Spatial variability in reef-fish assemblages in shallow and upper mesophotic coral ecosystems in the Philippines

The variability in reef-fish species assemblages was examined at three geographic locations in the Philippines (Apo, Abra and Patn), each showing varying levels of disturbances (low to high) at two depths, shallow-water reef (SWR; 8–20 m) and the upper mesophotic coral ecosystem (MCE; 30–35 m). Fish species assemblages varied among locations and between depths. Differences in fish assemblages among locations corresponded to the variability in benthic assemblages and levels of disturbances, wherein locations with higher coral cover and less disturbances had the highest fish species richness, abundance and biomass. Variation in fish assemblages between depths was also associated with changes in benthic assemblages and possibly inaccessibility to local fishing techniques. Fish species richness decreased with depth in all locations, but biomass increased only in the MCEs of Apo and Abra, which is a similar pattern exhibited in many MCEs. Our results suggest that despite location differences, depth had a relatively consistent influence on fish species assemblages, particularly in locations exposed to low and intermediate disturbance. Under high disturbance, MCEs exhibit similar vulnerability to SWRs.     

Geomorphology of mesophotic coral ecosystems: current perspectives on morphology, distribution, and mapping strategies

This paper presents a general review of the distribution of mesophotic coral ecosystems (MCEs) in relationship to geomorphology in US waters. It was specifically concerned with the depth range of 30–100 m, where more than 186,000 km² of potential seafloor area was identified within the US Gulf of Mexico/Florida, Caribbean, and main Hawaiian Islands. The geomorphology of MCEs was largely inherited from a variety of pre-existing structures of highly diverse origins, which, in combination with environmental stress and physical controls, restrict the distribution of MCEs. Sea-level history, along with depositional and erosional processes, played an integral role in formation of MCE settings. However, mapping the distribution of both potential MCE topography/substrate and existing MCE habitat is only beginning. Mapping techniques pertinent to understanding morphology and MCE distributions are discussed throughout this paper. Future investigations need to consider more cost-effective and remote methods (such as autonomous underwater vehicles (AUVs) and acoustics) in order to assess the distribution and extent of MCE habitat. Some understanding of the history of known MCEs through coring studies would help understand their initiation and response to environmental change over time, essential for assessing how they may be impacted by future environmental change.     

Community ecology of mesophotic coral reef ecosystems

Given the global degradation of shallow-water coral reef ecosystems resulting from anthropogenic activities, mesophotic coral reef ecosystems (MCEs) are gaining attention because they are generally considered a de facto refuge for shallow-water species. Despite their inferred importance, MCEs remain one of the most understudied reef habitats, and basic information on the taxonomic composition, depth range, habitat preferences, and abundance and distribution of MCE taxa is scarce. The processes that structure these communities are virtually unknown. Here, we provide a review of what is known about MCEs community ecology and outline essential gaps in our knowledge of these deeper water coral reef ecosystems. The primary findings of this review are as follows: (1) many dominant shallow-water species are absent from MCEs; (2) compared to shallow reefs, herbivores are relatively scarce, perhaps due to limited habitat complexity at depth; (3) changes in the dominant photosynthetic taxa with depth suggest adaptation and specialization to depth; (4) evidence regarding the importance of heterotrophy for zooxanthellate corals at depth is conflicting and inconclusive; and (5) decreased light with depth, but not temperature, appears to be the primary factor limiting the depth of MCEs. The majority of research done to date has been performed in the Caribbean, where some generalization can be made about the community structure and distribution of MCEs. The larger and more diverse Indo-Pacific remains largely unexplored with no apparent generalizations from the few sites that have been comparatively well studied. For MCEs, large gaps in knowledge remain on fundamental aspects of ecology. Advanced technologies must be harnessed and logistical challenges overcome to close this knowledge gap and empower resource managers to make informed decisions on conserving shallow-water and mesophotic coral reef ecosystems.     

