珊瑚病原微生物鉴定及其分子诊断技术进展

珊瑚礁生态系统是热带海洋最突出、最具代表性的生态系统,具有极高的生态价值和经济价值,然而由珊瑚疾病引起的珊瑚礁退化已经成为珊瑚礁生态系统的主要威胁之一。许多微生物(主要包括细菌、真菌、病毒)被认为与珊瑚疾病发生密切相关,确定珊瑚疾病的病原并建立其快速诊断的方法是开展珊瑚疾病流行病学调查和制定防控措施的必由之路。本文主要综述珊瑚疾病的病原微生物及其分子诊断技术的研究进展。     

珊瑚礁生态系统病毒研究进展

病毒对珊瑚礁生态系统中的生物进化、生物地球化学循环、珊瑚疾病等方面具有重要的生态影响。随着珊瑚礁的全球性退化,病毒在珊瑚礁生态系统中的功能与危害日益显现。综述了珊瑚礁生态系统中病毒的研究现状与进展,包括：（1）珊瑚礁病毒的多样性与分布特征（水体、宿主、核心病毒组）;（2）珊瑚礁病毒的生态功能（感染方式、促进生物进化、生物地球化学循环）;（3）珊瑚礁病毒对全球气候变化的响应（热压力、珊瑚疾病）。总体而言,珊瑚礁生态系统具有极高的病毒多样性,所发现的60个科占已知所有病毒科数量的58%。珊瑚的核心病毒组主要由双链DNA病毒、单链DNA病毒、单链逆转录病毒所组成,珊瑚黏液层对病毒具有富集作用。"Piggyback-the-Winner"（依附-胜利）是病毒在珊瑚礁中主要的生物动力学模式,其可通过水平基因迁移的方式促进礁区生物进化。病毒可通过裂解细菌与浮游藻类的途径参与珊瑚礁的生物地球化学循环,尤其是碳循环与氮循环过程。此外,病毒还具有介导珊瑚热白化与直接引发珊瑚疾病的能力,这会影响珊瑚礁生态系统应对气候变化的适应性与恢复力。基于国际上的研究进展综述,结合南海珊瑚礁生态现状提出以下研究方向,以期促进我国珊瑚礁病毒学的发展：（1）开展南海珊瑚礁中病毒多样性的识别及其时-空分布特征研究;（2）探索病毒对南海珊瑚热白化、珊瑚疾病的介导作用及其与气候变化的关系;（3）揭示病毒对南海珊瑚礁生物地球化学循环的贡献。     

The urgent need for robust coral disease diagnostics

Coral disease has emerged over recent decades as a significant threat to coral reef ecosystems, with declines in coral cover and diversity of Caribbean reefs providing an example of the potential impacts of disease at regional scales. If similar trends are to be mitigated or avoided on reefs worldwide, a deeper understanding of the factors underlying the origin and spread of coral diseases and the steps that can be taken to prevent, control, or reduce their impacts is required. In recent years, an increased focus on coral microbiology and the application of classic culture techniques and emerging molecular technologies has revealed several coral pathogens that could serve as targets for novel coral disease diagnostic tools. The ability to detect and quantify microbial agents identified as indicators of coral disease will aid in the elucidation of disease causation and facilitate coral disease detection and diagnosis, pathogen monitoring in individuals and ecosystems, and identification of pathogen sources, vectors, and reservoirs. This information will advance the field of coral disease research and contribute knowledge necessary for effective coral reef management. This paper establishes the need for sensitive and specific molecular-based coral pathogen detection, outlines the emerging technologies that could serve as the basis of a new generation of coral disease diagnostic assays, and addresses the unique challenges inherent to the application of these techniques to environmentally derived coral samples.     

