极地和深海环境中低温噬菌体研究进展

极地和深海是地球上较为独特的生态系统,生活在其中的生物由于长期处于低温、寡营养和黑暗封闭的环境中,大多缺乏基本的光合作用,而被认为是研究生命进化和地球环境演化等问题的＂活化石＂。在这样的极端环境中,低温噬菌体的丰度却很高,越来越多的证据表明它们在维持这类环境的生态平衡和调控生物地球化学循环等方面扮演着非常重要的角色。对极地与深海中低温噬菌体的研究进行简要综述。     

自然环境中T4型噬菌体g23基因多样性研究进展

摘要：过去的20多年,伴随着分子生物学技术在环境微生物研究中的应用,环境中细菌和真菌群落基因多样性及与其生存环境间的关系逐渐被揭示,但对于地球上广泛存在且数量巨大的生命体-噬菌体基因多样性研究还很少。本文以编码T4型噬菌体主要壳蛋白基因g23为目标,综述了近年来T4型噬菌体在海洋、湖泊和稻田中基因多样性的研究进展。研究结果表明T4型噬菌体g23基因分布与其生存环境关系很大,许多g23基因按获取环境不同划分为几个新类群。同时文中也指出了针对环境中T4型噬菌体g23基因研究应该注意的几点问题及未来的研究发展趋势。     

水环境中有机碳循环的重要驱动力-噬菌体

随着气候温暖化问题日益突出,维持全球碳平衡成为人类可持续发展的关键。在超过地球表面70%的水环境中,生物有机碳循环是所有元素循环中最重要的一环。噬菌体的分布十分广泛,且含量丰富,其丰度可达106~108/mL,仅海洋噬菌体的总量即可达1030个。噬菌体在维持生物有机碳循环中贡献巨大,据估算经由海洋病毒完成的可溶性有机碳就达到全球碳循环的26%。主要针对噬菌体在海洋、湖泊、冰尘穴及湿地有机碳循环的作用进行了综述。     

深海微生物多样性

海洋面积约占地球总面积的70％,平均深度3,800 m,海底平均压力38 MPa,海水以下更是包含有物理化学性质迥异的多种地质结构,例如海洋沉积物、洋壳、热液口以及冷泉等.这些性质迥异的地质结构环境造就了丰富的生物多样性,构成了地球上最大的微生物生态系统.深海海水中最主要的微生物类群是α-,γ-变形菌(Alpha-&Gammaproteobacteria),以及海洋古菌群I(Marine Group I).深海沉积物中微生物含量与有机物含量和距离大陆板块的距离相关,以异养微生物为主.深海冷泉区富集了厌氧甲烷氧化古菌ANME和硫酸盐还原菌(Deltaproteobacteria);深海热液区由于具有化学物质的多样性和快速的动态变化而导致形成微生物的高度多样性.洋壳主要由基性、超基性岩构成,含有丰富的矿物,其中不乏参与铁、锰、硫等关键代谢反应的化能自养微生物.同时,由于环境中99％以上的微生物没有已培养的亲缘种,因此对深海微生物的多样性、生理功能特性以及生物地球化学作用的理解和研究仍然存在巨大的挑战.本文将尝试从不同的深海环境分区来综述深海海水、沉积物、洋壳,以及冷泉区和热液口等特殊生态环境中微生物的分布和多样性.     

一种新的噬菌体基因多样性分子标记基因phoH研究进展

噬菌体作为结构最简单的生命体,不仅在调节寄主群落结构、遗传物质的水平移动方面作用巨大,同时也被证明在元素生物地球化学循环中具有非常重要的地位。尽管噬菌体的重要性越来越引起研究者的关注,但遗憾的是目前对于噬菌体基因多样性的研究还存在很大的局限性,发现并验证一种适合于研究噬菌体基因多样性的分子标记基因是环境病毒生态学研究的热点之一。介绍了一种新的分子标记基因-噬菌体辅助代谢磷酸盐调节基因pho H,并综述了近年来利用该基因揭示海洋海水、稻田田面水和沙漠石下生物中噬菌体基因多样性的研究进展。结果表明,噬菌体pho H基因分布与其生存环境关系密切,按获取环境不同pho H基因被划分为多个类群。最后对噬菌体pho H基因未来研究方向给予展望。     

