海洋微生物多样性及其分子生态学研究进展

海洋微生物多样性的深入研究将有助于微生物资源更好的开发和利用,海洋微生物多样性有很大的研究价值和研究空间。海洋中大多数微生物处于未可培养状态,在分子生态学基础上对海洋未可培养微生物进行研究是当今微生物多样性研究的主要方向。近年来相关研究进展迅速,研究方法不断更新。主要从分子生态学角度对微生物多样性研究现状进行概述并详细分析探讨了相关的研究方法,而且从分子生态学与海洋微生物多样性研究相结合的层面,对本领域的研究进行展望。旨在为海洋微生物多样性的研究及海洋资源的可持续开发与利用提供参考。     

中国海洋生物多样性的现状和展望

本文简要介绍中国海洋生物多样性的现状及未来。对中国海的物种多样性、遗传多样性、生态系统多样性、关键种及它们的生活区作了评述。展望将来,主要目标为推动海洋生物多样性的调查和研究,促进海洋生物多样性更好地服务于中国的持续利用。     

海洋古菌多样性研究进展

海洋古菌是海洋微生物中的一个大的类群,然而绝大多数的古菌不能分离培养.近年来分子生物学的方法广泛地应用于微生物多样性的研究中,研究发现,海洋古菌广泛地生活在各类海域环境中,而不仅仅是生活在极端的环境中.海洋古菌为海洋生态系统中主要的原核细胞成分,在海洋生态系统中的物质与能量循环中扮演着重要角色.主要阐述了生活在海洋不同环境中海洋古菌的多样性,有海洋浮游古菌的多样性、海底环境及海洋沉积物中古菌的多样性、附着或寄共生古菌多样性等的研究状况,以及研究海洋古菌多样性的分子生物学的主要方法.     

可培养海洋放线菌生物多样性的研究进展

海洋放线菌是新药开发和天然活性产物的重要来源,海洋放线菌的生物多样性是代谢产物功能多样性的基础,因此研究可培养放线菌的生物多样性具有重要的意义。综述了近年来可培养的海洋放线菌生物多样性的研究进展,尤其是海绵共附生放线菌、深海放线菌和海洋固有放线菌的研究进展,对可培养的海洋放线菌的分离培养方法,包括样品处理、培养基的选择等进行了重点介绍,并对未培养海洋放线菌的分离培养进行了探讨,强调了建立区域性海洋放线菌菌种及基因资源库的重要性。     

Low functional redundancy in coastal marine assemblages

The relationship between species and functional diversity remains poorly understood for nearly all ecosystem types, yet determining this relationship is critically important for developing both a mechanistic understanding of community assembly and appropriate expectations and approaches to protecting and restoring biological communities. Here we use two distinct data sets, one from kelp forests in the Channel Islands, California, and one from a global synthesis of marine reserves, to directly test how variation in species diversity translates into changes in functional diversity. We find strong positive relationships between species and functional diversity, and increased functional diversity of fish assemblages coinciding with recovery of species diversity in marine reserves, independent of the method used for classifying species in functional groups. These results indicate that low levels of redundancy in functional species traits exist across a suite of marine systems, and that fishing tends to remove whole functional groups from coastal marine ecosystems.     

Community structure and diversity of marine ascomycetes from coastal beaches of the southern Gulf of Mexico

Diversity of marine fungi in the Gulf of Mexico remains unknown for the most part, therefore the geographical distribution patterns of these microorganisms are mostly unknown too. Twelve sandy beaches located in this sea were sampled to evaluate the diversity of marine fungi, revealed by fruiting on natural substrata incubated in the laboratory for up to 12 months. Species richness and diversity differed between beaches, and corresponded with the presence of main and highly polluted river mouths, nearshore marine environments, and core industrial and port developments. Contaminants and local anthropogenic activities may be reducing the diversity of marine ascomycetes. Connections between beaches and different nearshore habitats explain the high diversity observed, since they represent a varied source of substrata for decomposition and heterogeneous environmental conditions. We recognized four main local species distribution patterns. Moreover, the constrained correspondence analysis showed that temperature is a major environmental variable affecting the distribution of these fungi. By a linear regression we showed a significant relationship between temperature and diversity.     

