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。     

冰尘结构特征及形成分析——以乌鲁木齐河源1号冰川为例

利用2007-2010年夏季在乌鲁木齐河源1号冰川采集的5个冰样, 对冰样中冰尘的特征、冰尘中蓝藻的种类及冰尘中无机矿物颗粒的粒度特征进行了分析研究. 研究表明: 冰尘为棕色球状聚合体, 粒径为0.27~3.5 mm, 分布在冰川消融区表面, 其组成成分为有机质、无机矿物颗粒和微生物. 冰尘有4种主要的内部结构: 类型Ⅰ, 具有同心层结构的冰尘;类型Ⅱ, 带有亚颗粒的冰尘;类型Ⅲ, 内部无明显结构的冰尘;类型Ⅳ, 中心位置处具有较大无机颗粒的冰尘. 冰尘中无机矿物颗粒的数量主要分布在d<3.5 μm的范围内, 且体积分布的粒径众数介于3~25 μm之间. 同时, 对冰尘中的蓝藻进行了16S rRNA基因序列的系统发育分析, 共从蓝藻16S rRNA基因文库中筛选了247个阳性克隆, RFLP分型得到10个不同的OTUs. BLAST比对, 系统发育分析将这10个OTUs归为颤藻目(Oscillatoriales)、色球藻目(Chroococcales)、未定种(Unclassified). 颤藻目为绝对优势类群, 占整个基因克隆文库的91%. 经估算, 冰尘中存在大量的有机物质和微生物, 无机矿物颗粒只占了很小的比例, 表明影响冰川消融区表面反照率的主要因素为冰尘中的有机部分, 包括有机物质和微生物.     

Morphometric relationships of penaeid shrimps in a coastal lagoon: Spatio-temporal variability and management implications

Spatio-temporal variability in the length-weight relationship of four sympatric shrimp species (Farfantepeneus aztecus, F. brasiliensis, F. duorarum, andF. notialis) was evaluated in the Celestun lagoon, Mexico. Monthly samples were taken throughout 2 yr in three hydrological zones (seaward, middle, and inner) and climatic seasons (Nortes, Dry, and Rainy). Significant intraspecific and interspecific differences in the length-weight relationships were detected among climatic seasons and hydrological zones, reflecting positive allometric growth.F. notialis registered the highest condition (weight at length), followed byF. duorarum, F. aztecus, andF. brasiliensis. The lowest values in condition were consistently registered during Nortes and at the seaward zone. All species showed a pattern consistent with a density-dependent effect on condition, that is a negative correlation between individual mean weight and total relative abundance. The immediate implication for managing this important multispecific coastal artisanal resource that is supported by our study is the restriction of fishing effort in the seaward zone, mainly during the Nortes seasons.     

Dietary Analysis of Marine Fish Species: Enhancing the Detection of Prey-Specific DNA Sequences via High-Throughput Sequencing Using Blocking Primers

Dietary studies of fish can enhance our understanding of predator-prey interactions and provide important insights into complex marine food webs. In this study, we performed dietary analyses of three commercially important fish species in South China: Acanthopagrus latus, Pampus argenteus, and Scomberomorus commerson. Two distinct fragments of the mitochondrial cytochrome c oxidase I (mtCOI) gene, a small (130 bp) and large (300 bp) amplicon, were amplified from the DNA extracted from the gut contents in the presence of blocking primers designed to inhibit the amplification of predator-specific DNA. The amplicons from each predator species were tagged with a unique indexing bar code and sequenced using the Illumina MiSeq platform. Our results showed that the three fish species consumed a wide variety of prey, including jellyfish, copepods, crustaceans, and fish. Seasonal variations in prey composition and species-selective predation were observed. Our approach of combining next-generation sequencing with blocking primers greatly enhanced the speed and resolution of the dietary analyses in marine fishes and could provide novel insights into marine ecosystems.     

Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence

Evolutionary trees are derived based on nucleic acid and protein sequences and the methods of numerical taxonomy. From 5S ribosomal RNA sequences, molecules that participate in protein synthesis, the order of branching of many prokaryote species and the nuclear and organellar components of eukaryote species are inferred. All oxygen-evolving forms, including the chloroplasts and blue-green algae, are to be found on a single branch; the mitochondria are found with the Rhodospirillaceae, nonsulfur photosynthetic bacteria; and the eukaryote cytoplasmic components are found with the archae-bacteria, including Thermoplasma and Sulfolobus. This tree clearly supports the symbiotic origin of the eukaryote organelles. There is much redundant information available from c-type cytochromes, cytochromes c′, 4Fe-4S ferredoxins and 5.8S rRNA molecules. A gene duplication of ferredoxin, probably predating all of the species divergences, permitted us to infer an ancestral molecule that can be placed on the tree to give the base. The heterotrophic anaerobes have a sequence most resembling the ancestral sequence, suggesting that the ancestor may have been a heterotroph. Ten prokaryote species occur on both the c-type and the c′-type cytochrome trees. There is only one inconsistency in the topologies of the two trees, which may reflect a gene transfer among prokaryotes confirming that, for these genes of fundamental importance, gene transfer followed by acceptance is rare. The eukaryote trees derived from 5S and 5.8S rRNA suggest that the earliest eukaryotes were unicellular and that the multicellular forms of plants, animals, fungi and slime molds arose independently.     

The Late Pleistocene megafauna of the Chulym River basin,southeastern West Siberian Plain: chronology and stable isotope composition

New data were obtained for the Chulym River basin in the southeastern part of the West Siberian Plain, one of the understudied parts of Siberia in terms of age and composition of carbon and nitrogen stable isotopes for Late Pleistocene megafauna. The ¹⁴C dates from the Sergeevo outcrop, the most complete section of Late Quaternary deposits in the region, are mostly greater than ~30 550 bp. Other localities yielded ¹⁴C values in the range from >44 500 to ~19 300 bp. The finite date of ~42 270 bp for the Khozarian steppe elephant (Mammuthus trogontherii chosaricus) from Asino is intriguing because previously it was not detected in the Late Pleistocene of Siberia after the last interglacial (Marine Isotope Stage 5e), ~115 000–130 000 years ago. Stable isotope data show both similarities and differences compared to the pre-Last Glacial Maximum megafaunal species in other parts of Siberia.     

Antibiotic resistance and genetic diversity in water-borne Enterobacteriaceae isolates from recreational and drinking water sources

A total of 240 water-borne bacteria including 72 Escherichia coli, 83 Enterobacter, 30 Klebsiella, 36 Salmonella and 19 Shigella spp. isolates from drinking and recreational water sources were assessed for antibiotic resistance and genetic diversity. Escherichia coli (88.89 %) and species of Enterobacter (86.75 %), Klebsiella (83.33 %) and Salmonella (100 %) were resistant to cefadroxil, while >94 % Shigella spp. were resistant to cefaclor and cefuroxime. Ofloxacin was the most effective antibiotic against isolates of all the genera. Multiple antibiotic resistance index identified dug well, pond and piped water supplies as high risk sources of enteric pathogens. Random amplified polymorphic DNA analysis and restriction fragment length polymorphism of amplified 16S rRNA gene were studied for genetic relatedness of Enterobacteriaceae isolates. Primer P1254 identified 10, 16, 4, 4 and 1 distinct random amplified polymorphic DNA group(s) of E. coli, Enterobacter, Klebsiella, Salmonella and Shigella species, respectively. Unlike random amplified polymorphic DNA, restriction fragment length polymorphism using AluI and HaeIII could not segregate isolates in different genetic profiles. 16S rRNA gene of three Enterobacter spp. strains from different sources with similar restriction fragment length polymorphism but different random amplified polymorphic DNA patterns was sequenced, and identified as Enterobacter hormaechei strains skg0061, 0062 and 0063. The sequence information has been submitted to GenBank (HQ322393-95). Biochemically similar but genetically diverse Enterobacteriaceae members from drinking and recreational water sources exhibited varying antibiotic sensitivity. Contamination of water sources with such multiple antibiotic-resistant enteric pathogens poses threat to human health.     