深海极端微生物菌群及代谢产物多样性的研究进展

海洋覆盖了地球表面积的四分之三,它不仅是生命的起源,而且还孕育了各种极端微生物。它们存在于海洋极端环境中,如热液喷口、热泉、咸湖和深海层等,由于生境太过恶劣,一度被认为是生命的禁区。随着人类对深海极端环境微生物研究的不断深入,已经探索到那里具有丰富的菌群资源和具有潜在价值的天然生物活性产物。这些极端微生物能够适应极高温、极低温、高压、高盐、高放射性和极度酸碱性等极端环境,具有特殊的生物多样性、遗传背景和代谢途径,能够产生各种具有特殊功能的酶类及其他活性物质,展现出巨大的研究价值和应用潜力。研究海洋极端微生物对探索生物多样性、新资源开发利用及对地球生物学研究等都具有重要意义。     

海洋微型底栖生物的多样性与地理分布

海洋微型底栖生物是指生活于海洋沉积物中及表面的所有单细胞原核和真核微型生物,包括原核微生物、真核微藻及原生动物等光合自养和异养的类群.与水体相比,海洋底栖生境孕育了形态和功能多样性更高的微型生物,在陆架浅海单位体积沉积物中其丰度较之水体中同类生物高一至几个数量级,而深海则孕育着特殊进化环境下新奇多样且数量庞大的微型底栖生物,是维持海洋生物多样性、海洋生态系统结构和功能不可或缺的部分.迄今对于微型生物是全球性还是限定性分布一直存在争议,对其解答受到分类研究欠缺及采样不足的制约.分子生物学从正反两方面提供了理论依据,但无法得出一个普遍接受的观点.海洋微型底栖生物的多样性研究侧重于物种多样性及群落结构与分子多样性,较为显著的进展体现在原核微生物的分子多样性及底栖真核微藻的物种多样性研究,对于海洋底栖原生动物的多样性研究则相较滞后.本文综述了国内外对海洋微型底栖生物各主要类群的分类学和多样性研究进展,探讨了各类群在全球的潜在物种多样性,并就我国未来加强海洋微型底栖生物多样性构成、分布与变动及驱动变化的因子以及底栖微食物网的研究提出了建议.     

海洋浮游介形类的多样性和生态学研究进展

海洋浮游介形类(ostracods)是一类分布较广的小型甲壳动物, 大多数是典型的有机碎屑摄食者, 本身又是中深层鱼类的饵料, 在海洋碳循环中起重要作用。目前海洋浮游介形类研究主要集中在海洋表层, 大约还有200—400 种的海洋浮游介形类未被发现, 尤其是栖息于深海的种类。今后介形类分类学研究的重要趋势之一是深海种类的发现。我国介形类研究起步晚, 积累少, 应加强我国不同海域深海介形类及其与环境关系的深入研究。文章综述了海洋浮游介形类的多样性和生态学等方面的研究进展, 重点概述了海腺萤科分类的发展, 比较分析了不同海域介形类的物种多样性和分布特征, 总结了浮游介形类的生态作用及其影响因素, 概括了我国海洋浮游介形类的研究现状, 以期为海洋生物多样性、海洋生物地球化学循环以及深海生态学等方面的研究提供基础依据。     

东北湿地沉积物中T4型噬菌体g23基因的多样性

【目的】揭示我国东北典型湿地沉积物中T4型噬菌体g23基因的多样性,明确湿地环境T4型噬菌体群落分布特征,为噬菌体生态学研究提供数据支撑。【方法】采用简并性引物MZIA1bis和MZIA6对采自东北6个地点不同类型湿地沉积物土壤DNA进行PCR扩增,采用克隆测序方法,解析沉积物中T4型噬菌体g23基因组成,通过UniFrac分析T4型噬菌体群落结构在湿地沉积物中与其他环境中的差异。【结果】在东北湿地沉积物中共得到262条不同的g23基因序列,构建的系统进化树分析表明,我国东北湿地沉积物T4型噬菌体g23基因分布与海洋、湖泊及稻田生态系统中g23基因亲缘关系较近,而与东北旱地黑土g23基因分布较远;以g23基因群集表征的T4型噬菌体群落在不同地点湿地中分异明显。【结论】东北湿地生态系统T4型噬菌体群落结构复杂多样,存在着一些未知的噬菌体类群。     

低温细菌与古菌的生物多样性及其冷适应机制

低温细菌与古菌广泛分布于地球的低温环境,包括南极、北极及高山地带的冻土、低温土壤和荒漠、冰川、湖泊、海冰,以及深海、冰洞和大气平流层等.栖息在这些低温环境中的细菌与古菌具有丰富的多样性,主要为α,p和γ-Proteobacteria分支、CFB类群分支和革兰氏阳性细菌分支等.由于低温环境中的微生物流动性低,因而是研究微生物地理学理想的生态系统,有助于理解地球微生物的多样性、分布规律乃至形成机制.由于长期生活在冰冻环境中,低温细菌与古菌形成了多种适应低温环境的生理机制,如它们通过细胞膜脂类的组成来调节膜的流动性以维持正常的细胞生理功能;利用相容性溶质、抗冻蛋白、冰核蛋白及抗冰核形成蛋白等实现低温保护作用;产生冷激蛋白、冷适应蛋白和DEAD-box RNA解旋酶保持低温下RNA的正确折叠、蛋白质翻译等重要的生命活动;另外还产生低温酶,提高能量产生和储存效率等以适应低温环境.随着DNA序列分析技术的飞速发展,各类组学方法也用于揭示微生物全局性的冷适应机制.     

