Role of the small-size fraction of mesozooplankton in the pelagic community of the northeastern part of the Black Sea in the autumn

The role of the small-size (SF; 0.1–0.5 mm) and large-size (LF; 0.5–20.0 mm) fractions in the biomass and abundance of mesozooplankton (0.1–20.0 mm) was assessed using the database of samples obtained during the cruises of RV Akvanavt in the northeastern Black Sea in November 2000 and October 2006. The mesozooplankton was collected by means of Juday nets (37/50, filtering gauze 160 μm) and Niskin bottles in two areas: (1) the shelf and continental slope (30–1480 m depth) and (2) the deep sea (depths of more than 1500 m). The plankton net was considerably less effective in collecting the SF of the mesozooplankton (by a factor of 30–36) than the Niskin bottles. When comparing the SF and LF, we estimated the abundance and biomass of the SF in the samples obtained with the Niskin bottles. The abundance of the SF in the deep-sea area was 2.5 times lower compared to the shelf and continental slope, and the LF abundance was 5.0 times lower in the same way. The abundance of the SF constituted 88% of the total mesozooplankton on the shelf and continental slope, and 78% in the deep-sea area. The biomass of the SF was higher as well on the shelf and continental slope. Meroplankton played a significant role in the SF zooplankton abundance (0.5 × 10³ + 0.16 ind. m⁻³) in this area. The SF grazing impact was 10% of the total mesozooplankton grazing on the shelf and continental slope, and 17% in the deepsea area. Appendicularia and nauplii of copepods had the greatest contribution to the mesozooplankton grazing among the SF group.     

基于宏基因组测序研究中太平洋海山富钴结壳区非培养微生物生态功能

富钴结壳是一种重要的海底矿产资源.富钴结壳是生物地球化学和微生物学的研究热点,但目前我们对富钴结壳区的微生物群落结构仍缺乏认识.本研究针对中太平洋海山富钴结壳区沉积物,采用非培养方法获得微生物基因组信息并分析其生态学功能.采用PCR的方法筛选得到78个带有16S rRNA基因的克隆.变形杆菌门和奇古菌门MGI类群分别为古菌和细菌的主要类群.测序并分析了9个带有16S rRNA 基因的fosmid克隆.这些克隆中含有较多的代谢相关和重金属抗性相关基因,表明多样的代谢和抗逆途径在微生物适应富钴结壳环境中发挥了重要作用.代谢途径分析表明,氮循环是富钴结壳区一种重要的生物地球化学过程.此外,发现多个水平基因转移事件,这些基因大部分转移自细菌,少量转移自古菌或植物.比较基因组分析表明,属于奇古菌门MGI类群的克隆W4-93包含一段共线性的基因簇.以上结果说明水平基因转移和基因组分歧进化在微生物适应深海环境过程中发挥了重要作用.     

深海生物原位实验与生态监测研究进展

深海在黑暗、高静水压、低温（黑烟囱等热液系统除外）和寡营养的极端环境下形成了特殊的生境。对深海生物/微生物的研究,不仅可以揭示各种深海生物的生理代谢特性和动态变化规律,而且有助于深海生物资源的开发利用,特别是深海微生物碳循环机制的相关研究可为全球实现碳中和目标提供新的路线图。研究深海生物的首要条件是获得大量保持原位特性的样本,然而传统深海采样手段的局限可能导致深海相关研究结果无法反映深海环境下真实的生命过程,亟需发展满足深海生物原位研究的采样方法和生态监测技术。本文对深海生物研究现状,相关科学问题和原位组学研究进展,以及原位生态监测装备研发和应用进行综述,并对深海原位生物实验室进行了展望。     

Nucleic acid concentrations (DNA,RNA) in the continental and deep-sea sediments of the eastern Mediterranean: relationships with seasonally varying organic inputs and bacterial dynamics