A precise and non-destructive method to calculate the surface area in living scleractinian corals using X-ray computed tomography and 3D modeling

The surface area of corals represents a major reference parameter for the standardization of flux rates, for coral growth investigations, and for investigations of coral metabolism. The methods currently used to determine the surface area of corals are rather approximate approaches lacking accuracy, or are invasive and often destructive methods that are inapplicable for experiments involving living corals. This study introduces a novel precise and non-destructive technique to quantify surface area in living coral colonies by applying computed tomography (CT) and subsequent 3D reconstruction. Living coral colonies of different taxa were scanned by conventional medical CT either in air or in sea water. Resulting data volumes were processed by 3D modeling software providing realistic 3D coral skeleton surface reconstructions, thus enabling surface area measurements. Comparisons of CT datasets obtained from calibration bodies and coral colonies proved the accuracy of the surface area determination. Surface area quantifications derived from two different surface rendering techniques applied for scanning living coral colonies showed congruent results (mean deviation ranging from 1.32 to 2.03%). The validity of surface area measurement was verified by repeated measurements of the same coral colonies by three test persons. No significant differences between all test persons in all coral genera and in both surface rendering techniques were found (independent sample t-test: all n.s.). Data analysis of a single coral colony required approximately 15 to 30 min for a trained user using the isosurface technique regardless of the complexity and growth form of the latter, rendering the method presented in this study as a time-saving and accurate method to quantify surface areas in both living coral colonies and bare coral skeletons. Communicated by Biology Editor Dr Michael Lesser     

珊瑚礁生态脆弱性评价--以泰国思仓岛为例

珊瑚礁生态系统受到环境变化、人类活动等各种因素的严重威胁,保护珊瑚礁生态系统是目前全球海洋生态保护的热点,对珊瑚礁开展定量的生态脆弱性评估能够为保护管理对策的制定提供重要科学依据。本研究选取泰国思仓岛作为研究区域,结合空间分析技术建立了具有通用性的珊瑚礁生态脆弱性评估方法。基于ESA模型构建了珊瑚礁生态脆弱性综合指数和评价指标体系,系统分析了思仓岛珊瑚礁脆弱性的来源、构成,并直观展现了脆弱性的区域空间分布。结果表明:思仓岛研究区东北侧的珊瑚礁生态脆弱性大于西南侧,当地珊瑚礁的关键影响因子分别为驳船排污、港口码头、水体透明度等。根据脆弱性评价的结果,提出了当地珊瑚礁保护与修复的空间分区管理对策。本研究为印度-太平洋区系珊瑚礁生态脆弱性评价提供了可行的示例,也为中国的珊瑚礁可持续管理研究提供了借鉴和参照。     

Increased light intensity induces heat shock protein Hsp60 in coral species

The effect of increased light intensity and heat stress on heat shock protein Hsp60 was examined in two coral species using a branched coral and a laminar coral, selected for their different resistance to environmental perturbation. Transient Hsp60 induction was observed in the laminar coral following either light or thermal stress. Sustained induction was observed when these stresses were combined. The branched coral exhibited comparatively weak transient Hsp60 induction after heat stress and no detectable induction following light stress, consistent with its susceptibility to bleaching in native environments compared to the laminar coral. Our observations also demonstrate that increased light intensity and heat stress exhibited a greater negative impact on the photosynthetic capacity of environmentally sensitive branched coral than the more resistant laminar coral. This supports a correlation between stress induction of Hsp60 and (a) ability to counter perturbation of photosynthetic capacity by light and heat stress and (b) resistance to environmentally induced coral bleaching.     

Large‐scale coral reef rehabilitation after blast fishing in Indonesia

The severely degraded condition of many coral reefs worldwide calls for active interventions to rehabilitate their physical and biological structure and function, in addition to effective management of fisheries and no‐take reserves. Rehabilitation efforts to stabilize reef substratum sufficiently to support coral growth have been limited in size. We documented a large coral reef rehabilitation in Indonesia aiming to restore ecosystem functions by increasing live coral cover on a reef severely damaged by blast fishing and coral mining. The project deployed small, modular, open structures to stabilize rubble and to support transplanted coral fragments. Between 2013 to 2015, approximately 11,000 structures covering 7,000 m² were deployed over 2 ha of a reef at a cost of US$174,000. Live coral cover on the structures increased from less than 10% initially to greater than 60% depending on depth, deployment date and location, and disturbances. The mean live coral cover in the rehabilitation area in October 2017 was higher than reported for reefs in many other areas in the Coral Triangle, including marine protected areas, but lower than in the no‐take reference reef. At least 42 coral species were observed growing on the structures. Surprisingly, during the massive coral bleaching in other regions during the 2014–2016 El Niño–Southern Oscillation event, bleaching in the rehabilitation area was less than 5% cover despite warm water (≥30°C). This project demonstrates that coral rehabilitation is achievable over large scales where coral reefs have been severely damaged and are under continuous anthropogenic disturbances in warming waters.     

