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。     

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.     

海洋微生物宏基因组工程进展与展望

据初步统计,生活于海洋环境包括大洋深处的微生物有100万种以上,构成了一个动态的遗传基因库,其中绝大多数微生物或者从来没有经过实验室培养,或者至今无法培养,因而其分类地位及其生态学功能尚未为人类所认识。随着16S rRNA序列分析与系统分类学的广泛应用,海洋微生物多样性研究领域已经发生了很可观的改变,这些变化极大的丰富了人们对的微生物多样性及其生态功能的认识和理解。这里结合笔者近十年来的工作实践,讨论近年来在海洋微生物资源开发利用方面的研究进展,提出一个带有自动化特征的宏基因组功能表达平台,探讨海洋微生物资源利用的新途径。可以预见在不久的将来,海洋环境宏基因组工程研究将在一定程度上使得传统未培养海洋微生物基因资源及其功能产物能够为人类所开发和利用。     

单细胞稳定同位素标记技术在固氮微生物中的应用研究

生物固氮是指固氮微生物将大气中氮气还原为生物可利用氨的过程,是环境中新氮的主要来源,调控初级生产力并影响氮储库的收支平衡。由于环境中大部分固氮微生物不可纯培养,不依赖培养且具有高空间分辨率水平的单细胞技术,成为研究固氮微生物的有力手段。~(15)N_2稳定同位素标记技术,以微生物对~(15)N的同化量或速率为依据,是表征微生物固氮活性的最直接手段。本文对~(15)N_2稳定同位素标记结合两种单细胞技术,即纳米二次离子质谱(Nano SIMS)和单细胞拉曼光谱,用于固氮微生物研究的最新进展进行了综述,内容包括揭示环境中高活性固氮微生物、空间分布、与其他生物的共生关系、细胞生理状态等,并进一步对近期发展的基于单细胞拉曼光谱的固氮微生物研究进行了展望。     

水圈微生物：推动地球重要元素循环的隐形巨人

正生活在水圈环境中的微生物数量巨大、遗传与代谢方式极为多样,它们驱动着地球上重要元素的循环。水圈微生物研究已经成为生命科学与地球科学的研究热点。国家自然科学基金委员会于2017年启动了"水圈微生物驱动地球元素循环的机制"重大研究计划(简称"水圈微生物"计划)。"水圈微生物"计划拟选择典型水圈生境,通过多学科交叉研究,借助新技术、新方法,揭示水圈微生物在物种、群落和生态水平驱动碳氮硫循环的机制及其环境响应,     

Characterization of Bacterial,Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems.     

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.     

Distribution and Diversity of Planktonic Fungi in the West Pacific Warm Pool

Fungi contribute substantially to biogeochemical cycles of terrestrial and marine habitats by decomposing matter and recycling nutrients. Yet, the diversity of their planktonic forms in the open ocean is poorly described. In this study, culture-independent and molecular approaches were applied to investigate fungal diversity and abundance derived from samples collected from a broad swath of the Pacific Warm Pool across major environmental gradients Our results revealed that planktonic fungi were molecularly diverse and their diversity patterns were related to major phytoplankton taxa and various nutrients including nitrate, nitrite, orthophosphate and silicic acid. Over 400 fungal phylotypes were recovered across this region and nearly half of them grouped into two major fungal lineages of Ascomycota and Basidiomycota, whose abundance varied among stations. These results suggest that planktonic fungi are a diverse and integral component of the marine microbial community and should be included in future marine microbial ecosystem models.     

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.     

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.     

我国海洋细菌新物种鉴定与资源研发进展

近年来国际上对海洋微生物资源的发掘方兴未艾。本文综述了2000年以来我国在海洋细菌新物种鉴定与资源研发方面的进展,统计分析了国内相关单位海洋细菌新物种鉴定发表的数量及多样性,介绍了国内相关科研机构在海洋细菌系统学方面的工作进展,以及国内海洋微生物资源保藏与开发现状。比较了世界范围内海洋细菌系统学研究进展,并探讨了海洋细菌分离培养的主要方法,最后小结了我国海洋细菌资源研究领域存在的问题及未来发展的前景,为其进一步研发利用提供参考。     

Metagenomics-based drug discovery and marine microbial diversity

As the global threat of drug-resistant pathogens continues to rise, new strategies and resources are required to accelerate and advance the drug discovery process. We believe that rapid progress in metagenomics has opened up a new era in the study of marine microbial diversity that enables direct access to the genomes of numerous uncultivable microorganisms. This review outlines recent developments and future trends in metagenomics-based drug discovery in marine microbial communities and their associated chemical prosperity.     