In order to study temporal variations of the genetic material in the continental shelf and deep-sea sediments of the extremely oligotrophic Cretan Sea, samples were collected on seasonal basis from August 1994 to September 1995, with a multiple corer, at seven stations (from 40 to 1540 m depth). Surface sediments (0–1 cm) were sub-sampled and analyzed for nucleic acid content (DNA, RNA) and bacterial density. DNA concentrations in the sediments were high (on annual average, 25.0 μg g^-1) and declined with increasing water depth, ranging from 3.5 to 55.2 μg g^-1. DNA concentrations displayed wide temporal changes also at bathyal depths confirming the recent view of the large variability of the deep-sea environments. Also RNA concentrations decreased with increasing water depth (range: 0.4–29.9 μg g^-1). The ratio of RNA to DNA did not show a clear spatial pattern but was characterized by significant changes between sampling periods. DNA concentrations were significantly correlated with protein and phytopigment concentrations in the sediment, indicating a possible relationship with the inputs of primary organic matter from the photic layer. Bacterial densities were generally high (range: 0.9–4.6×10⁸ cells g^-1) compared to other deep-sea environments and decreased with increasing water depth. Estimates of the bacterial contribution to the sedimentary genetic material indicated that bacterial-DNA accounted, on annual average, for a small fraction of the total DNA pool (4.3%) but that bacterial-RNA represented a significant fraction of the total sedimentary RNA (26%). Bacterial contribution to nucleic acids increased, even though irregularly, with increasing depth. In deep-sea sediments, changes in RNA concentrations appear to be largely dependent upon bacterial dynamics. Estimates of the overall living contribution to the DNA pools (i.e. microbial plus meiofaunal DNA) indicated that the large majority (about 90%) of the DNA in continental and deep-sea sediments of the eastern Mediterranean was detrital. The non-living DNA pools reach extremely high concentrations up to 0.41 g DNA m^-2 cm^-1. Thus, especially in deep benthic habitats, characterized by low inputs of labile organic compounds, detrital DNA could represent a suitable and high quality food source or a significant reservoir of nucleic acid precursors for benthic metabolism.     

大洋铁锰结核的微生物成矿过程及其研究进展

深海铁锰结核作为世界上潜在的巨大金属宝库已成为当今开发海底矿藏的热点，因而深入了解铁锰结核成矿过程成为其开发利用的先决条件。研究发现多金属铁锰结核中的铁锰矿物不仅仅是由单纯的物理作用形成的，同时也包含了海洋生物驱动的生物矿化的过程。本文介绍了运用分子生物学、矿物学和地球化学等多学科的研究方法对大洋中铁锰的生物成矿过程和成矿特征的研究。深海铁锰结核的生长速率缓慢且其生长演化伴随着微生物群落的活动，因此结核的生长过程同时也记录着不同时期微生物群落结构的变化并生成了大量的微生物化石。在铁和锰的生物矿化过程中，细菌可以通过酶促反应氧化Fe（Ⅱ）和Mn（Ⅱ），同时可能伴随生物能量的生成，此外微生物还可以通过非酶促反应的方式促进Fe和Mn的富集沉淀。这些研究表明生物矿化作用在大洋铁锰结核成矿过程中有巨大贡献，对大洋铁锰结核的生物成因过程提供更加全面准确的理解，从而为今后进一步充实大洋铁锰结核的生物矿化理论及其开发利用提供依据。     

Microbial ecology concerning to the degradation of nucleic acid in the marine environment

This article summarizes the author's current work on microbial degradation of nucleic acid. The aim of this work is to elucidate parts of the saprogenic process in the marine ecosystem through the study of the behavior of nucleic acid-hydrolyzing bacteria inhabiting seawater and sediments.Considerably large population of nucleic acid-hydrolyzing bacteria was found to occur in seawater and sediments. The main genera of these microbes areVibrio spp. in coastal seas, andPseudomonas spp. in the oceanic waters. As a result of microbial attack, nucleic acid components are released into seawater. The properties of extracellular nuclease produced by a marineVibrio sp. are well adapted to the seawater environment; consequently this enzyme has high activity and stability in seawater. By determining nuclease activity in seawater and sediments, the intensities of nucleic acid-hydrolysisin situ were evaluated.Distribution patterns of marine bacteria are also discussed in reference to the occurrence of phytoplankton in seawater.     

