漫谈海洋地微生物学

文章由地微生物学谈起,论述海洋地微生物学的研究历史及难度等。讨论海洋地微生物学内容及其环境的特点、研究现状及方向。文章寄希望于海洋环境、地质等地球科学家与微生物学家等的共同努力、密切配合,大力开拓我国的海洋地微生物学研究。

我国深海地微生物学研究状况分析

引用国际相关趋势论述我国深海地微生物学的研究状况和研究进展,包括介绍国际间相关研究的历史状况、动态,我国研究的主要课题、内容和成果。展望了我国本领域的前景。

地微生物学研究热点之一

地球表层或地球内部的一切极端环境中生存微生物是一个潜在的资源宝库。曾报道在温泉、深海热液出口交接处有嗜热细菌的存在，源于这些细菌含有很强的嗜极酶、如耐热酶、蛋白质及其他细胞组分，有些嗜热酶进入实用化，商品化。有的嗜热细菌全部基因组测序工作的完成，对嗜极酶基因组的研究与探索以及对嗜热菌适应极端环境的生存和繁衍与分子机制的研究有重要价值。这是深海火山口嗜热微生物研发的一个热点，也是地微生物学研究的新领域。英国“自然”(2005．元月)报道，地中海深处含盐量极高的4个盐盆地区，有一群活着的微生物，该地区水的含盐量极高，比酱油成2倍，这些微生物照样维持它们的生命活动。

海底热液活动区地微生物学研究中的分子生物学技术

海底热液活动区微生物生态及其相关研究一直是近年来海洋地微生物学研究的热点之一。有关发现不断挑战着人们对微生物的代谢机理、生存极限、元素地球化学循环作用等方面的传统认识。与传统的富集培养方法相比,主要基于16S rRNA基因和特征性功能基因系统的发育分析等技术为研究这一极端环境中栖息的微生物群落提供了更为系统和全面的手段。这些技术包括基因文库构建(16S rRNA和其它功能基因)、变性梯度凝胶电泳(DGGE)、末端限制性片段长度多态性分析(T-RFLP)、荧光原位杂交(FISH)以及定量PCR等。目前,上述技术手段广泛应用于全球海底热液活动区地微生物学的研究,在丰富地球物种多样性、调查微生物参与的元素地球化学循环过程、研究微生物与矿物的相互作用以及生命起源与演化等方面取得了大量的研究成果。简要介绍了常规分子生物学技术的基本原理及其在海底热液活动区地微生物学研究中的应用现状。

Recover vigorous cells of Magnetospirillum magneticum AMB-1 by capillary magnetic separation

Cultivable magnetotactic bacteria(MTB) in laboratory can provide sufficient samples for molecular microbiological and magnetic studies.However,a cold-stored MTB strain,such as Magnetospirillum magneticum AMB-1,often loses its ability to synthesize magnetosomes and consequently fails to sense the external magnetic field.It is therefore important to quickly recover vigorous bacteria cells that highly capable of magnetosome producing.In this study,a modified capillary magnetic separation system was designed to recover a deteriorating strain of Magnetospirillum magneticum AMB-1 that long-term cold-stored in a refrigerator.The results show that all cells obtained after a 3-cycle treatment were vigorous and had the ability to produce magnetosomes.Moreover,the 3rd-cycle recovered cells were able to form more magnetosome crystals.Compared with the colony formation method,this new method is time-saving,easily operated,and more efficient for recovering vigorous MTB cells.

Microaerobic iron oxidation and carbon assimilation and associated microbial community in paddy soil

Iron oxidation is a prevalent and important biogeochemical process in paddy soil,but little is known about whether and how microbially mediated iron oxidation is coupled with carbon assimilation,particularly under microaerobic conditions.Here,we investigated kinetics of CO_2 assimilation and Fe(Ⅱ)oxidation in an incubation experiment with paddy soil under suboxic conditions,and profiled the associated microbial community using DNA-stable isotope probing and 16S r RNA gene-based sequencing.The results showed that CO_2 assimilation and Fe(II)oxidation in the gradient tubes were predominantly mediated by the microbes enriched in the paddy soil,primarily Azospirillum and Magnetospirillum,as their relative abundances were higher in the^( 13)C heavy fractions compared to^( 12)C heavy fractions.This study provided direct evidence of chemoautotrophic microaerophiles linking iron oxidation and carbon assimilation at the oxic–anoxic interface in the paddy soil ecosystem.