海洋微生物多样性的研究进展

海洋微生物多样性（marine microorganisms diversity)是指所有海洋微生物种类、种内遗传变异和它们的生存环境的总称。本文介绍了海洋微生物多样性方面的研究和利用进展,包括研究微生物多样性方法的改进,有价值的海洋微生物功能性产品的开发;关于海洋微生物抗肿瘤、抗病毒药物的研究等。     

Diversity and biotechnological potential of the sponge-associated microbial consortia

Sponges are well known to harbor diverse microbes and represent a significant source of bioactive natural compounds derived from the marine environment. Recent studies of the microbial communities of marine sponges have uncovered previously undescribed species and an array of new chemical compounds. In contrast to natural compounds, studies on enzymes with biotechnological potential from microbes associated with sponges are rare although enzymes with novel activities that have potential medical and biotechnological applications have been identified from sponges and microbes associated with sponges. Both bacteria and fungi have been isolated from a wide range of marine sponge, but the diversity and symbiotic relationship of bacteria has been studied to a greater extent than that of fungi isolated from sponges. Molecular methods (e.g., rDNA, DGGE, and FISH) have revealed a great diversity of the unculturable bacteria and archaea. Metagenomic approaches have identified interesting metabolic pathways responsible for the production of natural compounds and may provide a new avenue to explore the microbial diversity and biotechnological potential of marine sponges. In addition, other eukaryotic organisms such as diatoms and unicellular algae from marine sponges are also being described using these molecular techniques. Many natural compounds derived from sponges are suspected to be of bacterial origin, but only a few studies have provided convincing evidence for symbiotic producers in sponges. Microbes in sponges exist in different associations with sponges including the true symbiosis. Fungi derived from marine sponges represent the single most prolific source of diverse bioactive marine fungal compounds found to date. There is a developing interest in determining the true diversity of fungi present in marine sponges and the nature of the association. Molecular methods will allow scientists to more accurately identify fungal species and determine actual diversity of sponge-associated fungi. This is especially important as greater cooperation between bacteriologists, mycologists, natural product chemists, and bioengineers is needed to provide a well-coordinated effort in studying the diversity, ecology, physiology, and association between bacteria, fungi, and other organisms present in marine sponges.     

Impact of supply-side ecology on consumer-mediated coexistence: evidence from a meta-analysis

Studies of marine nearshore hard substrates have demonstrated that consumers and abiotic disturbances can remove biomass, clearing space for species that are competitively subordinate and subsequently increasing diversity. However, studies often examine the impact of these space-opening forces on diversity in isolation from other potentially interacting factors. In marine systems, space can be closed by recruitment decoupled from local populations. Therefore, we investigated how recruitment influences the impacts of consumers on diversity with a meta-analysis of 27 experiments of community development involving sessile species on marine hard substrates. These studies allowed quantification of recruitment rates, consumer pressure, and species richness of primary space occupants. This meta-analysis demonstrated that consumers generally increase diversity at high levels of recruitment but decrease diversity at low levels of recruitment. Therefore, species diversity of sessile species is controlled by the interaction between forces that open (predation and herbivory) and close (recruitment) space.     

黄海海域海洋沉积物细菌多样性分析

【背景】海洋独特的环境造就了海洋生物的多样性,海洋沉积物中细菌对海洋环境具有至关重要的作用。【目的】研究陆地土壤和海洋沉积物间细菌群落相似性和差异性,以便更好地认识海洋细菌多样性,深入了解沉积物细菌在海洋环境中的潜在作用。【方法】从中国黄海海域及大连市大黑山脚下分别采集样品,以陆地土壤为对照,采用16SrRNA基因高通量测序技术分析海洋沉积物的细菌群落结构。【结果】海洋沉积物样品中芽孢杆菌纲(Bacilli)、鞘氨醇单胞菌属(Sphingomonas)和芽孢杆菌属(Bacillus)丰度高于陆地土壤样品;海洋沉积物中亚硝化单胞菌(unculturedbacterium f. Nitrosomonadaceae)和厌氧绳菌(uncultured bacterium f. Anaerolineaceae)丰度虽低于陆地土壤,但丰度值也均高于1%;样品分类学统计显示酸杆菌门(Acidobacteria)在海洋沉积物和陆地土壤样品中的序列丰度比例都较大,鞘氨醇单胞菌属(Sphingomonas)在海洋沉积物样品中的序列丰度大于陆地土壤样品。【结论】海洋沉积物细菌多样性可作为海洋环境恢复情况的重...     

