麻黄属的化石记录及早期多样性

买麻藤纲的系统演化位置数百年来一直是国际植物学界争论的焦点问题。有人认为，买麻藤纲是被子植物的姐妹群，但另有人认为该纲与裸子植物的关系更为密切。尽管存在争议，但是麻黄属（麻黄科）一直被公认为买麻藤纲的基部类群。由于其在植物界中的特殊位置，解剖学、形态和分类学、分子系统学与古植物学等多种学科已经对该属开展了多角度的研究工作。在对买麻藤纲系统发育和演化位置进行研究时，我们意识到麻黄属的历史记录问题不仅是对麻黄属进行其他研究中必须首先解决的关键问题，而且已成为当务之急。而要令人满意的地解决麻黄属的历史记录，必须弄清以下核心问题：①麻黄属的起源时间是什么? ②麻黄属的化石记录怎样? ③早期麻黄植物的多样性怎样? 我们在全世界搜集了麻黄属的全部化石文献，这给我们对该属历史记录进行研究提供了扎实的基础;我们在辽西热河生物群尖山沟组早白垩世地层采集到了保存完好的麻黄化石，这为我们对其历史记录的研究提供了新的材料。 在对该属进行深入的研究后，结合对在中国辽宁省西部尖山沟组早白垩世地层采集到的保存完好的麻黄化石的研究，得出结论如下： (1)麻黄科下原有的似麻黄属和异麻黄属的属征以及模式种的形态特征与麻黄属非常接近。似麻黄属与麻黄属的区别在于二者的时代不同，异麻黄属和麻黄属的差异在于异麻黄属的分枝式样兼具对生和互生。在综合对比后，将似麻黄属和异麻黄属归并入麻黄属中。 (2)根据繁殖器官的特征，对麻黄属下的化石记录进行了整理，结果发现，目前可以确认的麻黄属化石种共有7个，分别是Ephedra chenii (Cao et Wu) Liu, Li et Wang comb. nov., E. antiqua (Heer) Liu, Li et Wang comb. nov., E. xingxuei (Tao et Yang) Liu, Li et Wang comb. nov., E. lanceolata Liu, Ferguson, Li et Wang sp. nov., E. divisa Liu, Ferguson, Li et Wang sp. nov., E. ovata Liu, Ferguson, Li et Wang sp. nov., 以及E. tenera Liu, Li et Wang sp. nov.。其余的种由于性状不明确或缺乏繁殖部分的特征而被暂时搁置一边。 (3)在1.25亿年前，麻黄属在种子单位中苞片的形态、叶片的形态和大小以及叶脉式样等四个方面已经表现出了丰富的多样性。1.25亿年前，麻黄属叶片的最长可达35毫米，最宽可达45毫米，比现代植物的大（最长可达35毫米，最宽可达2毫米）;叶片的叶脉式样中在同时具有现在植物的平行脉和汇聚脉之外，还有分叉脉出现。种子单位中苞片的形态主要为鳞片状和披针形，这比现代植物窄;叶片的形态主要有四种类型（卵形、裂叶、披针形以及鳞片状），比现代植物中的两种类型（披针形和鳞片状）复杂。将1.25亿年前多样的麻黄属与现代麻黄植物对比，表明在过去的1.25亿年期间，麻黄属的演化过程为：性状的消失和物种的灭绝。 (4)对于麻黄属的起源时间，对现代麻黄植物叶绿体rbcL基因序列的分析得出的时间为8-32 百万年，而近期基于rbcL、rps4 以及ITS序列和麻黄属化石种子以及麻黄粉的分析，得出麻黄属的起源时间为1.1亿年。我们发现的保存完好的化石标本给出的可靠的直接证据表明，麻黄属植物早在1.25亿年前已经出现，而且当时已经表现出了丰富的多样性，说明麻黄属的起源时间可能会更早。

