Archaea,the tree of life,and cellular evolution in eukaryotes

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.     

微生物成矿

微生物对生命元素如碳、氮、硫、氧和金属离子的代谢作用能显著的改变微生物周边的外部环境和其内部环境。在一系列的生物地球化学过程中,微生物参与了矿产的沉积(生物成矿)或参与了矿石和岩石的溶解(生物风化)。生物成矿作用有两个途径：一个叫生物诱导成矿,通过这个过程,微生物分泌出代谢产物导致了之后的矿物颗粒的沉积;另一个叫生物控制成矿,在这个过程中,微生物在控制矿物成核和生长上起到了显著作用。微生物成因的矿物总体来说颗粒都很小和／或有着独特的同位素特征。最普遍的生物成因矿物有碳酸盐、硫化物和铁的氧化物。细胞表面和其分泌的胞外聚合物的结构可以为离子的浓缩、聚合和矿化提供模板,并起到重要作用。地球材料的仿生合成帮助我们了解了在人工条件下的生物成矿机制。此外,在地质环境中生物成因的矿物还可以作为一种生物信号,用来重建地球和其他行星的起源和演化。     

http://www.sciencedirect.com/science/article/pii/S1674987111001290

The Three Gorges Dam(TGD) of the Yangtze River.China,is one of the largest irrigation and hydroelectric engineering projects in the world.The effects of huge man-made projects like TGD on fauna and macrophyte are obvious,mainly through changes of water dynamics and flow pattern;however, it is less clear how microorganisms respond to such changes.This research was aimed to examine differences in microbial diversity at different seasons and locations(in front of and behind the TGD).In addition, differences between particle-attached and free-living communities were also examined.The community structures of total and potentially active microorganisms in the water columns behind and in front of the TGD were analyzed with the DNA- and RNA-based 16S rRNA gene phylogenetic approaches over three different seasons.Clone libraries of 16S rRNA genes were prepared after amplification from extracted DNA and.for some samples,after preparing cDNA from extracted rRNA.Differences were observed between sites at different seasons and between free-living and particle-attached communities.Both bacterial and archaeal communities were more diverse in summer than in winter, due to higher nutrient levels and warmer temperature in summer than in winter.Particle-attached microorganisms were more diverse than free-living communities,possibly because of higher nutrient levels and heterogeneous geochemical micro-environments in particles.Spatial variations in bacterial community structure were observed,i.e..the water reservoir behind the TGD(upstream) hosted more diverse bacterial populations than in front of the dam(downstream),because of diverse sources of sediments and waters from upstream to the reservoir.These results have important implications for our understanding of responses of microbial communities to environmental changes in river ecosystems affected by dam construction.     

Distribution of aliphatic des-A-triterpenoids in the Dajiuhu peat deposit, southern China

Aliphatic des-A-triterpenoids have been tentatively assigned in samples taken from a 260 cm thick peat sequence from the Dajiuhu Basin of southern China using gas chromatography–mass spectrometry (GC–MS). The compounds, possessing the carbon skeletons of oleanane, ursane or lupane, are generally considered as the microbial degradation products of plant triterpenoids under anoxic conditions. Abundant aliphatic des-A-triterpenoids were observed only in peat samples during the transitional period from the last glaciation to the early Holocene (9.5–11.6 cal ¹⁴C ka BP). Among these, des-A-lupane is the only saturated ring A-degraded compound, whilst mono- and di-unsaturated des-A-triterpenes are dominated by oleanane and ursane derivatives. The mono- and di-unsaturated des-A-triterpenes show a strong correlation (R² 0.94) in abundance, indicating that they may be derived from the same source or process. Des-A-lupane shows no correlation in abundance with the mono- or di-unsaturated des-A-triterpenes (R² < 0.25) and may be derived from a different source or process in the catchment. The period with abundant aliphatic des-A-triterpenoids corresponds to the interval with relatively high sedimentation rate (> 0.3 mm per year). These data indicate that the abundance of aliphatic des-A-triterpenoids in the Dajiuhu peat deposit in the early Holocene may result from the prevailing reducing conditions in the water table or surficial sediment and/or rapid preservation of the early diagenetic products. Our study highlights the potential application of des-A-triterpenes in the reconstruction of palaeoenvironments based on peat sequences.     

黑潮源区沉积物微生物多样性初步研究

从黑潮源区采集上层沉积物,进行DNA提取,以细菌和古菌的16S rDNA通用引物PCR扩增黑潮源区沉积物中细菌和古菌群落的16S rDNA,并构建细菌和古菌的16S rDNA文库,经限制性片段长度多态性分析(Restriction Fragment Length Polymorphism,RFLP),DNA序列测定和系统发育分析,对黑潮源区表层沉积物的细菌和古菌多样性进行了研究。研究结果表明:黑潮源区细菌包括了变形杆菌(Proteobacteria)、酸杆菌(Acidbacterium)、浮霉菌(Planctanycene)、疣微菌(Verrucomicro-bia)和Candidate division OP8和拟杆菌(Bacteroidetes)共6个类群,其中变形杆菌是优势类群。古菌包括了泉古菌(Crenarchaeota)和广古菌(Euryarchaeota),其中泉古菌占优势;泉古菌包括MCG、C3、MBGA和MGI 4个类群,而广古菌包括SAGMEG、MBGE和MEG 3个类群,其中MBGE是优势类群。     

Tectonomicrobiology: A new paradigm for geobiological research

Geomicrobiology is a sub-discipline of geobiology and emphasizes the interaction between microorganisms and their environment on Earth. There is a need to explicitly emphasize the biogeochemical processes performed by microorganisms associated with Earth’s tectonic activities, especially under the framework of the modern theory of plate tectonics. Tectonomicrobiology aims to create a better synergy between microbial and active tectonic processes. This explicit synergy should also foster better communications between solid Earth scientists and life scientists in terms of holistic Earth system dynamics at both tectonic and micro-scales.     