Microbial Biomass and Organic Nutrients in the Deep-Sea Sediments of the Central Indian Ocean Basin

In order to assess the impact of deep-sea mining on the in situ benthic life, we measured the microbial standing stock and concentration of organic nutrients in the deep-sea sediments of the Central Indian Ocean Basin in the Indian pioneer area. Sediments were collected using box core and grab samples during September 1996. The total bacterial numbers ranged from 10 10 -10 11 cells per g -1 dry weight sediment. There was a marginal decrease in the number of bacteria from surface to 30 cm depth, though the subsurface section registered a higher number than did the surface. The highest numbers were encountered at depths of 4-8 cm. The retrievable number of bacteria were two orders less in comparison with the direct total counts of bacteria. An almost homogeneous distribution of bacteria, total organic carbon, living biomass, and lipids throughout the depth of cores indicates active microbial and benthic processes in the deep sea sediments. On the other hand, a uniform distribution of total counts of bacteria, carbohydrates, and total organic carbon in all the cores indicates their stable nature and suggests that they can serve as useful parameters for long-term monitoring of the area after the benthic disturbance. Further studies on temporal variability in this region would not only verify the observed norms of distribution of these variables but would also help to understand restabilization processes after the simulated benthic disturbance.     

北极深海沉积物中细菌和古菌群落结构研究

在北极深海沉积物生态系统中,微生物的群落结构由有机质输入、能量的可用性及其他环境因素决定.然而,全球气候变暖及其导致的冰盖提前融化正在影响微生物的多样性.为描述北极深海沉积物中的微生物群落结构及其与环境因素的相关性,我们利用罗氏454对北极深海沉积物样品的16S rDNA扩增子进行了测序,对细菌和古菌群落的丰富度、成分、结构及其系统发育分类地位进行了描述.硫还原和化能有机营养类是细菌群落中的主要类群;而古细菌群落主要是由微生物的关系最为密切的氨氧化奇古菌门(96.66%)和产甲烷古生菌界(3.21%).这项研究描述了北极极点附近深海沉积物(> 3500米)中的微生物多样性,将为以后研究类似环境中微生物代谢过程和途径等功能分析奠定基础.     

Microbial Diversity of Deep-sea Sediments from Three Newly Discovered Hydrothermal Vent Fields in the Central Indian Ridge

Since the discovery of hydrothermal vents in the late 1970s, deep-sea hydrothermal vent fields have attracted great attention as biological hotspots. However, compared with other ocean ridges, the structure and function of microbial communities inhabiting vent fields in the Central Indian ridge (CIR) remain understudied. Here, we provide for the first time 16S rRNA gene-based comparative metagenomic analysis of the sediment-associated microbial communities from three newly discovered vent fields in the CIR. Sediment samples collected in the Invent B, Invent E and Onnuri vent fields varied in geochemical properties, elemental concentrations and associated microbial communities. Proteobacteria (Gammaproteobacteria) was the dominant phylum in Invent B and Onnuri vent fields. In contrast, Invent E mainly consisted of Chloroflexi and Euryarchaeota. Predicted functional profiling revealed that the microbial communities in the three vents are dominated by chemoheterotrophic functions. In addition, microbial communities capable of respiration of sulfur compounds, nitrification, nitrite oxidation, methylotrophy, and methanotropy were found to be the main chemolithoautotrophs. Compared to other vent fields, Invent E showed a predominance of archaeal methanogens suggesting it exhibits slightly different geochemistry. Multivariate analysis indicated that the biogeochemical and trace metal differences are reflected in the sediment microbial compositions of the three vent fields. This study expands our current understanding of the microbial community structure and potential ecological functions of the newly discovered hydrothermal vent fields in the CIR.