Approaches to investigating the ecology of plasmids in marine bacterial communities

To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.     

The latitudinal position of peak marine diversity in living and fossil biotas

Aim Peak marine taxonomic diversity has only rarely occurred at or near the equator during the Phanerozoic Eon, in contrast to the present‐day pattern. This fundamental difference is difficult to reconcile because the latitude at which peak diversity occurs for living marine taxa has not yet been explicitly determined at a broad taxonomic and spatial scale. Here, we attempt to determine this value in order to compare the contemporary and fossil patterns directly. Location Our data are global in coverage. Methods We used a literature compilation of 149 present‐day marine latitudinal diversity gradients. We summed the number of marine taxa that exhibited peak diversity within 10° latitudinal bins. In addition, we recorded locality data, general habitat (benthic/pelagic), and the taxonomic level of the study organisms. Results We found that peak diversity for most sampled marine taxa currently occurs between 10° and 20° N, even after correcting for a Northern Hemisphere sampling bias. Moreover, this peak position is a global phenomenon: it is found across habitats and higher taxa, within all sampled ocean basins, and on both sides of the Atlantic and Pacific oceans. Benthic taxa, which dominate our data, exhibit one peak at 10°–20° N, while pelagic taxa exhibit a peak at 10°–20° N and an additional peak at 10°–20° S, producing a distinct trough at the equator. Main conclusions Our data indicate that peak marine diversity for many taxa is currently within 10°–20° N rather than at the equator, and that this is not likely to result from either undersampling at lower latitudes or the pattern being dominated by a particular taxon. Possible explanations may include a coincidence with the intertropical convergence zone, a mid‐domain effect, abundant shallow marine habitat, or high ocean temperatures at latitudes nearest the equator. Regardless of its exact cause, the position of peak diversity should be considered a fundamental feature of the latitudinal diversity gradient that must be accounted for within attempts to explain the latter’s existence.     

Phylogenetic diversity of culturable fungi associated with the Hawaiian Sponges Suberites zeteki and Gelliodes fibrosa

Sponges are well documented to harbor large amounts of microbes. Both culture-dependent and molecular approaches have revealed remarkable bacterial diversity in marine sponges. Fungi are commonly isolated from marine sponges, yet no reports on phylogenetic diversity of sponge-inhabiting fungi exist. In this report, we investigated the phylogenetic diversity of culturable fungi from the Hawaiian alien marine sponges Suberites zeteki and Gelliodes fibrosa. A total of 44 independent isolates were recovered from these two sponge species, representing 7 orders and 22 genera of Ascomycota. The majority (58%) of fungal isolates from S. zeteki resided in the Pleosporales group, while the predominant isolates (52%) from G. fibrosa were members of the Hypocreales group. Though differing in fungal species composition and structure, culturable communities of these two sponges displayed similar phylogenetic diversity. At the genus level, only two genera Penicillium and Trichoderma in the Eurotiales and Hypocreales orders, respectively, were present in both sponge species. The other genera of the fungal isolates were associated with either S. zeteki or G. fibrosa. Some of these fungal genera had been isolated from sponges collected in other marine habitats, but more than half of these genera were identified for the first time in these two marine sponges. Overall, the diversity of culturable fungal communities from these two sponge species is much higher than that observed in studies of marine sponges from other areas. This is the first report of phylogenetic diversity of marine sponge-associated fungi and adds one more dimension to our current understanding of the phylogenetic diversity of sponge-symbiotic microbes.     