河北中新世球果和果实及云南、浙江上新世化石木研究

本研究以河北围场县广发永化石点早中新世地层中的球果和果实、浙江宁海县杜岙化石点早上新世地层中的半矿化化石木、云南寻甸县金所和先锋化石点晚上新世地层中的丝炭和褐煤化木材为研究对象，对这三个化石点数百个植物大化石的形态或解剖结构进行了详细研究，鉴定出6个新的化石种，4个新记录种，7个未定种;其中2个化石属为我国新记录。根据其结构特征探讨这些化石类群与相关化石和现代植物的系统关系。并依据其现代亲缘种生长的生态和气候范围，对化石点沉积时期的植被和气候类型进行了推测。 果实中含有多种有价值的分类和系统发育的信息，对于种子植物的演化和系统发育研究具有重要的意义。在河北围场县发现大量保存较好的松科球果和姜科化石，为我们进一步研究松科植物和姜科植物解剖结构，以及探讨其系统演化提供难得的机会和直接的证据，同时为该化石地的植被演替和地层对比研究提供更多的植物学证据。对河北围场县广发永化石点球果和果实的形态研究，鉴定出三种松科球果化石种和一种姜科植物。分别为围场松（Pinus weichangensis sp. nov.）、围场云杉（Picea weichangensis sp. nov.）、围场铁杉（Tsuga weichangensis sp. nov.）以及化石Spirematospermum属未定种。其中围场云杉、围场铁杉球果在形态上与相应现代类群具有明显的差异，可能代表已灭绝的种类。Spirematospermum属未定种为一绝灭类型，是该属在我国的首次记录。这四种化石类群发现，反映早中新世化石该化石点气候与现代完全不同，为湿润的暖温带和亚热带气候。 浙江省在地质结构上位于东亚大陆边缘，是环太平洋岩浆活动带的重要组成部分。宁海县属于浙东南区属华南地层区，其第三纪地层嵊县群在该区分布广泛，其古植物研究仅限于孢粉和叶化石。本报告中首次对该层铜岭祝组的木化石进行了报道。对浙江宁海杜岙化石点早上新世地层中化石木样品的解剖研究，鉴定出三种木材类型，为史马库栎型木Quercus shimakurae、Liqumdambar cf. hisauchi和蔷薇科未定种。前者与现代栎属槲栎类、后者与枫香树属分别具有密切的亲缘关系，是我国首次报道栎属和枫香树属化石木。 云南现今复杂的地势地貌，独特的气候，丰富的植物种类和多样的植被类型是经历了长达数百万年的地质构造运动和自然环境演变的结果。第三纪时期由于大陆板块运动导致印度板块与亚洲板块的对接和碰撞，其地壳构造运动异常活跃。其第三系陆相地层广泛分布于古生代褶皱区的200多个互不相连的中、小型盆地及中、新生代断陷和拗陷型山间盆地中，并蕴涵了丰富的植物化石，为我们研究植被和植物演化提供了众多的证据。本次研究基于云南中部寻甸县金所煤矿和先锋煤矿的大量褐煤化和丝炭化材料，为进一步恢复云南晚第三纪气候和植被提供更多的依据，尤其是丝炭材料保存了木材精细而真实的结构，为木材准确鉴定和演化提供了可靠的依据。根据对云南金所和先锋化石点晚上新世沉积中褐煤化材料和丝炭样品解剖结构的研究，鉴定出8种化石木，包括2种裸子植物，5种双子叶植物和1种单子叶植物;分属5科7属。化石类群包括松属（Pinus）五针松组未定种Section Cembra sp.、云杉属未定种Picea sp、寻甸含笑Michelia xundianensis sp. nov.、多角含笑 Michelia angulata sp. nov.、Lithocarpoxylon cf. radiporosum、Castanoradix sp.、寻甸珍珠花Lyonia xundianensis sp. nov.、竹亚科未定种Bambusoideae sp。根据现今这些化石对应类群的生长和分布的气候区域，沉积时期的气候与现代气候较为接近。