Intraspecific Variation in Growth of Marsh Macrophytes in Response to Salinity and Soil Type: Implications for Wetland Restoration

Genetic diversity within plant populations can influence plant community structure along environmental gradients. In wetland habitats, salinity and soil type are factors that can vary along gradients and therefore affect plant growth. To test for intraspecific growth variation in response to these factors, a greenhouse study was conducted using common plants that occur in northern Gulf of Mexico brackish and salt marshes. Individual plants of Distichlis spicata, Phragmites australis, Schoenoplectus californicus, and Schoenoplectus robustus were collected from several locations along the coast in Louisiana, USA. Plant identity, based on collection location, was used as a measure of intraspecific variability. Prepared soil mixtures were organic, silt, or clay, and salinity treatments were 0 or 18 psu. Significant intraspecific variation in stem number, total stem height, or biomass was found in all species. Within species, response to soil type varied, but increased salinity significantly decreased growth in all individuals. Findings indicate that inclusion of multiple genets within species is an important consideration for marsh restoration projects that include vegetation plantings. This strategy will facilitate establishment of plant communities that have the flexibility to adapt to changing environmental conditions and, therefore, are capable of persisting over time.     

Anaerobic Metabolism in Tidal Freshwater Wetlands: II. Effects of Plant Removal on Archaeal Microbial Communities

The interaction of plant and microbial communities are known to influence the dynamics of methane emission in wetlands. Plant manipulations were conducted in an organic rich (JB-organic) and a mineral rich (JB-mineral) site in a tidal freshwater wetland to determine if plant removal impacted archaeal populations. In concert, a suite of process-based measurements also determined the effects of plant removal on rates of methanogenesis and Fe-reduction. The microbial populations were analyzed with clone libraries of the SSU ribosomal RNA (rRNA) gene from selected plots, and terminal restriction length polymorphism (tRFLP) of the SSU rRNA and the methyl-coenzyme M reductase (mcrA) gene. Overall, methanogenesis dominated anaerobic carbon mineralization at both sites during the most active growing season. A total of 114 SSU rRNA clones from four different plots revealed a diversity of Euryarchaeota including representatives of the Methanomicrobiales, Methanosarcinales and Thermoplasmatales. The clone libraries were dominated by the Thaumarchaeota, accounting for 65 % of clones, although their diversity was low. A total of 112 tRFLP profiles were generated from 56 samples from 25 subplots; the patterns for both SSU rRNA and mcrA showed little variation between sites, either with plant treatment or with the growing season. Overall these results suggest that wetland soil archaeal populations were resilient to changes in the associated surface plant communities. The work also revealed the presence of novel, mesophilic Thaumarchaeota of unknown metabolic function.     