Higher species richness of octocorals in the upper mesophotic zone in Eilat (Gulf of Aqaba) compared to shallower reef zones

Mesophotic coral-reef ecosystems (MCEs), which comprise the light-dependent communities of corals and other organisms found at depths between 30 and ~ 150 m, have received very little study to date. However, current technological advances, such as remotely operated vehicles and closed-circuit rebreather diving, now enable their thorough investigation. Following the reef-building stony corals, octocorals are the second most common benthic component on many shallow reefs and a major component on deep reefs, the Red Sea included. This study is the first to examine octocoral community features on upper MCEs based on species-level identification and to compare them with the shallower reef zones. The study was carried out at Eilat (Gulf of Aqaba, northern Red Sea), comparing octocoral communities at two mesophotic reefs (30–45 m) and two shallow reef zones (reef flat and upper fore-reef) by belt transects. A total of 30 octocoral species were identified, with higher species richness on the upper MCEs compared to the shallower reefs. Although the MCEs were found to host a higher number of species than the shallower reefs, both featured a similar diversity. Each reef zone revealed a unique octocoral species composition and distinct community structure, with only 16% of the species shared by both the MCEs and the shallower reefs. This study has revealed an almost exclusive dominance of zooxanthellate species at the studied upper MCE reefs, thus indicating an adequate light regime for photosynthesis there. The findings should encourage similar studies on other reefs, aimed at understanding the spatiotemporal features and ecological role of octocorals in reef ecosystems down to the deepest limit of the MCEs.     

Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss

Effects of maternal cytoplasmic environment (MCE) on development rate in rainbow trout were evaluated within a quantitative trait loci (QTL) analysis framework. Previous research had identified QTL for development rate in doubled haploid (DH) progeny produced from a cross between the Oregon State University (OSU) and the Swanson (SW) River rainbow trout clonal lines. In this study, progeny for QTL mapping were produced from a cross between the OSU and Clearwater (CW) River clonal lines. Doubled haploids were produced from the OSU x CW F1 by androgenesis using eggs from different females (or MCEs); with androgenesis, the maternal nuclear genome was destroyed by irradiation and diploidy was restored by blocking the first embryonic cleavage by heat shock. All embryos were incubated at the same temperature and development rate quantified as time to hatch. Using a linkage map constructed primarily with AFLP markers, QTL mapping was performed, including MCE covariates and QTL x MCE effects in models for testing. The major QTL for development rate in the OSU x SW cross overlaps with the major QTL found in this OSU x CW cross; effects at this locus were the same across MCEs. Both MCE and QTL x MCE effects contribute to variability in development rate, but QTL x MCE were minor and detected only at small-effect QTL.     

Evaluation and mapping of the conservation significance of habitats using GIS: an example from Crete, Greece

To ensure the long-term future of NATURA 2000 sites across Europe, effective techniques are required for evaluating and monitoring their conservation significance. This paper describes a GIS-based method that uses multi-criteria evaluation (MCE) to determine the conservation significance of vegetation communities and habitats for a case study of a proposed NATURA 2000 site on the northwest coast of Crete, Greece. The method uses the most frequently used criteria for the selection of priority areas for nature conservation—species and habitat diversity, rarity of species and habitats, naturalness, threat of human disturbance and replaceability. For each community and corresponding habitat type, each criterion was scored according to field data and expert knowledge using a numerical scale. The final conservation score for each community was derived using MCE within a GIS and mapped. The results demonstrated that the method is an effective tool for evaluating and comparing conservation significance and could be applied to other sites across Europe and to monitor change.     

Theme section on “Mesophotic Coral Ecosystems: Characterization, Ecology, and Management”

Mesophotic coral ecosystems (MCEs) are characterized by the presence of light-dependent corals and associated communities that are typically found at depths ranging from 30 to 40 m and extending to over 150 m in tropical and subtropical regions. The dominant communities providing structural habitat in the mesophotic zone can be comprised of coral, sponge, and algal species. Because working in this depth range is constrained by traditional SCUBA limits, less is known about corals and associated organisms there compared to shallower coral communities. Following the first-ever gathering of international scientists to review and discuss existing knowledge of MCEs, this issue focuses on the ecological characterization, geomorphology, and concept of MCEs as refugia for shallow-water populations. The review and research papers comprising this special issue reflect the current scientific understanding of these ecosystems and the underlying mechanisms that regulate them, as well as potential resource management implications. It is important to understand the value and role of mesophotic coral ecosystems in tropical and subtropical regions as these areas face increasing environmental change and human impacts     

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m)

Mesophotic coral ecosystems (MCEs) are generally poorly studied, and our knowledge of lower MCEs (below 60 m depth) is largely limited to visual surveys. Here, we provide a first detailed assessment of the prokaryotic community associated with scleractinian corals over a depth gradient to the lower mesophotic realm (15–85 m). Specimens of three Caribbean coral species exhibiting differences in their depth distribution ranges (Agaricia grahamae, Madracis pharensis and Stephanocoenia intersepta) were collected with a manned submersible on the island of Curaçao, and their prokaryotic communities assessed using 16S rRNA gene sequencing analysis. Corals with narrower depth distribution ranges (depth-specialists) were associated with a stable prokaryotic community, whereas corals with a broader niche range (depth-generalists) revealed a higher variability in their prokaryotic community. The observed depth effects match previously described patterns in Symbiodinium depth zonation. This highlights the contribution of structured microbial communities over depth to the coral’s ability to colonize a broader depth range.     