Using Agent-Based Models to Aid Reef Restoration: Enhancing Coral Cover and Topographic Complexity through the Spatial Arrangement of Coral Transplants

High coral cover and topographic complexity are favorable qualities of a healthy coral reef. Because coral reef restoration is expensive and coral growth is naturally slow, there is a need to strategically arrange coral transplants to maximize coral cover and topographic complexity. Similarly, it is important to understand how differences in the life history characteristics of coral transplants can influence changes in the structural attributes of coral reefs. This study utilizes agent‐based computer modeling to explore the different spatial scenarios of coral transplantation using corals with contrasting r‐ and K‐selected life histories. Spatial indexes are used to compare coral cover and topographic complexity at incremental time scales, within which disturbance events are of minor importance in spatial structuring. The outcomes of the model suggest that even‐spaced grided transplanting arrangements provide the fastest increase in coral cover and three‐dimensional habitat space (topographic complexity) across large temporal scales (<30 years) for corals with r‐selected life history strategies.     

Early cellular changes are indicators of pre-bleaching thermal stress in the coral host

Thermal stress causes the coral-dinoflagellate symbiosis to disassociate and the coral tissues to whiten. The onset and occurrence of this coral bleaching is primarily defined via the dinoflagellate responses. Here we demonstrate that thermal stress responses occur in the coral host tissues in the days before the onset of coral bleaching. The observed sequence of thermal responses includes reductions in thickness of coral tissue layers and apoptosis of the cells prior to reductions in symbiont density. In the days before the onset of coral bleaching the outer coral tissue layer (epithelium) thickness reduces and apoptosis occurs within the gastrodermis. Two days following this, coinciding with an initial reduction of symbiont density (by approximately 25%), gastrodermal thickness decreased and apoptosis of host cells was identified in the epithelium. This was eventually followed by large reduction in symbiont density (by approximately 50%) consistent with coral bleaching. Both pro-apoptotic and anti-apoptotic genes are identified in the reef building coral Acropora aspera, demonstrating the necessary pathways are present for fine control of host apoptosis. Our study shows that defining periods of host stress based on the responses defined by dinoflagellate symbiont underestimates the importance of early cellular events and the cellular complexity of coral host.     

不同改良剂对珊瑚砂理化性质和氮素固持的影响

高碱环境和土壤养分的匮乏严重限制了我国热带珊瑚岛土壤环境下植物的生长适应能力,因此,珊瑚砂改良对促进珊瑚岛植被恢复,维持珊瑚岛生态环境可持续健康发展具有重要意义。该研究通过室内土柱模拟试验,对比了同一梯度下4种常用土壤改良材料(蛭石、珍珠岩、生物炭和钙基膨润土)对珊瑚砂理化性质、氮素淋溶以及总氮含量的影响。结果表明,与对照(CK)相比,施用生物炭使珊瑚砂pH显著降低1.4%,钙基膨润土、生物炭和蛭石能够显著提高珊瑚砂的阳离子交换量至CK的24.21、10.43和9.43倍。同时,施用生物炭、钙基膨润土和蛭石并不能降低以硝态氮形式为主的氮素淋失,但是能显著减少其他途径的氮素损失,从而达到促进珊瑚砂氮素固持的效果,3种改良剂施用下的珊瑚砂总氮损失相较于CK分别降低了40.92%、27.32%和25.09%。因此,施用生物炭、钙基膨润土和蛭石均能有效提高珊瑚砂土壤质量,对改良珊瑚砂和热带珊瑚岛植被恢复具有重要意义,其中生物炭的改良效果最为显著,是改良珊瑚砂的理想材料。     

Coral density and predation affect growth of a reef-building coral

The influence of predation on the growth of stony corals has gained increased attention, although the degree to which coral conspecific density can modify the effects of corallivores remains poorly studied. Here, a field experiment was used to quantify the independent and combined effects of coral colony density and coral predators on the skeletal growth of massive Porites. Predator exclusion increased coral growth by 20%. Increasing coral density increased growth by 30%. However, the effect of predators was independent of coral density. Possible alternative mechanisms for increased skeletal growth at higher colony density include changes in near-field flow, resulting in increases in photosynthetic activity, nutrient uptake, or the increased accessibility of coral mutualists.     

