The Santa Barbara Basin is a symbiosis oasis

It is generally agreed that the origin and initial diversification of Eucarya occurred in the late Archaean or Proterozoic Eons when atmospheric oxygen levels were low and the risk of DNA damage due to ultraviolet radiation was high. Because deep water provides refuge against ultraviolet radiation and early eukaryotes may have been aerotolerant anaerobes, deep-water dysoxic environments are likely settings for primeval eukaryotic diversification. Fossil evidence shows that deep-sea microbial mats, possibly of sulphur bacteria similar to Beggiatoa, existed during that time. Here we report on the eukaryotic community of a modern analogue, the Santa Barbara Basin (California, USA). The Beggiatoa mats of these severely dysoxic and sulphidic sediments support a surprisingly abundant protistan and metazoan meiofaunal community, most members of which harbour prokaryotic symbionts. Many of these taxa are new to science, and both microaerophilic and anaerobic taxa appear to be represented. Compared with nearby aerated sites, the Santa Barbara Basin is a 'symbiosis oasis' offering a new source of organisms for testing symbiosis hypotheses of eukaryogenesis.     

Interactions between marine microorganisms and their phages

Viruses are the most abundant biological entities in marine ecosystems. Most of them are phages that infect bacteria and archaea. Phages play important roles in causing the mortality of prokaryotic cells, structuring microbial communities, mediating horizontal gene transfer between different microbes, influencing the microbial food web process, and promoting biogeochemical cycles (such as C, N, etc.) in the ocean. Here we provided an overview of recent advances in research on the interactions between marine microorganisms and their phages, and suggest future research directions based on our understanding of the literature and our own work.     

Proteorhodopsin in the ubiquitous marine bacterium SAR11

Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 ('Pelagibacter ubique'), the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.     

Unsuspected diversity among marine aerobic anoxygenic phototrophs

Aerobic, anoxygenic, phototrophic bacteria containing bacteriochlorophyll a (Bchla) require oxygen for both growth and Bchla synthesis. Recent reports suggest that these bacteria are widely distributed in marine plankton, and that they may account for up to 5% of surface ocean photosynthetic electron transport and 11% of the total microbial community. Known planktonic anoxygenic phototrophs belong to only a few restricted groups within the Proteobacteria alpha-subclass. Here we report genomic analyses of the photosynthetic gene content and operon organization in naturally occurring marine bacteria. These photosynthetic gene clusters included some that most closely resembled those of Proteobacteria from the beta-subclass, which have never before been observed in marine environments. Furthermore, these photosynthetic genes were broadly distributed in marine plankton, and actively expressed in neritic bacterioplankton assemblages, indicating that the newly identified phototrophs were photosynthetically competent. Our data demonstrate that planktonic bacterial assemblages are not simply composed of one uniform, widespread class of anoxygenic phototrophs, as previously proposed; rather, these assemblages contain multiple, distantly related, photosynthetically active bacterial groups, including some unrelated to known and cultivated types.     

不同生活习性下原核生物基因组大小与GC含量的关系研究

 对原核生物基因组的研究显示,基因组GC含量与基因组大小和氧气偏好性等因素存在着一定的相关性。为了探索基因组大小与GC含量的相关性是否受原核生物生活习性的影响,选取了有代表性的411种原核生物（包括古细菌与真细菌）,分别从最适生长温度、氧气偏好性、运动特性、水生特性和寄生特性等因素进行分析,发现基因组大小与GC含量的相关性确实受这些因素的影响,而寄生原核生物中显示出最好的相关性。     

Effects of diatoms on reproduction and growth of marine copepods

Two hot spots in marine ecology, deleterious effects of diatoms and feeding selectivity of copepods, as well as new progress on these two issues achieved in the recent ten years, are reviewed. These two issues are considered correlated closely. Diatoms and their metabolites can induce deleterious effects on growth, reproduction and development of copepods, including increase of mortality and decrease of egg production, hatching and growth rates. Such negative effects, resulting from either chemical toxin or nutritional deficiency, can be conquered in natural environments by diverse feeding. It is therefore concluded that deleterious effects of diatoms observed in laboratory or during blooming period are only a special case that accommodation of feeding strategy of copepods is disabled. To understand their feeding strategy in natural environments is a prerequisite to explaining the mechanisms of deleterious effects caused by diatoms, and makes it possible to re-evaluate the energy flow in marine ecosystems.     