Deep reefs are not refugium for shallow‐water fish communities in the southwestern Atlantic

1. The deep reef refugia hypothesis (DRRH) predicts that deep reef ecosystems may act as refugium for the biota of disturbed shallow waters. Because deep reefs are among the most understudied habitats on Earth, formal tests of the DRRH remain scarce. If the DRRH is valid at the community level, the diversity of species, functions, and lineages of fish communities of shallow reefs should be encapsulated in deep reefs.
2. We tested the DRRH by assessing the taxonomic, functional, and phylogenetic diversity of 22 Brazilian fish communities between 2 and 62 m depth. We partitioned the gamma diversity of shallow (<30 m) and deep reefs (>30 m) into independent alpha and beta components, accounted for species’ abundance, and assessed whether beta patterns were mostly driven by spatial turnover or nestedness.
3. We recorded 3,821 fishes belonging to 85 species and 36 families. Contrary to DRRH expectations, only 48% of the species occurred in both shallow and deep reefs. Alpha diversity of rare species was higher in deep reefs as expected, but alpha diversity of typical and dominant species did not vary with depth. Alpha functional diversity was higher in deep reefs only for rare and typical species, but not for dominant species. Alpha phylogenetic diversity was consistently higher in deep reefs, supporting DRRH expectations.
4. Profiles of taxonomic, functional, and phylogenetic beta diversity indicated that deep reefs were not more heterogeneous than shallow reefs, contradicting expectations of biotic homogenization near sea surface. Furthermore, pairwise beta‐diversity analyses revealed that the patterns were mostly driven by spatial turnover rather than nestedness at any depth.
5. Conclusions. Although some results support the DRRH, most indicate that the shallow‐water reef fish diversity is not fully encapsulated in deep reefs. Every reef contributes significantly to the regional diversity and must be managed and protected accordingly.

     

An assessment of shallow and mesophotic reef brachyuran crab assemblages on the south shore of O‘ahu,Hawai‘i

Shallow coral reefs are extensively studied but, although scleractinian corals have been recorded to 165 m, little is known about other mesophotic coral reef ecosystem (MCE) inhabitants. Brachyuran crabs fill many ecological and trophic niches on reefs, making them ideal candidates for evaluating species composition among depths to ask whether MCEs host the same communities as shallower reef communities that have been well studied. Here we deployed autonomous reef monitoring structures for 2 yr on the south shore of O‘ahu along a depth gradient (12, 30, 60, and 90 m) to sample and assess brachyuran crab communities. A total of 663 brachyuran crabs representing 69 morphospecies (16 families) were found. Community composition was not significantly different within depths, but was highly stratified by depth. Each depth was distinct, but the 30 and 60 m depths were least dissimilar from one another. We show that deeper reefs host significantly different brachyuran communities, and at much lower total abundance, than shallow reefs in Hawai‘i, with 4–27 unique morphospecies per depth and only 3 of 69 morphospecies (~4 %) occurring across the entire depth range sampled.     

Fish and flow management in the Murray–Darling Basin: Directions for research

Effective natural resource management requires knowledge exchange between researchers and managers to support evidence‐based decision‐making. To achieve this, there is a need to align research with management and policy needs. This project aimed to identify the flow‐related ecological knowledge needs for freshwater fish to better inform environmental water management in the Murray–Darling Basin, south‐eastern Australia. Our major objective was to provide an up‐to‐date assessment of scientific research and integrate this with the knowledge requirements of relevant managers to guide future research. We reviewed the contemporary scientific literature and engaged managers specifically responsible for delivering flows for fish outcomes via a questionnaire and workshop. Research on fishes of the MDB has generally evolved from single locations and/or times to larger spatio‐temporal scales, including multiple sites, rivers and catchments. There has also been a trend from single life stage studies to incorporation of multiple life stages and population processes. There remain, however, significant deficiencies in knowledge for most native species, many of which are threatened. Four agreed key knowledge gaps were derived from the literature review and managers’ suggestions: (i) population dynamics, (ii) movement, dispersal and connectivity, (iii) survival and recruitment to adults and (iv) recruitment drivers. To inform policy and management, managers desired timely advice, based on robust research and monitoring. Fish species of most relevance to managers were those highly regarded by community stakeholders and whose life histories and population dynamics are potentially influenced by flow. Populations of these mostly large‐bodied, angling species (e.g. Murray Cod, Golden Perch and Silver Perch) have declined, often due to river regulation and, in conjunction with managers’ priorities, are relevant candidates for research to support the management of flow to rehabilitate fish populations in the MDB.     