Relative Importance of Coral Cover,Habitat Complexity and Diversity in Determining the Structure of Reef Fish Communities

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m² quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.     

Live coral repels a common reef fish ectoparasite

Coral reefs are undergoing rapid changes as living corals give way to dead coral on which other benthic organisms grow. This decline in live coral could influence habitat availability for fish parasites with benthic life stages. Gnathiid isopod larvae live in the substratum and are common blood-feeding parasites of reef fishes. We examined substrate associations and preferences of a common Caribbean gnathiid, Gnathia marleyi. Emergence traps set over predominantly live coral substrata captured significantly fewer gnathiids than traps set over dead coral substrata. In laboratory experiments, gnathiids preferred dead coral and sponge and tended to avoid contact with live coral. When live gnathiids were added to containers with dead or live coral, significantly fewer were recovered from the latter after 24 h. Our data therefore suggest that live coral is not suitable microhabitat for parasitic gnathiid isopods and that a decrease in live coral cover increases available habitat for gnathiids.     

Region‐wide temporal and spatial variation in Caribbean reef architecture: is coral cover the whole story?

The architectural complexity of coral reefs is largely generated by reef‐building corals, yet the effects of current regional‐scale declines in coral cover on reef complexity are poorly understood. In particular, both the extent to which declines in coral cover lead to declines in complexity and the length of time it takes for reefs to collapse following coral mortality are unknown. Here we assess the extent of temporal and spatial covariation between coral cover and reef architectural complexity using a Caribbean‐wide dataset of temporally replicated estimates spanning four decades. Both coral cover and architectural complexity have declined rapidly over time, with little evidence of a time‐lag. However, annual rates of change in coral cover and complexity do not covary, and levels of complexity vary greatly among reefs with similar coral cover. These findings suggest that the stressors influencing Caribbean reefs are sufficiently severe and widespread to produce similar regional‐scale declines in coral cover and reef complexity, even though reef architectural complexity is not a direct function of coral cover at local scales. Given that architectural complexity is not a simple function of coral cover, it is important that conservation monitoring and restoration give due consideration to both architecture and coral cover. This will help ensure that the ecosystem services supported by architectural complexity, such as nutrient recycling, dissipation of wave energy, fish production and diversity, are maintained and enhanced.     

珊瑚共生体碳代谢特征研究进展

珊瑚礁作为一种典型的海洋生态系统,具有巨大的固碳和储碳潜力。然而,目前对于珊瑚礁的净碳能力(碳释放与碳吸收)仍存在争议,主要归因于珊瑚共生体碳代谢的多样性和复杂性。珊瑚礁在生物钙化、呼吸过程中向大气释放二氧化碳(CO₂);但在生物合成和沉积过程中却可以将碳进行固定与埋藏;为此,珊瑚礁的碳源碳汇身份还有待明确。现有部分研究表明,共生体通过碳代谢可以促进珊瑚礁吸收大气中的CO₂。此外,珊瑚礁和海岸带蓝碳生态系统通常表现出很强的连通性,珊瑚共生体碳代谢能有效提高海岸带盐沼植被、海草床、海洋浮游植物等生物的碳汇功能。为了加深对珊瑚礁碳源-碳汇功能的理解,综述了珊瑚共生体的碳代谢特征,梳理了共生体中碳的关键生态过程(有机碳的迁移、无机碳的转化、两者的赋存状态),总结了细菌-虫黄藻-病毒在共生体碳代谢中的作用,评述了珊瑚礁碳源-碳汇特征及影响因子。旨在阐明珊瑚共生体碳代谢的关键过程,并基于此寻求有效的珊瑚礁碳增汇技术,形成以碳增量为主的珊瑚保护与修复技术,提升珊瑚礁在蓝碳生态系统中的贡献。     

Comparison of coral diversity between big and small atolls: a case study of Yongle atoll and Lingyang reef,Xisha Islands,central of South China Sea