     

好氧反硝化反应器中微生物群落的碳代谢特征

本文采用Biolog-ECO微平板技术,分析了不同水力停留时间(hydraulic retention time,HRT)5、6、7h和进水硝酸盐(NO3ˉ-N)浓度50、100、150mg/L时,好氧反硝化反应器微生物群落结构和代谢功能特征。研究结果表明:在同一进水硝酸盐浓度下,水力停留时间越长,微生物代谢活性越强(P0.05);在同一水力停留时间下,不同进水NO3ˉ-N浓度下微生物平均吸光值(用平均颜色变化率AWCD指示)的大小顺序为50150100mg/L(P0.05),说明进水NO3ˉ-N浓度对微生物代谢活性有一定影响。反应器内微生物对不同碳源的代谢利用由强到弱的顺序是:多聚物氨基类碳水化合物羧酸类胺类酚酸类。不同处理组的Shannon-Wiener指数、Simpson指数、Pielou指数、Mc Intosh指数相互之间差异显著(P0.05),其中HRT为7h、NO3ˉ-N为150mg/L以上处理组微生物多样性指数最高。本实验采用Biolog-ECO板来分析在好氧反硝化反应器中微生物的群落代谢特征,研究结果可为通过碳源调节生物滤池水处理效果提供科学依据,以此提高水处理效率。     

Symbiotic Relations of Sediment-Agglutinating Nematodes and Bacteria in Detrital Habitats: The Enzyme-Sharing Concept

Abstract. A new concept (‘enzyme sharing’) concerning the interaction of marine nematodes and microbes in the degradation of sedimentary detritus is presented. Elements of this concept are (1) the notorious tendency of many aquatic nematodes to agglutinate detrital particles by mucus secretions, (2) new observations on the stimulation of microbial growth by nematodes in agar plates, and (3) literature data on limited endogenous proteolytic capacities of aquatic nematodes.
Observations on nematode‐microbe associations in agar plates prompted the conceptual synthesis. In agar medium without the addition of any nutrients a spectacular growth of bacteria was visible on the sinusoidal crawling trails of nematodes only 2 – 3 days after introduction of the worms (species of Adoncholaimus, Anoplostoma and Sabatieria). Juveniles of Anoplostoma that hatched in the agar cultures left their minute trails in the medium and these were rapidly occupied by bacteria. The nematodes repeatedly visited their bacterial trails, which persisted as a peculiar biotic structure for more than one year and survived the nematodes.
In sterile agar preparations containing the fluorogenic methylumbelliferyl‐β‐glucoside in the presence of the nematode Adoncholaimus, an enhanced fluorescence of the medium was visible, indicating β‐glucosidase activity. We therefore assume that oncholaimid nematodes discharge enzymes that alone, or in concert with microbial activities, contribute to the hydrolytic cleavage of refractory polysaccharides containing β‐glucosidic bonds such as agar components and cellulose. The sugars thus produced may then be taken up by the nematodes and concomitantly support the conspicuous growth of microbes. Since we did not observe any feeding of the nematodes on the associated microbes in agar plates, we question the nutritive potential of intact microbial cells for a number of nematodes abounding in detrital habitats, and call attention to the significance of ambient dissolved or adsorbed organic monomeric nutrients.
Consequently, we perceive the puzzling perpetual accretion of detrital organic particles to sediment agglutinations by nematodes as an adaptation for operating an ‘enzymatic reactor’ for the production of dissolved nutrients. We hypothesise a relationship of mutual commensalism of nematodes and heterotrophic microbes in detrital habitats and propose the term ‘enzyme sharing’ for this relationship. Both parties invest in a common enzyme pool that decomposes organic detritus for their nutrition. We present here evidence that nematodes contribute β‐glucosidase, which is involved in the cellulase system. Data from the literature suggest that microbial enzymatic processing of detrital proteins yields amino acids available to nematodes, which apparently have no efficient proteolytic enzyme system in their intestines.     