Epimerase (Msed_0639) and Mutase (Msed_0638 and Msed_2055) Convert (S)-Methylmalonyl-Coenzyme A (CoA) to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle

Crenarchaeotal genomes encode the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle for carbon dioxide fixation. Of the 13 enzymes putatively comprising the cycle, several of them, including methylmalonyl-coenzyme A (CoA) epimerase (MCE) and methylmalonyl-CoA mutase (MCM), which convert (S)-methylmalonyl-CoA to succinyl-CoA, have not been confirmed and characterized biochemically. In the genome of Metallosphaera sedula (optimal temperature [T(opt)], 73°C), the gene encoding MCE (Msed_0639) is adjacent to that encoding the catalytic subunit of MCM-α (Msed_0638), while the gene for the coenzyme B(12)-binding subunit of MCM (MCM-β) is located remotely (Msed_2055). The expression of all three genes was significantly upregulated under autotrophic compared to heterotrophic growth conditions, implying a role in CO(2) fixation. Recombinant forms of MCE and MCM were produced in Escherichia coli; soluble, active MCM was produced only if MCM-α and MCM-β were coexpressed. MCE is a homodimer and MCM is a heterotetramer (α(2)β(2)) with specific activities of 218 and 2.2 μmol/min/mg, respectively, at 75°C. The heterotetrameric MCM differs from the homo- or heterodimeric orthologs in other organisms. MCE was activated by divalent cations (Ni(2+), Co(2+), and Mg(2+)), and the predicted metal binding/active sites were identified through sequence alignments with less-thermophilic MCEs. The conserved coenzyme B(12)-binding motif (DXHXXG-SXL-GG) was identified in M. sedula MCM-β. The two enzymes together catalyzed the two-step conversion of (S)-methylmalonyl-CoA to succinyl-CoA, consistent with their proposed role in the 3-HP/4-HB cycle. Based on the highly conserved occurrence of single copies of MCE and MCM in Sulfolobaceae genomes, the M. sedula enzymes are likely to be representatives of these enzymes in the 3-HP/4-HB cycle in crenarchaeal thermoacidophiles.     

RNAi‐based GM plants: food for thought for risk assessors

RNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi‐based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here.     

Importance of spatio–temporal connectivity to maintain species experiencing range shifts

Climate change can affect the habitat resources available to species by changing habitat quantity, suitability and spatial configuration, which largely determine population persistence in the landscape. In this context, dispersal is a central process for species to track their niche. Assessments of the amount of reachable habitat (ARH) using static snap-shots do not account, however, for the temporal overlap of habitat patches that may enhance stepping-stone effects. Here, we quantified the impacts of climate change on the ARH using a spatio–temporal connectivity model. We first explored the importance of spatio–temporal connectivity relative to purely spatial connectivity in a changing climate by generating virtual species distributions and analyzed the relative effects of changes in habitat quantity, suitability and configuration. Then, we studied the importance of spatio–temporal connectivity in three vertebrate species with divergent responses to climate change in North America (grey wolf, Canadian lynx and white-tailed deer). We found that the spatio–temporal connectivity could enhance the stepping-stone effect for species predicted to experience range contractions, and the relative importance of the spatio–temporal connectivity increased with the reduction in habitat quantity and suitability. Conversely, for species that are likely to expand their ranges, spatio–temporal connectivity had no additional contribution to improve the ARH. We also found that changes in habitat amount (quantity and suitability) were more influential than changes in habitat configuration in determining the relative importance of spatio–temporal connectivity. We conclude that spatio–temporal connectivity may provide less biased and more realistic estimates of habitat connectivity than purely spatial connectivity.     

Conservation genomics of natural and managed populations: building a conceptual and practical framework

The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time‐consuming. To address this gap, a recent workshop entitled ‘ConGen 2015’ was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges.     