Acid mine drainage biogeochemistry at Iron Mountain,California

The Richmond Mine at Iron Mountain, Shasta County, California, USA provides an excellent opportunity to study the chemical and biological controls on acid mine drainage (AMD) generation in situ, and to identify key factors controlling solution chemistry. Here we integrate four years of field-based geochemical data with 16S rRNA gene clone libraries and rRNA probe-based studies of microbial population structure, cultivation-based metabolic experiments, arsenopyrite surface colonization experiments, and results of intermediate sulfur species kinetics experiments to describe the Richmond Mine AMD system. Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation of approximately 1 × 10⁵ to 2 × 10⁵ moles pyrite/day contains up to 24 g/1 Fe, several g/1 Zn and hundreds of mg/l Cu. Geochemical conditions change markedly over time, and are reflected in changes in microbial populations. Molecular analyses of 232 small subunit ribosomal RNA (16S rRNA) gene sequences from six sites during a sampling time when lower temperature (<32°C), higher pH (>0.8) conditions predominated show the dominance of Fe-oxidizing prokaryotes such as Ferroplasma and Leptospirillum in the primary drainage communities. Leptospirillum group III accounts for the majority of Leptospirillum sequences, which we attribute to anomalous physical and geochemical regimes at that time. A couple of sites peripheral to the main drainage, "Red Pool" and a pyrite "Slump," were even higher in pH (>1) and the community compositions reflected this change in geochemical conditions. Several novel lineages were identified within the archaeal Thermoplasmatales order associated with the pyrite slump, and the Red Pool (pH 1.4) contained the only population of Acidithiobacillus. Relatively small populations of Sulfobacillus spp. and Acidithiobacillus caldus may metabolize elemental sulfur as an intermediate species in the oxidation of pyritic sulfide to sulfate. Experiments show that elemental sulfur which forms on pyrite surfaces is resistant to most oxidants; its solublization by unattached cells may indicate involvement of a microbially derived electron shuttle. The detachment of thiosulfate (S₂O₃^2-) as a leaving group in pyrite oxidation should result in the formation and persistence of tetrathionate in low pH ferric iron-rich AMD solutions. However, tetrathionate is not observed. Although a S₂O₃^2--like species may form as a surface-bound intermediate, data suggest that Fe³⁺ oxidizes the majority of sulfur to sulfate on the surface of pyrite. This may explain why microorganisms that can utilize intermediate sulfur species are scarce compared to Fe-oxidizing taxa at the Richmond Mine site.

     

Comparative Phylogeography of North American Atlantic Salt Marsh Communities

Identifying differential population structure within metacommunities is key toward describing the mechanisms that maintain biodiversity in natural systems. At both local and regional scales on the North American Atlantic coast, we assessed phylogeographic and genetic diversity patterns of six common salt marsh invertebrates using equivalent sampling schemes and sequence data from the same mitochondrial locus. In general, our results suggest little genetic structure across four previously sampled biogeographic regions and a slight increase in genetic diversity from northern to southern areas; however, two of the species (Geukensia demissa and Uca pugilator) exhibited significant differentiation between the northernmost populations and other regions, consistent with a number of previous studies. Although the minimal genetic structure recovered in this community is consistent with expectations based on the larval life history of the species examined, confirmation of this result suggests that latitudinal shifts in ecological interactions in salt marsh systems are environmentally driven, rather than due to heritable adaptation.     

Short sequence effect of ancient DNA on mammoth phylogenetic analyses

The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.     

Morphological,demographic and genetic traces of Upper Palaeolithic human impact on limpet assemblages in North Iberia

Human activities have an impact on extant biotic communities, and may have had just as important an impact in the past. We assess human impact on limpet assemblages during the Upper Palaeolithic in Asturias (north‐west Spain). The intensely exploited genus Patella exhibited a marked size decrease and a change in species assemblage composition, substituting the larger species P. vulgata for the smaller P. depressa. The present Patella assemblages in the upper tidal level exhibit the same pattern as those of the Epipalaeolithic (approx. 12 000 to 6000 years before the present). Although climate change may have contributed to such species replacement, spatial differences between close areas with different densities of Palaeolithic human settlements indicate unequivocal human impact. Present Patella species sampled from the region exhibit genetic signatures of past bottlenecks in mitochondrial DNA, which also indicate recent demographic expansion, suggesting that old impacts have been sufficiently important to leave genetic traces in current populations. Copyright © 2011 John Wiley & Sons, Ltd.     

Genetic Variation in the Common Reed, <Emphasis Type="Italic">Phragmites australis</Emphasis>, in the Mississippi River Delta Marshes: Evidence for Multiple Introductions