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

DNA polymerase δ (Polδ) plays a crucial and versatile role in DNA replication and DNA repair processes. Vent shrimp Rimicaris exoculata is the primary megafaunal community living in hydrothermal vents. In this study, the Polδ from shrimp Rimicaris exoculata was cloned, expressed and characterized. The results showed that the Polδ catalytic subunit (POLD1), 852 amino acids in length, shared high homology with crayfish Procambarus clarkii and shrimp Oratosquilla oratoria. The recombinant POLD1 expressed in Escherichia coli showed that the enzyme was active in a range of 20°C to 40°C with an optimum temperature at 25°C and in a wide range of pH with an optimum at pH 6.0. The activities of POLD1 were significantly enhanced in the presence of Triton-X 100, Tween 20 and Mn2+. The K_m (dNTP) value of POLD1 was 4.7 μmol/L. The present study would be helpful to reveal the characterization of Polδ of deep-sea vent animals.     

北极地区深海微生物研究进展及对策

对北极地区深海微生物研究进展进行了综述和展望分析,并提出强化我国北极深海微生物研究的对策,以期为相关研究和决策提供参考。综述表明北极深海微生物具有丰富的多样性,是数量巨大的遗传基因资源承载者,群落结构表现出显著的空间分布差异,在北极深海食物链中可能发挥着基础性作用。展望分析提出聚焦北极深海这一特殊的极端环境,开展微生物多样性和地理分布特征研究、新颖遗传生化功能挖掘以及多尺度生态系统下微生物与环境变化的研究具有重要意义和价值。建议我国顶层布局、构建北极深海微生物协同研究体系,提升专用配套仪器装备保障能力,全面推进相关研究工作。     

Deep-Sea Nodules and Co-rich Mn Crusts

The mining of deep-sea manganese nodules has been a topic of interest since J.L. Mero undertook his preliminary studies in the 1960s to evaluate the prospects for mining deep-sea nodules. Despite the great deal of investment in deep-sea mining over more than 40 years, there has still been no successful attempt to mine the deep-sea nodules on a commercial scale. One of the major problems is that the nodules cannot be brought to the surface with the necessary amounts of recoverable nickel, cobalt and zinc to warrant the initial high investment necessary for this operation. It therefore appears that in the short term, deep-sea manganese and Co-rich Mn crusts will not be mined on a commercial scale in the foreseeable future. Nonetheless, investigations of deep-sea mineral deposits by a number of nations will continue and enable us to understand the deep-sea environment in increasing detail, which is necessary in view of the great extent of the deep oceans which cover an area of about 66% of the Earth's surface.     

Estimates of ocean wavelength and direction from X-and L-band synthetic aperture radar data collected during the Marineland experiment

Simultaneously obtainedX- andL-band synthetic aperture radar (SAR) data collected during the Marineland Experiment were spectrally analyzed by fast Fourier transform (FFT) techniques to estimate ocean wavelength and direction. An eight-sided flight pattern was flown over the same ocean area in order to study the sensitivity of the spectral estimate on radar look direction. These spectral estimates were compared with in situ wave measurements made by a pitch-and-roll buoy. The comparison revealed that theX-band SAR detected all gravity waves independent of radar look direction, while theL-band SAR detected all range-traveling gravity waves but failed to detect waves in three of four cases in which the waves were traveling within 25° of the azimuth direction. The analysis also indicates that azimuth-traveling waves appear longer and more range-traveling in the SAR imagery than observed by in situ instrumentation. It is postulated that degraded azimuth resolution due to scatterer motion is responsible for these observations.     