<Emphasis Type="Italic">Euphyllia paradivisa</Emphasis>, a successful mesophotic coral in the northern Gulf of Eilat/Aqaba,Red Sea

Mesophotic coral ecosystems (MCEs) host a thriving community of biota that has remained virtually unexplored. Here we report for the first time on a large population of the endangered coral species Euphyllia paradivisa from the MCEs of the Gulf of Eilat/Aqaba (GOE/A), Red Sea. The mesophotic zone in some parts of the study site harbors a specialized coral community predominantly comprising E. paradivisa (73 % of the total coral cover), distributed from 36 to 72 m depth. Here we sought to elucidate the strict distribution but high abundance of E. paradivisa in the MCEs at the GOE/A. We present 4 yr of observations and experiments that provide insight into the physiological plasticity of E. paradivisa: its low mortality rates at high light intensities, high competitive abilities, successful symbiont adaptation to the shallow-water environment, and tolerance to bleaching conditions or survival during prolonged bleaching. Despite its ability to survive under high irradiance in shallow water, E. paradivisa is not found in the shallow reef of the GOE/A. We suggest several factors that may explain the high abundance and exclusivity of E. paradivisa in the MCE: its heterotrophic capabilities; its high competition abilities; the possibility of it finding a deep-reef refuge there from fish predation; and its concomitant adaptation to this environment.     

记忆水平依赖的海马-前额叶神经节律交互

海马(HPC)和前额叶皮层(PFC)的协同作用是记忆加工过程的关键,其相互作用对学习和记忆功能至关重要.大量证据表明,情景记忆的形成、巩固与检索依赖于特征神经节律在PFC和HPC脑区间的同步作用,这些节律包括theta节律、gamma节律和sharp wave ripples (SWRs)节律等.在精神类疾病中患者往往伴随出现学习记忆功能障碍,基于人类和动物的脑电研究均发现以上3种神经节律在HPC和PFC之间的同步性下降,可能作为反映精神病理下认知功能障碍的重要指标.本文从HPC-PFC网络中的神经节律研究出发,总结了theta节律、gamma节律和SWRs节律在两脑区间的协调交互模式在情景记忆中的作用,以及精神分裂症和抑郁症状态下HPC-PFC通路上神经节律的异常表现及其潜在损伤机制,为今后精神疾病的快速诊断提供客观依据.     

Beyond species distribution modeling: A landscape genetics approach to investigating range shifts under future climate change

Understanding how biodiversity will respond to future climate change is a major conservation and societal challenge. Climate change is predicted to force many species to shift their ranges in pursuit of suitable conditions. This study aims to use landscape genetics, the study of the effects of environmental heterogeneity on the spatial distribution of genetic variation, as a predictive tool to assess how species will shift their ranges to track climatic changes and inform conservation measures that will facilitate movement. The approach is based on three steps: 1) using species distribution models (SDMs) to predict suitable ranges under future climate change, 2) using the landscape genetics framework to identify landscape variables that impede or facilitate movement, and 3) extrapolating the effect of landscape connectivity on range shifts in response to future climate change. I show how this approach can be implemented using the publicly available genetic dataset of the grey long-eared bat, Plecotus austriacus, in the Iberian Peninsula. Forest cover gradient was the main landscape variable affecting genetic connectivity between colonies. Forest availability is likely to limit future range shifts in response to climate change, primarily over the central plateau, but important range shift pathways have been identified along the eastern and western coasts. I provide outputs that can be directly used by conservation managers and review the viability of the approach. Using landscape genetics as a predictive tool in combination with SDMs enables the identification of potential pathways, whose loss can affect the ability of species to shift their range into future climatically suitable areas, and the appropriate conservation management measures to increase landscape connectivity and facilitate movement.     

Mesophotic coral ecosystems in the Hawaiian Archipelago

Efforts to map coral reef ecosystems in the Hawaiian Archipelago using optical imagery have revealed the presence of numerous scleractinian, zoothanthellate coral reefs at depths of 30–130+ m, most of which were previously undiscovered. Such coral reefs and their associated communities have been recently defined as mesophotic coral ecosystems (MCEs). Several types of MCEs are found in Hawai‘i, each of which dominates a different depth range and is characterized by a unique pattern of coral community structure and colony morphology. Although MCEs are documented near both ends of the archipelago and on many of the islands in between, the maximum depth and prevalence of MCEs in Hawai‘i were found to decline with increasing latitude. The Main Hawaiian Islands (MHI) had significantly deeper and greater percentages of scleractinian coral, and peaks in cover of both scleractinian corals and macroalgae occurred within depth bins 20 m deeper than in the Northwestern Hawaiian Islands (NWHI). Across the archipelago, as depth increased the combined percentage of living cover of mega benthic taxa declined sharply with increasing depth below 70 m, despite the widespread availability of hard substrate.