A review of the influence of biogeography,riverine linkages,and marine connectivity on fish assemblages in evolving lagoons and lakes of coastal southern Africa

The Holocene evolution of eight South African coastal lakes and lagoons is examined and related to changes in fish composition over that period. Historical and current connectivity with riverine and marine environments are the primary determinants of present‐day fish assemblages in these systems. A small and remarkably consistent group of relict estuarine species have persisted in these coastal lakes and lagoons. The loss or reduction of connectivity with the sea has impacted on the diversity of marine fishes in all eight study systems, with no marine fishes occurring in those water bodies where connectivity has been completely broken (e.g. Sibaya, Groenvlei). In systems that have retained tenuous linkages with the sea (e.g., Verlorenvlei, Wilderness lakes), elements of the marine fish assemblage have persisted, especially the presence of facultative catadromous species. Freshwater fish diversity in coastal lakes and lagoons is a function of historical and present biogeography and salinity. From a freshwater biogeography perspective, the inflowing rivers of the four temperate systems reviewed here contain three or fewer native freshwater fishes, while the subtropical lakes that are fed by river systems contain up to 40 freshwater fish species. Thus, the significantly higher fish species diversity in subtropical versus temperate coastal lakes and lagoons comes as no surprise. Fish species diversity has been increased further in some systems (e.g., Groenvlei) by alien fish introductions. However, the impacts of fish introductions and translocations have not been studied in the coastal lakes and lagoons of South Africa. In these closed systems, it is probable that predation impacts on small estuarine fishes are significant. The recent alien fish introductions is an example of the growing threats to these systems during the Anthropocene, a period when human activities have had significant negative impacts and show potential to match the changes recorded during the entire Holocene.     

Microbes on the edge of global biosphere]

The search for life on the edge of global biosphere is a frontier to bridge conventional bio/ecology and exo/astrobiology. This communication reviews the foci of microbiological studies on the inhabitants of the selected "edges", i.e., deep-sea, deep subsurface and Antarctic habitats. The deep-sea is characterized as the no-light (non-photosynthetic) habitat, and the primary production is mostly due to the chemosynthetic autotrophy at the hydrothermal vents and methane-rich seeps. Formation of the chemosynthesis-dependent animal communities in the deep leads to the idea that such communities may be found in "ocean" of the Jovian satellite, Europa. The oxygen minimal layer (OML) in mid-water provides another field of deep-sea research. Modern OML is a relatively thin layer, found between the water depth of 200 and 1000 m, but was much thicker during the periods of oceanic anoxia events (OAEs) in the past. The history of oceanic biosphere is regarded as the cycle of OAE and non-OAE periods, and the remnants of the past OAEs may be seen in the modem OML. Anoxic (no-O2) condition is also characteristic of deep subsurface biosphere. Microorganisms in deep subsurface biosphere exploit every available oxidant, or terminal electron acceptor (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Subsurface of hydrothermal vents, or sub-vent biosphere, may house brine (high salt) habitats and halophilic microorganisms. Some sub-vent halophiles were phylogenetically closely similar to the ones found in the Antarctic habitats which are extremely dry by the liophilizing climate. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, has been a target of "life in extreme environments" and is about to be drill-penetrated for microbiological studies. These 'microbiological platforms' will provide new knowledge about the diversity and potential of the Earth's life and facilitate the capability of astrobiologial exploration.     

Recently discovered landlocked basins in Indonesia reveal high habitat diversity in anchialine systems

In this article, the variability of physical settings of anchialine systems in Indonesia is discussed together with the consequences these settings have for the environment and biota within the systems. Exploration in two karstic areas (Berau, East Kalimantan and Raja Ampat, West Papua) has resulted in the discovery of 20 previously unknown anchialine systems in Indonesia. Based on parameters such as bathymetry, size, coastline, salinity, water temperature, pH, degree of connection to the sea, and the presence-absence of selected key taxa we distinguish three types of (non-cave) anchialine systems in the Indo-Pacific: (1) Marine lakes with large and deep basins containing brackish to almost fully marine waters. Marine lakes show a range in the degree of connection to the sea with the result that the higher the connection the more the lake resembles a lagoon in both water chemistry and biota, while the more isolated lakes have brackish water and contain unique species that are rarely found in the adjacent sea. (2) Anchialine pools with small and shallow basins containing brackish water and low diversity of macrofauna. (3) Blue pools in chasms that contain water with a clear halocline and are possibly connected to anchialine caves. Study of the many unique features of anchialine systems will enhance our understanding of the physical and ecological processes responsible for diversification in tropical shallow marine environments.     

Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms]

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".     

Resource diversity promotes among‐individual diet variation,but not genomic diversity,in lake stickleback

Many generalist species consist of specialised individuals that use different resources. This within‐population niche variation can stabilise population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favour ecological diversity among consumers (via disruptive selection or plasticity). Alternatively, niche variation might be a side‐effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate‐sized lakes support generalist stickleback populations using an even mixture of the two prey types, and exhibit greater among‐individual variation in diet and morphology. In contrast, genomic diversity increases with lake size. Thus, phenotypic diversity and neutral genetic polymorphism are decoupled: trophic diversity being greatest in intermediate‐sized lakes with high resource diversity, whereas neutral genetic diversity is greatest in the largest lakes.     

Genetic structure of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis> L.) from the Hardangervidda mountain plateau (Norway) analyzed by microsatellite DNA: a basis for conservation guidelines

The Hardangervidda in southern Norway, the largest mountain plateau in Europe, has thousands of lakes and streams, mainly between 1000 and 1300 m above sea level, where brown trout is the only fish species. To describe the current genetic diversity of brown trout in this area, a total of 863 fish from 20 lakes were genotyped with eleven microsatellites. Most diversity is within lake populations, but diversity among geographical groups and populations within groups was significant, too. Neighbor-joining, principle coordinate analysis and Bayesian clustering show three major geographic groups in accordance with the river systems. Bias was caused by recent stocking in two lakes. Low/no genetic differentiation among some populations indicates that intermixing is common when lakes are well-connected, as was also shown by assignment test. We recommend preserving the genetic diversity of brown trout in this unique area by managing stocking in lake systems according to genetic structure.     

Evidence for an active rare biosphere within freshwater protists community

Studies on the active rare biosphere at the RNA level are mainly focused on Bacteria and Archaea and fail to include the protists, which are involved in the main biogeochemical cycles of the earth. In this study, the richness, composition and activity of the rare protistan biosphere were determined from a temporal survey of two lakes by pyrosequencing. In these ecosystems, the always rare OTUs represented 77.2% of the total OTUs and 76.6% of the phylogenetic diversity. From the various phylogenetic indices computed, the phylogenetic units (PUs) constituted exclusively by always rare OTUs were discriminated from the other PUs. Therefore, the rare biosphere included mainly taxa that are distant from the reference databases compared to the dominant ones. In addition, the rarest OTUs represented 59.8% of the active biosphere depicted by rRNA and the activity (rRNA:rDNA ratio) increased with the rarity. The high rRNA:rDNA ratio determined in the rare fraction highlights that some protists were active at low abundances and contribute to ecosystem functioning. Interestingly, the always rare and active OTUs were characterized by seasonal changes in relation with the main environmental parameters measured. In conclusion, the rare eukaryotes represent an active, dynamic and overlooked fraction in the lacustrine ecosystems.     

Fluidized muds: a novel setting for the generation of biosphere diversity through geologic time*

Reworked and fluidized fine‐grained deposits in energetic settings are a major modern‐day feature of river deltas and estuaries. Similar environments were probably settings for microbial evolution on the early Earth. These sedimentary systems act as efficient biogeochemical reactors with high bacterial phylogenetic diversity and functional redundancy. They are temporally rather than spatially structured, with repeated cycling of redox conditions and successive stages of microbial metabolic processes. Intense reworking of the fluidized bed entrains bacteria from varied habitats providing new, diverse genetic materials to contribute to horizontal gene transfer events and the creation of new bacterial ecotypes. These vast mud environments may act as exporters and promoters of biosphere diversity and novel adaptations, potentially on a globally important scale.     

Cold-adapted archaea

Many archaea are extremophiles. They thrive at high temperatures, at high pressure and in concentrated acidic environments. Nevertheless, the largest proportion and greatest diversity of archaea exist in cold environments. Most of the Earth's biosphere is cold, and archaea represent a significant fraction of the biomass. Although psychrophilic archaea have long been the neglected majority, the study of these microorganisms is beginning to come of age. This review casts a spotlight on the ecology, adaptation biology and unique science that is being realized from studies on cold-adapted archaea.