A suspended-particle rosette multi-sampler for discrete biogeochemical sampling in low-particle-density waters

To enable detailed investigations of early stage hydrothermal plume formation and abiotic and biotic plume processes we developed a new oceanographic tool. The Suspended Particulate Rosette sampling system has been designed to collect geochemical and microbial samples from the rising portion of deep-sea hydrothermal plumes. It can be deployed on a remotely operated vehicle for sampling rising plumes, on a wire-deployed water rosette for spatially discrete sampling of non-buoyant hydrothermal plumes, or on a fixed mooring in a hydrothermal vent field for time series sampling. It has performed successfully during both its first mooring deployment at the East Pacific Rise and its first remotely-operated vehicle deployments along the Mid-Atlantic Ridge. It is currently capable of rapidly filtering 24 discrete large-water-volume samples (30–100 L per sample) for suspended particles during a single deployment (e.g. >90 L per sample at 4–7 L per minute through 1 μm pore diameter polycarbonate filters). The Suspended Particulate Rosette sampler has been designed with a long-term goal of seafloor observatory deployments, where it can be used to collect samples in response to tectonic or other events. It is compatible with in situ optical sensors, such as laser Raman or visible reflectance spectroscopy systems, enabling in situ particle analysis immediately after sample collection and before the particles alter or degrade.     

Ex situ cultivation of Aplysinaaerophoba close to in situ conditions: ecological, biochemical and histological aspects

Sponges provide the largest number of biologically active natural products known from the marine environment and continue to be a very well studied phylum of marine fauna. The Mediterranean sponge Aplysina aerophoba accumulates brominated isoxazoline alkaloids such as Aplysinamisin-1, Aerophobin-2, Isofistularin-3 and the biotransformation product Aeroplysinin-1, which possesses, for example, antibiotic and cytotoxic properties. Until now, it is still being discussed which organisms – the sponge itself or associated microorganisms – are responsible for metabolite production. For cultivating Aplysina individuals under ex situ conditions, we surveyed relevant ecological factors in situ and controlled them in our aquarium system. We maintained A. aerophoba for more than 9 months and analysed changes of metabolite content and composition, microbial association as well as morphology in situ and ex situ under different light exposure. Although sponges showed slight reduction during maintenance, ex situ cultivation similar to in situ conditions provides a promising method to keep sponges and obtain their bioactive metabolites.     

中印度洋海盆富稀土沉积地球化学特征及富集机制研究

本文对中印度洋海盆深海富稀土沉积区两根柱样GC02和GC06开展了沉积物涂片观察,X-射线衍射分析,主量、微量和稀土元素分析,以及单矿物原位微区地球化学分析等,探讨了其地球化学特征、物质来源及稀土元素（REY）的富集机制。结果表明,GC02柱状沉积物类型为钙质黏土和沸石黏土,GC06柱状沉积物类型为钙质黏土、含沸石黏土和沸石黏土。稀土元素主要在含沸石黏土和沸石黏土中富集。北美页岩标准化（NASC）配分模式指示沉积物的REY主要来源于海水,矿物学和地球化学等特征表明该地区沉积物陆源组分可能主要源于澳大利亚的风尘物质。元素相关性和CaO/P₂O₅比值等指示了深海富稀土沉积中REY的主要赋存矿物为生物磷灰石（鱼牙/骨等）,其次为铁锰微结核。本文总结和探讨了深海富稀土沉积的形成机制,完善了深海富稀土沉积形成过程的概念模型。     

黄河三角洲退化湿地微生物特性的研究

本研究通过DAPI染色法、FDA染色法和稀释平板法对黄河三角洲退化湿地微生物特性进行研究,在分析土壤盐度和植物根际效应对微生物特性影响的基础上,探讨了微生物群落的垂直分布特征,并对可培养耐盐微生物进行了初步分离。结果表明,土壤盐度与微生物数量、活性及多样性呈显著负相关性(P<0.01)。耐盐细菌在耐盐微生物中占绝对优势,放线菌次之,真菌最少;微生物群落具有明显的垂直分布特征,数量、活性和多样性均随土层深度的增加而下降。五种植物(碱蓬、柽柳、芦苇、白茅、茵陈蒿)根际微生物群落的数量、活性及多样性明显高于非根际微生物群落;与柽柳、芦苇、白茅、茵陈蒿相比,碱蓬的根际效应最强。这些结果可为进一步开发利用滨海湿地微生物资源,形成修复退化湿地盐碱化土壤的植物-微生物耦合系统提供必要的理论依据。