A guide to the deep-water sponges of the Aleutian Island Archipelago

The first dedicated collections of deep-water (>80 m) sponges from the central Aleutian Islands revealed a rich fauna including 28 novel species and geographical range extensions for 53 others. Based on these collections and the published literature, we now confirm the presence of 125 species (or subspecies)of deep-water sponges in the Aleutian Islands. Clearly the deep-water sponge fauna of the Aleutian Islands is extraordinarily rich and largely understudied. Submersible observations revealed that sponges, rather than deep-water corals, are the dominant feature shaping benthic habitats in the region and that they provide important refuge habitat for many species of fish and invertebrates including juvenile rockfish (Sebastes spp.) and king crabs (Lithodes sp). Examination of video footage collected along 127 km of the seafloor further indicate that there are likely hundreds of species still uncollected from the region, and many unknown to science. Furthermore, sponges are extremely fragile and easily damaged by contact with fishing gear. High rates of fishery bycatch clearly indicate a strong interaction between existing fisheries and sponge habitat. Bycatch in fisheries and fisheries-independent surveys can be a major source of information on the location of the sponge fauna, but current monitoring programs are greatly hampered by the inability of deck personnel to identify bycatch. This guide contains detailed species descriptions for 112 sponges collected in Alaska, principally in the central Aleutian Islands. It addresses bycatch identification challenges by providing fisheries observers and scientists with the information necessary to adequately identify sponge fauna. Using that identification data, areas of high abundance can be mapped and the locations of indicator species of vulnerable marine ecosystems can be determined. The guide is also designed for use by scientists making observations of the fauna in situ with submersibles, including remotely operated vehicles and autonomous underwater vehicles.

杉科植物的表皮结构研究及古环境重建

全球古近纪和新近纪气候波动明显，很多科学家对古近纪和新近纪生物演化和气候演变规律的定量研究给予了相当的重视。杉科植物有长期发展的历史、少数的现存种和丰富的化石记录，成为指示古环境的理想植物之一。利用杉科植物重建古环境，首先要对化石植物进行正确的分类鉴定。杉科各属枝叶形态特征变异幅度较大，且枝叶排列和形态特征近似，有时各属之间存在交叉特征。杉科化石标本通常仅保存枝叶形式，且多个属的化石标本经常发现于同一地层，因而分类鉴定比较困难。植物的叶表皮结构是压型植物化石细胞信息的重要来源，是属种分类鉴定重要依据之一。本文在以往研究的基础上，完整分析了杉科9属现生植物的表皮特征，建立了杉科化石植物分类鉴定的现生植物的表皮特征参照系。 杉科植物的叶多为条形、钻形、鳞形或披针形，同种植物有1种、2种甚至3种叶型。其中水杉属的叶交互对生，其它属的叶螺旋状互生。水杉属的多数表皮细胞垂周壁明显弯曲，落羽杉属和杉木属有时微呈波状，其他属的表皮细胞垂周壁直。多数植物的叶片近轴面和远轴面的气孔数量和分布不同。一般来说，条形叶和披针形叶的远轴面气孔分布状况和气孔数量稳定，远轴面的中部最稳定。条形叶远轴面的气孔分布于中脉两侧，形成纵向的气孔带。条形叶近轴面气孔分布状况和气孔数量变化大，近轴面的气孔数量有时与远轴面近似，但多数情况下比远轴面少，有时整个叶片的近轴面仅少数几个气孔或没有气孔分布。钻形叶的近轴面和远轴面的气孔数量近似，或叶片近轴面的气孔数量比远轴面的气孔数量多，气孔分布范围也比远轴面气孔分布范围广。气孔椭圆形，落羽杉属植物和水松鳞形叶的气孔长轴方向与叶片长轴垂直或斜向排列，柳杉属植物的气孔多斜向排列，水松的条形叶和条状钻形叶的气孔多平行向排列。落羽杉属和柳杉属以外的杉科植物的气孔长轴多数与叶片长轴平行。在扫描电子显微镜下的密叶杉属植物叶片角质层的内表面，副卫细胞和表皮细胞的垂周壁与叶表面的角度一致，且副卫细胞的形态与表皮细胞类似，这种特殊气孔器被称为A-型气孔器。杉科植物中水杉属、落羽杉属和杉木属的气孔器近似密叶杉的这种A-型气孔器。台湾杉属、柳杉属、水松属、红杉属和巨杉属植物的气孔器与这种A-型气孔器不同，这几属的副卫细胞垂周壁表皮细胞的垂周壁方向不同，且副卫细胞的形态与表皮细胞的形态明显不同。因而气孔所有副卫细胞组成呈明显的圆盘状，保卫细胞在盘子的中央。综合分析植物的枝叶形态和表皮特征可以区分杉科各属。 本文研究了采自抚顺始新世的杉科植物标本，经枝叶特征、表皮结构和球果鳞片等特征分析为水松属的欧洲水松。论文分析了中国东北地区古温度定量研究结果与杉科植物的相关性。抚顺植物群发现有化石水杉M. occidentalis、中华红杉和欧洲水松，根据这三种化石植物的年均温度和年降水量，通过共存分析，推测抚顺始新世的年均温为12.1-17℃，年降水量为1199.6-2231mm。