Light stimulates growth of proteorhodopsin-containing marine Flavobacteria

Proteorhodopsins are bacterial light-dependent proton pumps. Their discovery within genomic material from uncultivated marine bacterioplankton caused considerable excitement because it indicated a potential phototrophic function within these organisms, which had previously been considered strictly chemotrophic. Subsequent studies established that sequences encoding proteorhodopsin are broadly distributed throughout the world's oceans. Nevertheless, the role of proteorhodopsins in native marine bacteria is still unknown. Here we show, from an analysis of the complete genomes of three marine Flavobacteria, that cultivated bacteria in the phylum Bacteroidetes, one of the principal components of marine bacterioplankton, contain proteorhodopsin. Moreover, growth experiments in both natural and artificial seawater (low in labile organic matter, which is typical of the world's oceans) establish that exposure to light results in a marked increase in the cell yield of one such bacterium (Dokdonia sp. strain MED134) when compared with cells grown in darkness. Thus, our results show that the phototrophy conferred by proteorhodopsin can provide critical amounts of energy, not only for respiration and maintenance but also for active growth of marine bacterioplankton in their natural environment.     

Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.     

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.     

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.     

Bacterial carbon processing by generalist species in the coastal ocean

The assimilation and mineralization of dissolved organic carbon (DOC) by marine bacterioplankton is a major process in the ocean carbon cycle. However, little information exists on the specific metabolic functions of participating bacteria and on whether individual taxa specialize on particular components of the marine DOC pool. Here we use experimental metagenomics to show that coastal communities are populated by taxa capable of metabolizing a wide variety of organic carbon compounds. Genomic DNA captured from bacterial community subsets metabolizing a single model component of the DOC pool (either dimethylsulphoniopropionate or vanillate) showed substantial overlap in gene composition as well as a diversity of carbon-processing capabilities beyond the selected phenotypes. Our direct measure of niche breadth for bacterial functional assemblages indicates that, in accordance with ecological theory, heterogeneity in the composition and supply of organic carbon to coastal oceans may favour generalist bacteria. In the important interplay between microbial community structure and biogeochemical cycling, coastal heterotrophic communities may be controlled less by transient changes in the carbon reservoir that they process and more by factors such as trophic interactions and physical conditions.     

Genomic perspectives in microbial oceanography

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.     

大庆油田聚驱后油藏细菌群落演替规律研究

应用分子生态学方法,研究了大庆油田聚驱后油藏微生物调剖过程中细菌群落结构变化规律。从大庆油田聚驱油藏样品中提取总DNA,扩增其16S rDNA片段,PCR-DGGE实验,通过切胶测序分析研究了细菌群落结构演替规律。微生物调剖试验结果显示,日产液下降3吨,日产油量提高11吨,含水量下降4吨。PCR-DGGE结果显示,北-2-4-P49主要的优势种群为假单胞菌属(Pseudomonas sp.)、不动杆菌属(Acinetobacter sp.)、梭菌属(Clostridia bacterium)、热微菌属(Thermomicrobium sp.)、厚壁菌属(Firmicutes bacterium)和一些未知菌属。细菌多样性丰富,群落结构变化较大。对微生物调剖前后细菌群落结构的研究可以为微生物采油过程提供技术指导和实际参考。     

Advances in the study of helminth mitochondrial genomes and their associated applications

Helminths, including flatworms and roundworms, are abundant organisms that have a variety of life histories. Of these, the genera Schistosoma, Echinococcus, Trichinella are notable parasites of veterinary and medical importance, and cause substantial socio- economic losses throughout China and the rest of the world. Genetic markers in the mitochondrial (mt) genome have proven use- ful for systematic, ecological, evolutionary and population studies, and the growth of mt genomic research has increased in the last two decades. Technological improvements, such as the long-polymerase chain reaction method and high-throughput se- quencing have allowed minute amounts of DNA from single worms, biopsy samples or microscopic organisms to be used for whole mt genome characterization. To facilitate the retrieval, annotation and analyses of mitochondrial features, multiple data- bases and specific software have also been designed and established. This review focuses on current progress, applications and perspectives regarding helminth mt genomics. To date, the complete mt genomes for 93 species of helminths have been sequenced and analyzed. Analyses of the mt genes, including gene content, arrangement, composition and variation have revealed unique features among the helminths when compared with other metazoans. This provides important data concerning their functional and comparative mitochondrial genomics, molecular taxonomy and characterization, population genetics and systematics, and evolu- tionary history. Moreover, mt genome data for parasitic helminths are important for diagnosis, epidemiology and ecology of in- fections. Mitochondrial genome data offer a rich source of markers for the systematics and population genetics of socioeconomi- cally important parasitic helminths of humans and other animals.     

Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity

Picoplankton--cells with a diameter of less than 3 microm--are the dominant contributors to both primary production and biomass in open oceanic regions. However, compared with the prokaryotes, the eukaryotic component of picoplankton is still poorly known. Recent discoveries of new eukaryotic algal taxa based on picoplankton cultures suggest the existence of many undiscovered taxa. Conventional approaches based on phenotypic criteria have limitations in depicting picoplankton composition due to their tiny size and lack of distinctive taxonomic characters. Here we analyse, using an approach that has been very successful for prokaryotes but has so far seldom been applied to eukaryotes, 35 full sequences of the small-subunit (18S) ribosomal RNA gene derived from a picoplanktonic assemblage collected at a depth of 75 m in the equatorial Pacific Ocean, and show that there is a high diversity of picoeukaryotes. Most of the sequences were previously unknown but could still be assigned to important marine phyla including prasinophytes, haptophytes, dinoflagellates, stramenopiles, choanoflagellates and acantharians. We also found a novel lineage, closely related to dinoflagellates and not previously described.     

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.     

响叶杨（杨属）叶绿体基因组测序与比较分析

本研究中,我们对响叶杨的叶绿体基因组进行测序和组装,并将其与杨属其他11个叶绿体基因组进行比较分析.结果表明,响叶杨叶绿体基因组全长158,591bp,其中两个反向重复序列区(IR)长度均为27,667bp,长单拷贝序列区(LSC)和短单拷贝序列区(SSC)长度分别为84,634和18,623bp.通过对杨属12个物种的叶绿体基因组进行比较,只发现了6个相对较大的插入缺失,因此整体而言,杨属的叶绿体基因组结构是高度保守的.系统发育分析结果显示,杨属中12个物种组成了3个具有高支持率的进化支,响叶杨与其他白杨组物种聚为一支,并且与银白杨的亲缘关系最近.本研究基于叶绿体基因组数据揭示了杨属的进化历史,将有助于进一步开展杨属植物基于叶绿体DNA序列数据的群体遗传学及其他分子生态学研究.     

Aerobic anoxygenic phototrophic bacteria and their roles in marine ecosystems

Aerobic anoxygenic phototrophic bacteria(AAPB) are characterized by the following physiological and ecological features. A mother AAPB cell can unusually divide into 3 daughter cells and looks like a “Y” during the division. AAPB cells sometimes adhere together forming a free-floating population. Most of the known AAPB species are obligately aerobic. Bacteriochlorophyll a (BChl a) is the only photosynthetic pigment in AAPB, and the number of BChl a molecules in an AAPB cell is much less than that in an anaerobic phototrophic bacterial cell, while the accessorial pigments carotenoids in AAPB are abundant in concentration and diverse in species. In addition to the common magnesium containing BChl a, a zinc-containing BChla was also seen in AAPB. AAPB have light harvesting complex I but usually lack light harvesting complex II. Although AAPB featur in photosynthesis, their growth is not necessarily lightdependent. There is a mechanism controlling the photosynthesis approach. AAPB are widely distributed in marine environments especially in oligotrophic oceans accounting for a substantial portion of the total biomass and playing a unique role in the cycle of carbon and other biogenic elements. Besides the contribution to primary production, AAPB also have great potentials in bioremediation of polluted environments. Studies on AAPB would be of great value in understanding the evolution of photosynthesis and the structure and function of marine ecosystems.     

First insights into the biodiversity and biogeography of the Southern Ocean deep sea

Shallow marine benthic communities around Antarctica show high levels of endemism, gigantism, slow growth, longevity and late maturity, as well as adaptive radiations that have generated considerable biodiversity in some taxa. The deeper parts of the Southern Ocean exhibit some unique environmental features, including a very deep continental shelf and a weakly stratified water column, and are the source for much of the deep water in the world ocean. These features suggest that deep-sea faunas around the Antarctic may be related both to adjacent shelf communities and to those in other oceans. Unlike shallow-water Antarctic benthic communities, however, little is known about life in this vast deep-sea region. Here, we report new data from recent sampling expeditions in the deep Weddell Sea and adjacent areas (748-6,348 m water depth) that reveal high levels of new biodiversity; for example, 674 isopods species, of which 585 were new to science. Bathymetric and biogeographic trends varied between taxa. In groups such as the isopods and polychaetes, slope assemblages included species that have invaded from the shelf. In other taxa, the shelf and slope assemblages were more distinct. Abyssal faunas tended to have stronger links to other oceans, particularly the Atlantic, but mainly in taxa with good dispersal capabilities, such as the Foraminifera. The isopods, ostracods and nematodes, which are poor dispersers, include many species currently known only from the Southern Ocean. Our findings challenge suggestions that deep-sea diversity is depressed in the Southern Ocean and provide a basis for exploring the evolutionary significance of the varied biogeographic patterns observed in this remote environment.     

SAR11 marine bacteria require exogenous reduced sulphur for growth

Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms. An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate, our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.