Why are there so few fish in the sea?

The most dramatic gradient in global biodiversity is between marine and terrestrial environments. Terrestrial environments contain approximately 75-85% of all estimated species, but occupy only 30 per cent of the Earth's surface (and only approx. 1-10% by volume), whereas marine environments occupy a larger area and volume, but have a smaller fraction of Earth's estimated diversity. Many hypotheses have been proposed to explain this disparity, but there have been few large-scale quantitative tests. Here, we analyse patterns of diversity in actinopterygian (ray-finned) fishes, the most species-rich clade of marine vertebrates, containing 96 per cent of fish species. Despite the much greater area and productivity of marine environments, actinopterygian richness is similar in freshwater and marine habitats (15 150 versus 14 740 species). Net diversification rates (speciation-extinction) are similar in predominantly freshwater and saltwater clades. Both habitats are dominated by two hyperdiverse but relatively recent clades (Ostariophysi and Percomorpha). Remarkably, trait reconstructions (for both living and fossil taxa) suggest that all extant marine actinopterygians were derived from a freshwater ancestor, indicating a role for ancient extinction in explaining low marine richness. Finally, by analysing an entirely aquatic group, we are able to better sort among potential hypotheses for explaining the paradoxically low diversity of marine environments.     

Regional effects as important determinants of local diversity in both marine and terrestrial systems

Community ecologists have struggled to create unified theories across diverse ecosystems, but it has been difficult to acertain whether marine and terrestrial communities differ in the mechanisms responsible for structure and dynamics. One apparent difference between marine and terrestrial ecology is that the influence of regional processes on local populations and communities is better established in the marine literature. We examine three potential explanations: 1) influential early studies emphasized local interactions in terrestrial communities and regional dispersal in marine communities. 2) regional‐scale processes are actually more important in marine than in terrestrial communities. 3) recruitment from a regional species pool is easier to study in marine than terrestrial communities. We conclude that these are interrelated, but that the second and especially the third explanations are more important than the first. We also conclude that in both marine and terrestrial systems, there are ways to improve our understanding of regional influences on local community diversity. In particular, we advocate examining local vs regional diversity relationships at localities within environmentally similar regions that differ in their diversity either because of their sizes or their varying degrees of isolation from a species source.     

Do new reconstructions clarify the relationships between the Phanerozoic diversity dynamics of marine invertebrates and long-term eustatic trends?

A relationship between global sea levels and the diversity of marine invertebrates throughout the Phanerozoic remains an urgent matter for debates. Its recognition depends on a proper selection of diversity and eustatic curves. A comparison of changes in the revised sample-standardized generic diversity and long-term global sea-level changes provides a weaker evidence for a direct covarying relationship than established earlier, although the eustatic control on diversity dynamics of marine invertebrates was important during ∼74% of the Phanerozoic. Multiple causation of biodiversity changes, data bias, erroneous reconstructions, and conceptual misinterpretations are likely explanations of observed difference between the new biodiversity and eustatic curves.     

Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high‐throughput sequencing sets

Fungi are everywhere and interact with humans in countless ways, but a large group of fungi called ‘Cryptomycota’ has escaped detection until very recently. Still, the extent of diversity and ecological habits of this group remain largely unknown. We interrogated publically available 18S rRNA gene datasets, obtained via high‐throughput sequencing from marine and freshwater samples, for Cryptomycota sequences. Contrary to previous work, we found evidence of substantial Cryptomycota diversity in the marine upper water column. Additionally, we produced a sequencing set from a groundwater aquifer, an environment unrepresented among 18S rRNA gene pyrosequencing sets. The Cryptomycota community in this aquifer sample appears distinct from the community in both freshwater and marine environments with evidence of a unique aquifer clade. This study significantly expands the boundary of known Cryptomycota sequence diversity and characterizes the phylogenetic distribution of this diversity in aquatic environments. Furthermore, the approach utilized is generalizable to discovery of novel micro‐eukaryotic diversity from any lineage.     