买麻藤目的化石记录及其与 被子植物起源关系的探讨

二十世纪初，前人在中国的东北地区发现了大量保存完好的动物化石，其中以狼鳍鱼最具代表性，科学家将在该地区发现的化石生物群命名为“热河生物群”。“热河”这一名称得名于该化石群的经典产地，即当时的热河省东部地区。建国后，热河省被撤消，其西部划归河北省，东部划归辽宁省。原热河生物群的经典产地因此落在了今天辽宁省的西部，即辽西地区。但是，“热河生物群”这一在地质古生物学界具有深刻影响的名称仍然保留着，而且近几年来在该地区又有大量的鸟类以及恐龙的化石被发现。该地区现在已经成为世界级的古生物宝库。通过不同的方法对该地区进行时代测定的结果认为该地区的时代为白垩纪早期。 与发现众多、研究深入的动物群相比，在该地区开展的植物学研究起步较晚，但在最近几年取得了很大的进展。目前为止，已经发现的植物类群就有苔藓、蕨类、银杏、苏铁、松柏类和被子植物。其中，银杏、苏铁、松柏类尤为丰富。理论上，被子植物也正是从该生物群所代表的白垩纪早期开始出现并逐步走向繁荣的。近年来在热河生物群中就有不少关于被子植物早期类群的报道，如古果属A rchaefructus和里海果属Hyrcantha等。传统上认为，买麻藤目植物与被子植物起源的关系非常密切，但是最近的分子系统学研究却将该类群推离了被子植物，而作为裸子植物高等类群松柏类的姐妹群对待。但是，在热河生物群中的一些新买麻藤目植物的化石标本与被子植物早期类型化石标本的发现却提供了新的思路或证据。如近年来，我国学者已经在该生物群中报道的麻黄科下的2属4种。这些发现的类群都与买麻藤植物的基部类群麻黄属密切相关。这种新发现带来的证据或许可以为被子植物起源这一世界难题的解决提供新的思路。 在对前人关于买麻藤目植物化石标本的研究进行整理的时候，我们发现我们的部分化石与前人发表的一个种Ephedrites chenii在标本的形态学特征方面完全相同。但是在对该类群及其所在的属与麻黄的现代类群作对比研究后发现，该种植物的繁殖器官的特征完全符合麻黄属的特征，因此将该类群转移到麻黄属中作为新组合对待。另外，根据前人对该种在种加词的命名上的修改，我们将该新组合命名为Ephedra cheniae。 在调查该生物群中的买麻藤植物时，我们发现在部分化石类群中出现了前人没有记载过的新性状，比如在麻黄科类植物中发现了互生的分枝方式，并据此命名一个新的单种属Alloephedra xingxuei。为了探讨互生分枝这一性状对于麻黄科的分类意义，我们调查了国内外不少标本馆中的标本，并在野外做了取样统计。结果发现，在不少现代麻黄的枝条上都出现了不同程度的分枝发育不均衡，表现为在同一节上对生的两个分枝中一侧分枝能够正常发育而另一侧发育迟缓甚至不发育，这种不均衡的发育造成了在现代麻黄中出现了类似互生的分枝状况。在整理前人对麻黄分枝方式研究的基础上，结合我们对野外类群形态学性状的调查，我们认为由于在同一节上对生的两个分枝中一侧延迟或不发育而引起的类似互生的性状是较为广泛存在的，它不应该成为属一级的分类依据，而只能作为种一级的分类依据对待。因此我们将AHoephedra xingxuei转移到麻黄属中作为新组合Ephedra xingxuei处理。 除此之外，我们也发现了不少其他的买麻藤目化石标本，在对买麻藤目以往的化石记录了解以及对这些标本形态学性状把握的基础上，我们将这些新发现的化石标本放置在麻黄科麻黄属中作为新种对待，并根据其叶片以及苞片的特征分别将他们命名为披针叶麻黄（Ephedra lanceoleta）、裂叶麻黄（Ephedra divisa），卵叶麻黄（Ephedra ovata）以及双苞麻黄（Ephedra bibracta）。 与此同时，我们也发现了保存完好的被子植物的化石标本。该标本中具有5个离生的心皮、分枝方式兼具侧生和二叉分枝两种、并具有多裂的叶片。在辽西地区同时代发现的被子植物早期类型共有两个，分别是Archaefructus和Hyrcantha。其中前者具有许多个离生的螺旋状排列在可育枝的顶端1cm内的子房／心皮，而后者只有2-4个子房／心皮。在对我们新发现的化石标本与这两个被子植物的早期类型在叶片形态、分枝式样、果实大小、果实构成、果实排布、心 皮数目等形态学特征对比的基础上，我们认为新的化石标本描述了一个被子植物早期类群的新形态，并根据其具有五个心皮以及多裂的叶片的特征，命名为裂叶文采果Wentsaia divisa gen.＆sp. nov。 由于我们有幸能在辽西同时发现了买麻藤植物的化石标本和被子植物早期类型的标本，这就给了我们一个讨论二者在起源关系方面的机会。在对二者的营养器官特征、繁殖器官结构组成、繁殖器官性别构成以及对二者生活环境理解进行对比的基础上，我们认为，买麻藤目植物的早期类型与被子植物的早期类型之间存在相关性。但是就目前的证据而言，尚无法推测二者之间是否存在性状上的演化关系，而该问题的解决需要更多的化石证据的积累。