Microbiostratigraphy and depositional environment of Eocene Shahbazan deposits at Chenareh section,southwest of Iran

The Shahbazan Formation was deposited in the foreland basin in southwestern Iran( Lorestan Basin). In this research,microbiostratigraphy and depositional environmental implications related to the Shahbazan Formation at the northern flank of Chenaerh anticline are discussed. Carbonate sequences of the Shahbazan Formation consist mainly of large benthic foraminifera along with other skeletal and non-skeletal components.Two biozones have been recognized by distribution of large foraminifera in the studied area that indicate middle Eocene age( Lutetian). Based on analysis of large benthic foraminiferal assemblages and microfacies features,7 different microfacies have been recognized,which can be grouped into three depositional environments: inner,middle and outer ramps.

The geobiological formation process of the marine source rocks in the Middle Permian Chihsia Formation of South China

The Chihsia Formation is one of the four sets of regional marine hydrocarbon source rocks from South China.In the past two decades,detailed geochemical and sedimentological studies have been carried out to investigate its origination,which have demonstrated that the high primary productivity plays a primary role in the deposition of sediments enriched in the organic matter.However,the mechanism of this high productivity and the path of the deposition and burial of the organic matter have always been a mystery.Based on the previous studies on the Shangsi Section in Guangyuan City,Sichuan Province,we proposed that the development of the equatorial upwelling due to the sea level rise is responsible for the relatively high productivity in the Chihsia Formation.The sea waters with high nutrient were transported by the sub-surface currents along the equator.High organic carbon flux was deposited on the deeper shelf,and then decomposed by bacteria,leading to the occurrence of anaerobic respiration.The metabolism of the microorganisms consumed the dissolved oxygen in waters,which was in favor of the preservation of the organic matter.This suggested geobiological model integrating with paleoclimatology,paleoceanography and geomicrobiology will help us to understand the causes of this particular sedimentary sequence.

Progress and perspective on frontiers of geobiology

Geobiology is a new discipline on the crossing interface between earth science and life science, and aims to understand the in- teraction and co-evolution between organisms and environments. On the basis of the latest international achievements, the new data presented in the Beijing geobiology forum sponsored by Chinese Academy of Sciences in 2013, and the papers in this special issue, here we present an overview of the progress and perspectives on three important frontiers, including geobiology of the critical periods in Earth history, geomicrobes and their responses and feedbacks to global environmental changes, and geobiology in extreme environments. Knowledge is greatly improved about the close relationship of some significant biotic events such as origin, radiation, extinction, and recovery of organisms with the deep Earth processes and the resultant envi- ronmental processes among oceans, land, and atmosphere in the critical periods, although the specific dynamics of the co-evolution between ancient life and paleoenvironments is still largely unknown. A variety of geomicrobial functional groups were found to respond sensitively to paleoenvironmental changes, which enable the establishment of proxies for paleoenvi- ronmental reconstruction, and to play active roles on the Earth environmental changes via elemental biogeochemical cycles and mineral bio-transforrnations, but to be deciphered are the mechanisms of these functional groups that change paleoenvi- ronmental conditions. Microbes of potential geobiology significance were found and isolated from some extreme environments with their biological properties partly understood, but little is known about their geobiological functions to change Earth envi- ronments. The biotic processes to alter or modify the environments are thus proposed to be the very issue geobiology aims to decipher in the future. Geobiology will greatly extend the temporal and spatial scope of biotic research on Earth and beyond. It has great potential of application in the domains of resource exploration and global change. To achieve these aims needs coor- dinative multidisciplinary studies concerning geomicrobiology and related themes, database and modeling of biogeochemical cycles, typical geological environments, and coupling of biological, physical, and chemical processes.

Mineral weathering and element cycling in soil-microorganism-plant system

Soil is an essential part of the critical zone,and soil-microbe-plant system serves as a key link among lithosphere,biosphere,atmosphere and hydrosphere.As one of the habitats with the richest biodiversity,soil plays a critical role in element biogeochemistry on the earth surface(weathered crust).Here we review the soil biological processes that are relevant to mineral weathering,element cycling,and transformation,with an emphasis on rock weathering mediated by soil microbes,plant root and the rhizosphere.