Lipidomics in archaeal membrane adaptation to environmental stresses and growth conditions: A review of culture-based physiological studies

Membrane lipids are thought to be a crucial part of the homeoviscous adaptation of archaea to extreme conditions.This article reviews the recent lipidomic studies of physiological membrane adaptations of archaea, assesses the biomolecular basis of an organic paleothermometer, TEX86, and contemplates the future directions of archaeal lipidomics. The studies of extremophilic archaea have revealed that at least three different molecular mechanisms are involved in membrane adaptation of archaea:(1) regulation of the number of cyclopentane rings of caldarchaeol,(2) alteration of the diether-to-tetraether lipid ratio,and(3) variation of the proportion of saturated and unsaturated lipids. However, most of the studies have focused on a limited number of archaeal ether-linked lipids, such as glycerol dialkyl glycerol tetraethers(GDGTs), which only represent a fraction of the entire lipidome. Environmental factors such as growth temperature and pH have been most frequently reported, but biotic factors, including growth phases, nutrition, and enzymatic activities affecting the membrane lipid composition are often overlooked. Membrane lipids of mesophilic ammonia-oxidizing marine Thaumarchaeota have been applied in the reconstruction of past sea surface temperatures. However, recent culture-based physiological studies have demonstrated that non-thermal biotic factors, including dissolved oxygen, ammonia oxidation rate and the growth rate, are the main drivers of GDGT cyclization in Nitrosopumilus maritimus. Moreover, other related strains or ecotypes exhibit a markedly different set of stress adaptations. A trend is now developing to examine the whole lipid profile(lipidome) for studies of archaeal physiology and biochemistry related to lipid biosynthesis(lipidomics) to gain a better understanding of the biological mechanisms underpinning the applications of membrane lipid-based proxies in biogeochemical or ecological research.     

Spectral characteristics of dissolved organic matter in sediment pore water from Pearl River Estuary

As key parts of land-sea transition zones,estuary ecosystems play a very important role in the ocean carbon cycle processes.The sources,degradation,and preservation of dissolved organic matter(DOM)in estuaries have long been the subject of intense study.To examine the aforementioned issues,this study examined three-dimensional fluorescence spectroscopy and ultraviolet-visible absorption spectroscopy to determine the spatial distribution and sources of DOM in the pore water of three sedimentary cores from the Pearl River Estuary(S1,S2 and S3,with increasing salinity).Using the parallel factor analysis(PARAFAC)method to analyze the three-dimensional fluorescence spectrum data,five fluorescent components were obtained—three humic-like components(C1,C3,and C4),and two protein-like components(C2 and C5).C2 exhibited a significant positive correlation with the sediment microbial deoxyribose nucleic acid(DNA)concentration(R~2=0.69,P<0.01),indicating that the protein-like component C2 might be derived from the catabolism of in situ microbes.C5 displayed a relatively weak correlation with DNA concentration(R~2=0.40,P<0.05),presumably due to the incorporation of phenolic compounds,which have a fluorescence peak very similar to that of protein-like components.The source of humic-like fluorescent components is extremely complex.The content at station S1 was relatively high(1.45–8.83 R.U.),which implies that terrestrial inputs had a significant influence.The three humic-like components showed similar distributions at S2 and S3,and the fluorescence intensity was rather low;this result indicates that the DOM at these two stations was more likely affected by the metabolism of algae and microorganisms.The humification index(HIX)and the fluorescence intensity of protein-like components increased and decreased,respectively,with depth.There was a significant positive correlation between the relative content of protein-like components and the spectral slope ratio(SR),which indicates that DOM transitioned from low-molecular-weight protein-like components in the surface sediment to high-molecular-weight humic-like components in the subsurface.This study provides valuable information for understanding the pore water size/reactivity(PWSR)model of DOM and its biochemical processes occurring in estuary sediments.     

对重金属和辐射污染的土壤和地下水的微生物修复

由重金属和辐射产生的环境污染在世界范围内产生了一系列问题.利用特殊的微生物如金属还原和耐金属细菌对环境中的金属和辐射污染进行处理具有非常好的前景.现场的生物修复的成功应用将对清除污染环境中的重金属和辐射提供潜在方法.最近的研究还关注于了解在微生物群体内重金属和辐射对微生物的作用.生物毯和生物膜是在生物修复中具有代表性的两种微生物群落的机能.金属的种类和价态变化、转移过程以及微生物代谢作用是对金属和辐射生物修复的三种重要的组成部分.结合以上三方面,可以更好的了解自然中的微生物和生物修复过程之间的关系.