An ecological characterization of the Stellwagen Bank National Marine Sanctuary Region: oceanographic, biogeographic, and contaminants assessment

The mission of NOAA’s National Marine Sanctuary Program (NMSP) is to serve as the trustee for a system of marine protected areas, to conserve, protect, and enhance their biodiversity, ecological integrity, and cultural legacy while facilitating compatible uses. Since 1972, thirteen National Marine Sanctuaries, representing a wide variety of ocean environments, have been established, each with management goals tuned to their unique diversity. Extending from Cape Ann to Cape Cod across the mouth of Massachusetts Bay, Stellwagen Bank National Marine Sanctuary (NMS) encompasses 2,181 square kilometers of highly productive, diverse, and culturally unique Federal waters. As a result of its varied seafloor topography, oceanographic conditions, and high primary productivity, Stellwagen Bank NMS is utilized by diverse assemblages of seabirds, marine mammals, invertebrates, and fish species, as well as containing a number of maritime heritage resources. Furthermore, it is a region of cultural significance, highlighted by the recent discovery of several historic shipwrecks. Officially designated in 1992, Stellwagen Bank became the Nation’s twelfth National Marine Sanctuary in order to protect these and other unique biological, geological, oceanographic, and cultural features of the region. The Stellwagen Bank NMS is in the midst of its first management plan review since designation. The management plan review process, required by law, is designed to evaluate, enhance, and guide the development of future research efforts, education and outreach, and the management approaches used by Sanctuaries. Given the ecological and physical complexity of Stellwagen Bank NMS, burgeoning anthropogenic impacts to the region, and competing human and biological uses, the review process was challenged to assimilate and analyze the wealth of existing scientific knowledge in a framework which could enhance management decision-making. Unquestionably, the Gulf of Maine, Massachusetts Bay, and Stellwagen Bank-proper are extremely well studied systems, and in many regards, the scientific information available greatly exceeds that which is available for other Sanctuaries. However, the propensity of scientific information reinforces the need to utilize a comprehensive analytical approach to synthesize and explore linkages between disparate information on physical, biological, and chemical processes, while identifying topics needing further study. Given this requirement, a partnership was established between NOAA’s National Marine Sanctuary Program (NMSP) and the National Centers for Coastal Ocean Science (NCCOS) so as to leverage existing NOAA technical expertise to assist the Sanctuary in developing additional ecological assessment products which would benefit the management plan review process.

