense biological, cultural and economic importance, but has also rapidly degraded over the last 30 years. Improved spatial information on reef geomorphic zonation and benthic cover type (including coral type) is critical to support scientific work to understand how the GBR is changing, and to support resource management decisions that enable conservation of the reef and its essential ecosystem services. Yet, no comprehensive maps exist that detail the geomorphic zonation or benthic cover for the GBR’s ~ 3000 reefs. This study presents three new types of shallow reef maps for 237 reefs in the central Cairns Management Region of the GBR Marine Park (GBRMP), explores how the detailed habitat maps created compared to current maps and posits how the new maps may support and refine current critical key science outputs and management challenges. Geomorphic Zonation, Benthic Cover and Coral Type habitat maps were created using a unique combined object-based image analysis and ecological modelling approach that incorporated satellite imagery, limited field data and key reef physical attributes (depth, slope, waves) using a previously peer-reviewed mapping approach developed for the Capricorn Bunker Group reefs, Southern GBR. The mapping approach was consistent and repeatable, suggesting applicability to mapping all 3000 reefs in the GBRMP. Compared to existing maps that only outline each reef, the increase in detail provided by these new habitat maps enabled discrete characterisation of each reef’s geomorphology and benthic composition. With the new habitat maps, areas within each reef can be identified as either coral habitat or not coral habitat. This has not been possible previously. As such, a model of coral ecological and biophysical processes that depends on bottom reflectance of sand and coral areas can be fine-tuned. Similarly, for reef restoration, nursery structures are commonly placed in non-coral habitats, and/or coral larvae are dispersed in areas of known coral habitat. The new habitat maps presented permit more accurate identification of these areas such that restoration projects can be targeted more effectively. These findings confirm the need to now apply this mapping approach to the full extent of the GBR.

The Habitats and Biodiversity of Watamu Marine National Park: Evaluating Our Knowledge of One of East Africa's Oldest Marine Protected Areas

Watamu Marine National Park (WMNP) is one of the oldest no-take Marine Protected Areas (MPAs) in the world. Since its establishment in 1968, it has been the subject of a number of scientific studies as well as suffering from a range of modern threats to coastal marine habitats. The current state and conservation value of WMNP is documented in terms of habitat, biodiversity, and available scientific literature. There were 101 published references relating to WMNP found, which mostly focus on coral reef ecology, with less attention to other topics, such as biodiversity, socio-economics, or the ecology of non-coral reef habitats. The habitat map produced of WMNP is the first to show this level of detail and the only habitat map of a Kenyan MPA. Nine habitat categories were mapped; revealing that the most dominant habitat type is seagrass and the least is coral reef. Species lists were collected for fish, echinoderms, molluscs, crustaceans, corals, and seagrass, and species abundances were used to estimate total species richness, species diversity and sampling completeness. There were 18 species across all groups that fall into a category of conservation concern (other than Least Concern or Not Evaluated) on the IUCN Red List and 8 species found which are currently undescribed. The findings of this paper emphasise the importance of non-coral habitats in the WMNP, such as seagrass beds, and the need for more research into the ecology and conservation importance of these habitats. The information provided in this paper provides a comprehensive overview to any scientist or conservationist wanting to carry out further work in WMNP.

Distribution and habitat association of benthic fish on the Condor seamount (NE Atlantic, Azores) from in situ observations

Distribution of fish assemblages and habitat associations of demersal fishes on the Condor seamount were investigated by analyzing in situ video imagery acquired by the Remotely-Operated Vehicles ROV SP300 and Luso 6000. A total of 51 fish taxa from 32 families were inventoried. Zooplanktivores (10 species) were the most abundant group followed by carnivores (23 species) and benthivores (18 species). Non-metric multidimensional scaling (MDS) analyses were performed on dive segments to visualize the spatial relationships between species and habitat type, substrate type or depth, with depth being the most significant parameter influencing fish distribution. Four major fish groups were identified from their vertical distribution alone: summit species (generally to <300m depth); broad ranging species (ca. from 200 to 800m); intermediate ranging slope species (ca. from 400m to 800–850m); and deeper species (800–850–1100m). The fish fauna observed at the summit is more abundant (15.2fish/100m2) and habitat-specialized than the fish observed along the seamount slope. Down the seamount slope, the summit fish assemblage is gradually replaced as depth increases, with an overall reduction in abundance. On the summit, three species (Callanthias ruber, Anthias anthias and Lappanella fasciata) had higher affinity to coral habitats compared to non-coral habitats. A coherent specialized fish assemblage associated to coral habitats could not be identified, because most species were observed also in non-coral areas. On the seamount's slope (300–1100m), no relationship between fish and coral habitats could be identified, although these might occur at larger scales. This study shows that in situ video imagery complements traditional fishing surveys, by providing information on unknown or rarely seen species, being fundamental for the development of more comprehensive ecosystem-based management towards a sustainable use of the marine environment.