Unlocking the diversity and biotechnological potential of marine surface associated microbial communities

Marine sessile eukaryotic hosts provide a unique surface for microbial colonisation. Chemically mediated interactions between the host and colonising microorganisms, interactions between microorganisms in the biofilm community and surface-specific physical and chemical conditions impact differently on the diversity and function of surface-associated microbial assemblages compared with those in planktonic systems. Understanding the diversity and ecology of surface-associated microbial communities will greatly contribute to the discovery of next-generation, bioactive compounds. On the basis of recent conceptual and technological advances insights into the microbiology of marine living surfaces are improving and novel bioactives, including those previously ascribed as host derived, are now revealed to be produced by members of the surface-associated microbial community.     

海洋环境中难培养微生物的寡营养培养

海洋中存在着丰富的微生物资源, 但迄今为止能够在实验室培养的微生物却不到1%, 而且能够通过培养得到的环境优势种更少, 这成为当代环境微生物学研究和海洋资源开发的最大障碍。过去十多年来, 通过不断改进培养方法和检测手段, 发明了许多新颖独特的技术, 提高了培养效率。特别是通过海洋微生物的寡营养培养技术, 分离并命名了一些难培养微生物, 给予人们极大的启发。海洋微生物资源的可持续性开发和利用, 是21世纪人类发展的重要方向, 是我们研究海洋微观世界的基础, 值得微生物学界同仁的共同关注。     

Microbial structuring of marine ecosystems

Despite the impressive advances that have been made in assessing the diversity of marine microorganisms, the mechanisms that underlie the participation of microorganisms in marine food webs and biogeochemical cycles are poorly understood. Here, we stress the need to examine the biochemical interactions of microorganisms with ocean systems at the nanometre to millimetre scale--a scale that is relevant to microbial activities. The local impact of microorganisms on biogeochemical cycles must then be scaled up to make useful predictions of how marine ecosystems in the whole ocean might respond to global change. This approach to microbial oceanography is not only helpful, but is in fact indispensable.     

Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales

In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S–50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.     

我国海洋微生物菌种资源保藏与共享服务现状

海洋微生物多样性丰富。我国近年来在海洋微生物多样性调查、资源获取与开发利用等多方面取得重要进展。为促进资源的可持续高效利用,建立了专业的海洋微生物菌种保藏中心,目前库藏海洋微生物菌种2. 2万株。本文介绍了目前中国海洋微生物菌种保藏管理中心库藏资源概况与共享利用情况,以共享记录为基础,从已共享菌株的多样性、库藏资源共享利用以及共享用户等方面开展了统计分析。统计结果显示,共享菌株中超过80%为细菌,其次依次为丝状真菌、酵母、古菌及噬菌体。在菌株水平,已共享细菌覆盖了库藏细菌的28%;在种的水平,已共享细菌覆盖了库藏细菌的47%,包括变形菌纲3 178株,芽胞杆菌纲951株,放线菌纲817株。目前,库藏资源总共享比例约为30%,覆盖了库藏57%的属和49%的种。共享用户目前达266家,其中国内用户244家,国外用户22家。为大洋课题、国家973课题、863课题、自然基金、行业公益性项目、科技支撑及企业项目等各种科技计划,提供了重要的菌种资源保障。据不完全统计,共支撑发表SCI论文达500余篇。中国海洋微生物菌种保藏管理中心在菌株资源的收集、整理和共享等方面,为我国的科研事业提供了大量的资源支撑,取得了较好的社会效益。     

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs

Extracellular enzymes produced by heterotrophic microbial communities are major drivers of carbon and nutrient cycling in terrestrial, freshwater, and marine environments. Although carbon and nutrient cycles are coupled on global scales, studies of extracellular enzymes associated with terrestrial, freshwater, and marine microbial communities are not often compared across ecosystems. In part, this disconnect arises because the environmental parameters that control enzyme activities in terrestrial and freshwater systems, such as temperature, pH, and moisture content, have little explanatory power for patterns of enzyme activities in marine systems. Instead, factors such as the functional diversity of microbial communities may explain varying patterns of enzyme activities observed in the ocean to date. In any case, many studies across systems focus on similar issues that highlight the commonalities of microbial community organization. Examples include the effective lifetime of enzymes released into the environment; the extent to which microbial communities coordinate enzyme expression to decompose complex organic substrates; and the influence of microbial community composition on enzyme activities and kinetics. Here we review the often-disparate research foci in terrestrial, freshwater, and marine environments. We consider the extent to which environmental factors may regulate extracellular enzyme activities within each ecosystem, and highlight commonalities and current methodological challenges to identify research questions that may aid in integrating cross-system perspectives in the future.     

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.     

Marine sponges as microbial fermenters

The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent findings regarding diversity, biogeography and population dynamics of sponge-associated microbiota, and the data are discussed within the larger context of the microbiology of the ocean.