Atmospheric nutrient input to coastal areas: reducing the uncertainties

A significant fraction of the total nitrogen entering coastal and estuarine ecosystems along the eastern U.S. coast arises from atmospheric deposition; however, the exact role of atmospherically derived nitrogen in the decline of the health of coastal, estuarine, and inland waters is still uncertain. From the perspective of coastal ecosystem eutrophication, nitrogen compounds from the air, along with nitrogen from sewage, industrial effluent, and fertilizers, become a source of nutrients to the receiving ecosystem. Eutrophication, however, is only one of the detrimental impacts of the emission of nitrogen containing compounds to the atmosphere. Other adverse effects include the production of tropospheric ozone, acid deposition, and decreased visibility (photochemical smog). Assessments of the coastal eutrophication problem indicate that the atmospheric deposition loading is most important in the region extending from Albemarle/Parnlico Sounds to the Gulf of Maine; however, these assessments are based on model outputs supported by a meager amount of actual data. The data shortage is severe. The National Research Council specifically mentions the atmospheric role in its recent publication for the Committee on Environmental and Natural Resources, Priorities for Coastal Ecosystem Science (1994). It states that, "Problems associated with changes in the quantity and quality of inputs to coastal environments from runoff and atmospheric deposition are particularly important [to coastal ecosystem integrity]. These include nutrient loading from agriculture and fossil fuel combustion, habitat losses from eutrophication, widespread contamination by toxic materials, changes in riverborne sediment, and alteration of coastal hydrodynamics. "

Habitat availability and heterogeneity and the Indo-Pacific warm pool as predictors of marine species richness in the tropical Indo-Pacific

Range overlap patterns were observed in a dataset of 10,446 expert-derived marine species distribution maps, including 8,295 coastal fishes, 1,212 invertebrates (crustaceans and molluscs), 820 reef-building corals, 50 seagrasses and 69 mangroves. Distributions of tropical Indo-Pacific shore fishes revealed a concentration of species richness in the northern apex and central region of the Coral Triangle epicenter of marine biodiversity. This pattern was supported by distributions of invertebrates and habitat-forming primary producers. Habitat availability, heterogeneity and sea surface temperatures were highly correlated with species richness across spatial grains ranging from 23,000 to 5,100,000 km2 with and without correction for autocorrelation. The consistent retention of habitat variables in our predictive models supports the area of refuge hypothesis which posits reduced extinction rates in the Coral Triangle. This does not preclude support for a center of origin hypothesis that suggests increased speciation in the region may contribute to species richness. In addition, consistent retention of sea surface temperatures in models suggests that available kinetic energy may also be an important factor in shaping patterns of marine species richness. Kinetic energy may hasten rates of both extinction and speciation. The position of the Indo-Pacific Warm Pool to the east of the Coral Triangle in central Oceania and a pattern of increasing species richness from this region into the central and northern parts of the Coral Triangle suggests peripheral speciation with enhanced survival in the cooler parts of the Coral Triangle that also have highly concentrated available habitat. These results indicate that conservation of habitat availability and heterogeneity is important to reduce extinction and that changes in sea surface temperatures may influence the evolutionary potential of the region.

Assessment of natural resource conditions in and adjacent to Dry Tortugas National Park

This project characterized and assessed the condition of coastal water resources in the Dry Tortugas National Park (DRTO) located in the Florida Keys. The goal of the assessment was to: (1) identify the state of knowledge of natural resources that exist within the DRTO, (2) summarize the state of knowledge about natural and anthropogenic stressors and threats that affected these resources, and (3) describe strategies being implemented by DRTO managers to meet their resource management goals. The park, located in the Straits of Florida 113 km (70 miles) west of Key West, is relatively small (269 square kilometers) with seven small islands and extensive shallow water coral reefs. Significant natural resources within DRTO include coastal and oceanic waters, coral reefs, reef fisheries, seagrass beds, and sea turtle and bird nesting habitats. This report focuses on marine natural resources identified by DRTO resource managers and researchers as being vitally important to the Tortugas region and the wider South Florida ecosystem. Selected marine resources included physical resources (geology, oceanography, and water quality) and biological resources (coral reef and hardbottom benthic assemblages, seagrass and algal communities, reef fishes and macro invertebrates, and wildlife [sea turtles and sea-birds]). In the past few decades, some of these resources have deteriorated because of natural and anthropogenic factors that are local and global in scale. To meet mandated goals (Chapter 1), resource managers need information on: (1) the types and condition of natural and cultural resources that occur within the park and (2) the stressors and threats that can affect those resources. This report synthesizes and summarizes information on: (1) the status of marine natural resources occurring at DRTO; and (2) types of stressors and threats currently affecting those resources at the DRTO. Based on published information, the assessment suggests that marine resources at DRTO and its surrounding region are affected by several stressors, many of which act synergistically. Of the nine resource components assessed, one resource category – water quality – received an ecological condition ranking of "Good"; two components – the nonliving portion of coral reef and hardbottom and reef fishes – received a rating of "Caution"; and two components – the biotic components of coral reef and hardbottom substrates and sea turtles – received a rating of "Significant concern" (Table E-1). Seagrass and algal communities and seabirds were unrated for ecological condition because the available information was inadequate. The stressor category of tropical storms was the dominant and most prevalent stressor in the Tortugas region; it affected all of the resource components assessed in this report. Commercial and recreational fishing were also dominant stressors and affected 78% of the resource components assessed. The most stressed resource was the biotic component of coral reef and hardbottom resources, which was affected by 76% of the stressors. Water quality was the least affected; it was negatively affected by 12% of stressors. The systematic assessment of marine natural resources and stressors in the Tortugas region pointed to several gaps in the information. For example, of the nine marine resource components reviewed in this report, the living component of coral reefs and hardbottom resources had the best rated information with 25% of stressor categories rated "Good" for information richness. In contrast, the there was a paucity of information for seagrass and algal communities and sea birds resource components.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