Role of prey availability in microhabitat preferences of juvenile coral trout (Plectropomus: Serranidae)

Availability of specific microhabitat exerts a strong influence on recruitment and abundance of coral reef fishes, but the ecological basis for microhabitat selection is not always clear. This study used a combination of field-based sampling and aquarium-based experiments to test microhabitat preferences of juvenile coral trout (mostly, Plectropomus maculatus), and assess whether microhabitat selection is related to prey access. In the field, coral trout use live Acropora corals situated over sand 3 times more than any other microhabitat, even through these specific microhabitats accounted for only 12.8% of habitat area. Field-based surveys revealed that live coral habitats support higher densities of potential prey species (71.73individuals per m2±8.4SE for fish; 423.36individuals per m2±91.8SE for crustacean) compared to dead corals (21.92individuals per m2±3.9SE for fish; 146.67individuals per m2±38.1SE for crustacean). Furthermore, structural microhabitats on sand have higher densities of prey (57.61individuals per m2±9.6SE for fish; 539.04individuals per m2±79.0SE for crustacean) compared to comparable microhabitats on consolidated carbonate substrata (36.05individuals per m2±6.7SE for fish; 129.36individuals per m2±15.9SE for crustacean). In the absence of prey, juvenile coral trout did not distinguish between live versus dead corals (37.18%±8.2SE and 35.48%±6.1SE), but both of these microhabitats were preferred over rubble (16.21%±3.5SE), macroalgae (11.09%±6.1SE) and sand (0%). In tank-based studies of prey use, juvenile coral trout consumed prey fishes that associate with non-coral habitats (e.g., Eviota zebrina; 33.28%±3.4SE) and mid water species (e.g., Aioliops tetrophthalmus; 47.97%±2.8SE), but did not consume those fishes with an obligate association with live corals (4.7%±1.9SE; 6.03%±2.2SE; 7.9%±2.8SE). Our results suggest that studies of microhabitat preferences should consider both the structure and location of specific microhabitats. It is presumed that structural microhabitats are essential for evading predators, while occupation of live corals positioned over sandy substrata maximizes accessibility to a diverse array of potential prey fishes and crustaceans.

Evolution of microhabitat association and morphology in a diverse group of cryptobenthic coral reef fishes (Teleostei: Gobiidae: Eviota)

Gobies (Teleostei: Gobiidae) are an extremely diverse and widely distributed group and are the second most species rich family of vertebrates. Ecological drivers are key to the evolutionary success of the Gobiidae. However, ecological and phylogenetic data are lacking for many diverse genera of gobies. Our study investigated the evolution of microhabitat association across the phylogeny of 18 species of dwarfgobies (genus Eviota), an abundant and diverse group of coral reef fishes. In addition, we also explore the evolution of pectoral fin-ray branching and sensory head pores to determine the relationship between morphological evolution and microhabitat shifts. Our results demonstrate that Eviota species switched multiple times from a facultative hard-coral association to inhabiting rubble or mixed sand/rubble habitat. We found no obvious relationship between microhabitat shifts and changes in pectoral fin-ray branching or reduction in sensory pores, with the latter character being highly homoplasious throughout the genus. The relative flexibility in coral-association in Eviota combined with the ability to move into non-coral habitats suggests a genetic capacity for ecological release in contrast to the strict obligate coral-dwelling relationship commonly observed in closely related coral gobies, thus promoting co-existence through fine scale niche partitioning. The variation in microhabitat association may facilitate opportunistic ecological speciation, and species persistence in the face of environmental change. This increased speciation opportunity, in concert with a high resilience to extinction, may explain the exceptionally high diversity seen in Eviota compared to related genera in the family.

Inter- and intra-habitat bacterial diversity associated with cold-water corals

The discovery of large ecosystems of cold-water corals (CWC), stretching along continental margins in depths of hundreds to thousands of meters, has raised many questions regarding their ecology, biodiversity and relevance as deep-sea hard-ground habitat. This study represents the first investigation that explicitly targets bacterial diversity from distinct microbial habitats associated with the cosmopolitan reef-building coral Lophelia pertusa, and also compares natural (fjord) and controlled (aquarium) conditions. Coral skeleton surface, coral mucus, ambient seawater and reef sediments clearly showed habitat-specific differences in community structure and operational taxonomic unit (OTU) number. Especially in the natural environment, bacterial communities associated with coral-generated habitats were significantly more diverse than those present in the surrounding, non-coral habitats, or those in artificial coral living conditions (fjord vs aquarium). These findings strongly indicate characteristic coral-microbe associations and, furthermore, suggest that the variety of coral-generated habitats within reef systems promotes microbial diversity in the deep ocean.

Distribution and abundance of fish in deep-sea coral habitats

Experimental fishing with long-lines and gillnets was conducted on the continental shelf off southwestern Norway between 150 and 350 m depth. Abundance and distribution of redfish (Sebastes marinus L., 1758), ling (Molva molva L., 1758), and tusk (Brosme brosme Ascanius, 1772) were quantified in Lophelia pertusa (L., 1758) coral reefs and in non-coral habitats. The largest catches of redfish were made with long-line fleets set in coral reef habitats. Ling and tusk were also most numerous in coral habitats, although not statistically significant. Fish caught in coral habitats tended to be larger in size than in non-coral habitats. The diet of redfish, tusk and ling included the same prey groups in all habitats, but they differed at the species level. Lophelia-reefs may provide a profitable feeding place for tusk. For the planktivorous Sebastes, on the other hand, their affinity to the reefs seems primarily to be related to the physical structure offered by the reefs.