The South China Sea (SCS) includes large areas of extensive coral reef development but its reefs are still poorly known. Yongle atoll is the biggest typical atoll in the Xisha Islands, central of SCS. Lingyang Reef is an isolated small atoll within the whole big Yongle atoll. A total of 144 and 119 coral species were recorded at big Yongle atoll and small Lingyang Reef, respectively. The real coral richness might be higher because species accumulation curve did not saturate. The coral diversity pattern was similar between big Yongle atoll and small Lingyang Reef. Coral communities fell into three clusters, consistent with their habitats on reef slope, reef flat and lagoon slope. The highest coral diversity was observed on reef slopes and the lowest coral diversity was found on lagoon slope. Genera richness was a better proxy for representing coral species diversity on both the big and small atoll but percent live coral cover was not a robust proxy on the small atoll, which only explained 24% of species diversity. This study demonstrated high coral diversity with consistent pattern along habitat types, as has been shown from many other reefs. While far from exhaustive, the study allows first glimpses on how much biodiversity is contained on SCS coral reefs, and hopes to give an impetus to their conservation. The study also suggests that simplified surveys at a small scale and the use of genera richness as an effective proxy for overall diversity can indeed provide important information to rapidly monitor and evaluate the coral diversity in remote locations.     

Influence of habitat degradation on fish replenishment

Temperature-induced coral bleaching is a major threat to the biodiversity of coral reef ecosystems. While reductions in species diversity and abundance of fish communities have been documented following coral bleaching, the mechanisms that underlie these changes are poorly understood. The present study examined the impacts of coral bleaching on the early life-history processes of coral reef fishes. Daily monitoring of fish settlement patterns found that ten times as many fish settled to healthy coral than sub-lethally bleached coral. Species diversity of settling fishes was least on bleached coral and greatest on dead coral, with healthy coral having intermediate levels of diversity. Laboratory experiments using light-trap caught juveniles showed that different damselfish species chose among healthy, bleached and dead coral habitats using different combinations of visual and olfactory cues. The live coral specialist, Pomacentrus moluccensis, preferred live coral and avoided bleached and dead coral, using mostly visual cues to inform their habitat choice. The habitat generalist, Pomacentrus amboinensis, also preferred live coral and avoided bleached and dead coral but selected these habitats using both visual and olfactory cues. Trials with another habitat generalist, Dischistodus sp., suggested that vision played a significant role. A 20 days field experiment that manipulated densities of P. moluccensis on healthy and bleached coral heads found an influence of fish density on juvenile weight and growth, but no significant influence of habitat quality. These results suggests that coral bleaching will affect settlement patterns and species distributions by influencing the visual and olfactory cues that reef fish larvae use to make settlement choices. Furthermore, increased fish density within the remaining healthy coral habitats could play an important role in influencing population dynamics.     

Sunlight and water transparency: cornerstones in coral research

Reef-building corals throughout the world are considered endangered. The evidence is a decline in coral health and reduced coral cover. Competing hypotheses for the cause of coral loss include removal of grazers, nutrient enrichment, disease, coral bleaching, increase in temperature, and excess light/ultraviolet exposure. We suggest that light limitation as a second order effect of anthropogenic activity (e.g. sediment resuspension and nutrient enrichment) is a valid and tractable hypothesis. This experimental field and laboratory study demonstrates that corals of the Florida reefs are functioning close to the compensation point where respiration (of coral polyp plus zooxanthellae) consumes the products of photosynthesis of the zooxanthellae, with little if any remaining for growth. We extend this work into an optical nomograph that is useful for predicting coral loss and recovery. The nomograph is designed to elucidate compensation depth for waters of various transparencies.     

Is CITES an effective tool for monitoring trade in corals?

 Despite a legal obligation to do so there is a widespread failure to record coral species on CITES trade permits. The complexity of coral taxonomy and the volume of coral specimens in trade mean that in practice this obligation will never be met, and so it may be sensible to ensure that the identification of genera is as accurate as possible. The accuracy of non-specialists in identifying coral genera using four existing guides was tested experimentally. Only three of ten genera were identified to more than 67% accuracy and none of the guides was ideally suited for coral specimens in trade. A guide designed specifically for this purpose and a change in emphasis under CITES to genera rather than species would therefore improve the effectiveness of CITES in monitoring the international coral trade. Accepted: 11 August 1999