Mitochondrial DNA variation in Northeast Atlantic and Mediterranean populations of Norway lobster, Nephrops norvegicus

Analysis of the genetic structure of the Norway lobster (Nephrops norvegicus), a marine crustacean with high commercial value, was undertaken to gain information regarding the differentiation of Atlantic from Mediterranean populations of marine invertebrates. Restriction fragment length polymorphism analysis of two mitochondrial DNA segments, 3.6 kilobases in total, was performed. Twelve populations from the North Sea, Irish Sea, Portuguese coast and Aegean Sea were analysed. Low levels of differentiation were found among them (F(ST) = 0.018, P < 0.001) and there were no signs of an Atlantic-Mediterranean divide or of an isolation-by-distance scheme of differentiation. Possible reasons for these low levels of differentiation can be found in the recent expansion of N. norvegicus populations. This is supported by the mismatch distribution of pairwise haplotype differences, as well as by the high mean haplotype diversity (h = 0.93) combined with medium nucleotide diversity (pi = 0.0057) (in comparison to values for marine crustaceans or teleosts) found in this study. This combination of high levels of haplotype diversity with moderate to low levels of nucleotide diversity has also been frequently attributed to a recent time of divergence for various marine species. No evidence was found for a Mediterranean refugium during glaciation periods, separate from the Atlantic, as has been reported for some marine species. The Irish Sea population was the most differentiated as a result of reduced levels of diversity. Results are also discussed in the light of future management of N. norvegicus stocks.     

莱州湾东岸潮下带大型底栖动物群落beta多样性格局及其驱动因素

群落β多样性格局的形成与维持机制一直是群落生态学研究的热点与核心。然而, 与陆生生态系统相比, 海洋生态系统尤其是海洋底栖生态系统中生物群落β多样性的研究明显滞后。本研究从分类(即物种组成)和功能(即性状组成)两个方面出发, 应用Mantel分析和基于矩阵的多元回归(multiple regression on distance matrices, MRM)分析, 探究了莱州湾东岸潮下带大型底栖动物群落β多样性及其周转(turnover)和嵌套(nestedness)组分与环境因子和空间距离的关系, 揭示了环境过滤和扩散限制两种生态学过程对其群落构建机制的影响。结果显示: (1)莱州湾东岸潮下带大型底栖动物群落的分类与功能性状β多样性均维持在较高水平且均以周转组分占主导, 表明研究区域大型底栖动物群落在物种和功能性状组成上差异较大, 而这种差异大部分来自物种或功能性状在空间或群落间的更替; (2)空间地理距离对大型底栖动物群落分类与功能性状β多样性及其组分无显著影响(Mantel检验, P > 0.05), 表明扩散限制对莱州湾东岸潮下带大型底栖动物群落的影响有限; (3) MRM分析表明, 沉积物总有机质(total organic matter, TOM)和粉砂含量显著影响大型底栖动物群落分类β多样性, 而TOM则显著影响功能性状β多样性。上述结果表明, 环境过滤是驱动莱州湾东岸潮下带大型底栖动物群落构建机制的首要因素。本研究阐明了莱州湾东岸潮下带大型底栖动物群落构建机制, 同时也为理解我国其他海域大型底栖动物群落的形成与维持机制提供了参考。     

Diversity and biogeography of marine actinobacteria

The actinomycetes, although not all the Actinobacteria, are easy to isolate from the marine environment. However, their ecological role in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate strains for search and discovery of new drugs. However, the marine environment has become a prime resource in search and discovery for novel natural products and biological diversity, and marine actinomycetes turn out to be important contributors. Similarly, striking advances have been made in marine microbial ecology using molecular techniques and metagenomics, and actinobacteria emerge as an often significant, sometimes even dominant, environmental clade. Both approaches - cultivation methods and molecular techniques - are leading to new insights into marine actinobacterial biodiversity and biogeography. Very different views of actinobacterial diversity emerge from these, however, and the true extent and biogeography of this are still not clear. These are important for developing natural product search and discovery strategies, and biogeography is a hot topic for microbial ecologists.