Fish and habitat community assessments on North Carolina shipwrecks: potential sites for detecting climate change in the graveyard of the Atlantic

The Monitor National Marine Sanctuary (MNMS) was the nation’s first sanctuary, originally established in 1975 to protect the famous civil war ironclad shipwreck, the USS Monitor. Since 2008, sanctuary sponsored archeological research has branched out to include historically significant U-boats and World War II shipwrecks within the larger Graveyard of the Atlantic off the coast of North Carolina. These shipwrecks are not only important for their cultural value, but also as habitat for a wide diversity of fishes, invertebrates and algal species. Additionally, due to their unique location within an important area for biological productivity, the sanctuary and other culturally valuable shipwrecks within the Graveyard of the Atlantic are potential sites for examining community change. For this reason, from June 8-30, 2010, biological and ecological investigations were conducted at four World War II shipwrecks (Keshena, City of Atlanta, Dixie Arrow, EM Clark), as part of the MNMS 2010 Battle of the Atlantic (BOTA) research project. At each shipwreck site, fish community surveys were conducted and benthic photo-quadrats were collected to characterize the mobile conspicuous fish, smaller prey fish, and sessile invertebrate and algal communities. In addition, temperature sensors were placed at all four shipwrecks previously mentioned, as well as an additional shipwreck, the Manuela. The data, which establishes a baseline condition to use in future assessments, suggest strong differences in both the fish and benthic communities among the surveyed shipwrecks based on the oceanographic zone (depth). In order to establish these shipwrecks as sites for detecting community change it is suggested that a subset of locations across the shelf be selected and repeatedly sampled over time. In order to reduce variability within sites for both the benthic and fish communities, a significant number of surveys should be conducted at each location. This sampling strategy will account for the natural differences in community structure that exist across the shelf due to the oceanographic regime, and allow robust statistical analyses of community differences over time.

A survey of deep-water coral and sponge habitats along the west coast of the US using a remotely operated vehicle: NOAA Fisheries Survey Vessel (FSV)'Bell M. Shimada', November 1-5, 2010

Remotely operated vehicle (ROV) surveys were conducted from NOAA’s state-of-the-art Fisheries Survey Vessel (FSV) Bell M. Shimada during a six-day transit November 1-5, 2010 between San Diego, CA and Seattle, WA. The objective of this survey was to locate and characterize deep-sea coral and sponge ecosystems at several recommended sites in support of NOAA’s Coral Reef Conservation Program. Deep-sea corals and sponges were photographed and collected whenever possible using the Southwest Fisheries Science Center’s (SWFSC) Phantom ROV ‘Sebastes’ (Fig. 1). The surveyed sites were recommended by National Marine Sanctuary (NMS) scientists at Monterey Bay NMS, Gulf of the Farallones NMS, and Olympic Coast NMS (Fig. 2). The specific sites were: Sur Canyon, The Football, Coquille Bank, and Olympic Coast NMS. During each dive, the ROV collected digital still images, video, navigation, and along-track conductivity-temperature-depth (CTD), and optode data. Video and high-resolution photographs were used to quantify abundance of corals, sponges, and associated fishes and invertebrates to the lowest practicable taxonomic level, and also to classify the seabed by substrate type. A reference laser system was used to quantify area searched and estimate the density of benthic fauna.