Microbial roles equivalent to geological agents of high temperature and pressure in deep Earth

Microbes not only show sensitive responses to environmental changes but also play important roles in geochemical and geophysical systems. It is well known that microbes have caused major changes in surface environments and biogeochemical cycles through Earth history. Microbial processes can also induce the synthesis of certain minerals under Earth-surface conditions that previously were believed to form only under high temperatures and pressures in the deep Earth. For example, microbes can promote the conversion of smectite to illite, synthesis of authigenic plagioclase, precipitation of dolomite, and biotransformation of geolipids. These effects of microbes are due to their large surface/volume ratios, enzyme production, and abundant functional groups. Microbial catalyzation of chemical reactions proceeds through reaction-specific enzymes, a decrease in Gibbs' s free energy, and/or break through the dynamics reaction thresholds via their metabolisms and physiology. Microbes can lower the surface free energy of mineral nuclei via biophysical adsorption due to their large surface/volume ratios and abundant functional groups. The mineral precipitation and transformation processes induced by microbes are functionally equivalent to geological processes operating at high temperatures and pressures in the deep Earth, suggesting that microbial processes can serve as analogs to deep abiotic processes that are difficult to observe.

Biomarker evidence for biotic and environmental change across the Cambrian Series 2–Series 3 boundary at the Wuliu- Zengjiayan section, Guizhou, China

The Wuliu-Zengjiayan section in Jianhe County, Guizhou Province, China has been suggested as a potential Global Stratotype Section and Point(GSSP) for the defined base of Cambrian Series 3. A molecular organic geochemical study on the Cambrian Series 2Series 3 boundary interval was carried out to reveal the biotic and environmental change during this transition. The hydrocarbons extracted from the Kaili Formation were proved to be indigenous. The various geochemical proxies such as biomarker parameter, δ13Corg, atomic H/C value of kerogen, and TOC content, co-vary along with the sedimentary column, and show a quick and significant change just across the Cambrian Series 2Series 3 boundary. The less abundance of isoprenoid hydrocarbons, the relative enrichment of midchain monomethyl branched alkanes(mmb-alkanes), the relatively negative value of δ13Corg, and the higher TOC contents may suggest that the upper Cambrian Series 2 was deposited in a relatively reducing environment with a higher organic input from cyanobacteria-predominated benthic microbial mats. On the other hand, the relative enrichment of isoprenoid hydrocarbons, the less abundance of mmb-alkanes, the relatively positive value of δ13Corg, the lower TOC contents, and the lower atomic H/C values of kerogen are combined to indicate an enhanced phytoplankton production and an increased oxygen content and nutrients in the ocean during the early Cambrian Series 3, which could have benefited the explosion of the Kaili Biota. The Wuliu-Zengjiayan section may provide a typical case to understand the co-variation of marine microbe, animal, and environment.

The research of typical microbial functional group reveals a new oceanic carbon sequestration mechanism——A case of innovative method promoting scientific discovery

Marine microbes are major drivers of marine biogeochemical cycles and play critical roles in the ecosystems. Aerobic anoxygenic phototrophic bacteria(AAPB) are an important bacterial functional group with capability of harvesting light energy and wide distribution, and appear to have a particular role in the ocean's carbon cycling. Yet the global pattern of AAPB distribution was controversial at the beginning of the 21 st century due to the defects of the AAPB enumeration methods. An advanced time-series observation-based infrared epifluorescence microscopy(TIREM) approach was established to amend the existing AAPB quantitative deviation and led to the accurate enumeration of AAPB in marine environments. The abundance of AAPB and AAPB% were higher in coastal and continental shelf waters than in oceanic waters, which does not support the idea that AAPB are specifically adapted to oligotrophic conditions due to photosynthesis in AAPB acting a supplement to their organic carbon respiration. Further investigation revealed that dependence of AAPB on dissolved organic carbon produced by phytoplankton(PDOC) may limit their competition and control AAPB distribution. So, the selection of carbon sources by AAPB indicated that they can effectively fractionate the carbon flow in the sea. Enlightened by these findings, the following studies on the interactions between marine microbes and DOC led to the discovery of a new mechanism of marine carbon sequestration—the Microbial Carbon Pump(MCP). The conceptual framework of MCP addresses the sources and mechanism of the vast DOC reservoir in the ocean and represents a breakthrough in the theory of ocean carbon sequestration.

Genomics,metagenomics,and microbial oceanography—A sea of opportunities

Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean science.Microbial oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine ecosystems.The application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem function.Here we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.