Influence of hard bottom morphology on fish assemblages of the continental shelf off Georgia, southeastern USA

Various reef types worldwide have inconsistent relationships among fish assemblage parameters and benthic characteristics, thus there is a need to identify factors driving assemblage structure specific to each reef type and locale. Limestone ledges are known to be key habitats for bottom fish on the continental shelf of the southeastern USA, however, the specific factors that link them to fish assemblages have not been quantified. Bottom fishes and habitat characteristics on ledges were surveyed at a study site located centrally in the southeastern USA continental shelf. Species richness, diversity, abundance, and biomass of fish were higher at ledges than on flat bottom. Species richness, abundance, and biomass of fish were well explained by ledge variables including percent cover of sessile invertebrates, total height, and height of undercut recesses. Multivariate analyses based on biomass of individual species at ledges revealed two fish assemblages associated with four ledge types. One assemblage was associated with ledges that were tall, heavily colonized with sessile invertebrates, large in area, and did or did not have undercuts. The other assemblage was associated with ledges that were short, not undercut, smaller in area, and were or were not heavily colonized by invertebrates. Seafloor classification schemes presently used in the region do not adequately capture hard bottom diversity to identify the location and extent of essential fish habitats for ecological and fisheries purposes. Given that ledges cover only ∼1% to 5% of the southeastern USA continental shelf, they merit the highest levels of consideration in regional research, conservation, and management plans.

Chemical contaminants in the coral Porites astreoides from southwest Puerto Rico

This report presents an initial characterization of chemical contamination in coral tissues (Porites astreoides) from southwest Puerto Rico. It is the second technical report from a project to characterize chemical contaminants and assess linkages between contamination and coral condition. The first report quantified chemical contaminants in sediments from southwest Puerto Rico. This document summarizes the analysis of nearly 150 chemical contaminants in coral tissues. Although only eight coral samples were collected, some observations can be made on the correlations between observed tissue and sediment contaminant concentrations. The concentrations of polycyclic aromatic hydrocarbons (PAHs), typically associated with petroleum spills and the combustion of fossil fuels, and polychlorinated biphenyls (PCBs) in the coral tissues were comparable to concentrations found in adjacent sediments. However, the concentration of a chemical contaminant (e.g., PAHs) in the coral tissues at a particular site was not a good predictor of what was in the adjacent sediments. In addition, the types of PAHs found in the coral tissues were somewhat different (higher ratios of alkylated PAHs) than in sediments. The levels of PCBs and DDT in coral tissues appeared higher just outside of Guanica Bay, and there was evidence of a downstream concentration gradient for these two contaminant classes. The trace elements copper, zinc and nickel were frequently detected in coral tissues, and the concentration in the corals was usually comparable to that found in adjacent sediments. Chromium was an exception in that it was not detected in any of the coral tissues analyzed. Additional work is needed to assess how spatial patterns in chemical contamination affect coral condition, abundance and distribution.

Field manual for investigating coral disease outbreaks

Coral reefs throughout their circumtropical range are declining at an accelerating rate. Recent predictions indicate that 20% of the world’s reefs have been degraded, another 24% are under imminent risk of collapse, and if current estimates hold, by 2030, 26% of the world’s reefs will be lost (Wilkinson 2004). Recent changes to these ecosystems have included losses of apex predators, reductions of important herbivorous fishes and invertebrates, and precipitous declines in living coral cover, with many reefs now dominated by macroalgae. Causes have been described in broad sweeping terms: global climate change, over-fishing and destructive fishing, land-based sources of pollution, sedimentation, hurricanes, mass bleaching events and disease. Recognition that corals can succumb to disease was first reported in the early 1970’s. Then it was a unique observation, with relatively few isolated reports until the mid 1990’s. Today disease has spread to over 150 species of coral, reported from 65 countries throughout all of the world’s tropical oceans (WCMC Global Coral Disease Database). While disease continues to increase in frequency and distribution throughout the world, definitive causes of coral diseases have remained elusive for the most part, with reef managers not sufficiently armed to combat it.