Multiple introductions are believed to play an important role in increasing genetic diversity and adaptability of invasive species, but there are few well-documented examples. The common reed, Phragmites australis, has dramatically increased in tidal wetlands throughout the USA in the past century due primarily to the introduction of a Eurasian lineage. In the Mississippi River “Balize” delta, P. australis is the dominant vegetation where monotypic stands of an introduced form blanket the outer marshes. The delta’s interior marshes, on the other hand, are more vegetatively diverse, serving as important waterfowl foraging habitat. Recent encroachment by various phenotypic forms of P. australis into the interior marshes led to this study examining genetic variation in these stands. Our results revealed four chloroplast DNA haplotypes that also segregate based on microsatellite variation. Three of these are closely related and introduced, but differ relative to time and likely mode of introduction. The “Delta” type (haplotype M1), which is unique to the region and the most common lineage, displays considerable microsatellite diversity. The Eurasian introduced lineage of P. australis (haplotype M), which is invasive elsewhere in North America, is increasing its distribution in the delta. A novel haplotype, AD, was also identified which is phenotypically and genetically similar to haplotype M. Despite the close relatedness, we found no evidence for inter-haplotype gene exchange at the nuclear level, suggesting that intraspecific hybridization is not a contributing factor to these invasions. The site provides a unique opportunity for researchers to understand the dynamics of multiple P. australis invasions.     

基于线粒体COI基因序列探讨鸭嘴舌形贝地理分布

从河北秦皇岛采集的用无水乙醇保存的鸭嘴舌形贝(Lingula anatina)样品中提取了DNA,经PCR扩增后进行克隆,得到了2条长度为682 bp的线粒体细胞色素C氧化酶第I亚基(COI)基因片段。调用GenBank中日本有明海和中国香港的鸭嘴舌形贝同源序列,用邻接法和贝叶斯法构建了系统发育树,结果表明:秦皇岛地区的鸭嘴舌形贝与日本有明海的鸭嘴舌形贝形成姊妹群,具有较近的亲缘关系,与香港的鸭嘴舌形贝亲缘关系较远。初步分析认为西太平洋地区鸭嘴舌形贝现有的地理分布并不是由浮游幼虫的扩散引起的,不同地区鸭嘴舌形贝的差异可能跟地理隔离有关。     

Theoretical and natural strain patterns in ductile simple shear zones

A simple empirical model representing the variation of shear strain throughout a simple shear zone allows us to determine the evolution of finite strain as well as the progressive shape changes of passive markers. Theoretical strain patterns (intensity and orientation of finite strain trajectories, deformed shapes of initially planar, equidimensional and non-equidimensional passive markers) compare remarkably well with patterns observed in natural and experimental zones of ductile simple shear (intensity and orientation of schistosity, shape changes of markers, foliation developed by deformation of markers).The deformed shapes of initially equidimensional and non-equidimensional passive markers is controlled by a coefficient P, the product of

1. (1) the ratio between marker size and shear zone thickness

2. (2) the shear gradient across the zone.

For small values of P (approximately P < 2), the original markers change nearly into ellipses, while large values of P lead to “ retort” shaped markers.This theoretical study also allows us to predict, throughout a simple shear zone, various relationships between the principal finite strain trajectory, planar passive markers and foliations developed by deformation of initially equidimensional passive markers.     

Delaware Bay and Chesapeake Bay populations of the horseshoe crabLimulus polyphemus are genetically distinct

The Delaware Bay contains the world’s largest population of horseshoe crabs, which constitute an ecologically significant component of this estuarine ecosystem. The North Atlantic speciesLimulus polyphemus has an extensive geographical distribution, ranging from New England to the Gulf of Mexico. Recent assessments of the Delaware Bay population based on beach spawning and trawling data have suggested a considerable decrease in the number of adult animals since 1990. Considerable debate has centered on the accuracy of these estimates and their impact on marine fisheries management planning. Compounding this problem is the lack of information concerning the genetic structure of Atlantic horseshoe crab populations. This study assessed patterns of genetic variation within and between the horseshoe crab populations of Delaware Bay and Chesapeake Bay, using both Random Amplification of Polymorphic DNA (RAPD) and DNA sequence analysis of the mitochondrial cytochrome oxidase I gene (COI). We examined 41 animals from Delaware Bay and 14 animals from the eastern shore of Chesapeake Bay. To provide high quality, uncontaminated genomic DNA for RAPD analysis, DNA was isolated from hemocytes by direct cardiac puncture, purified by spin column chromatography, and quantified by agarose gel electrophoresis. RAPD fingerprints revealed a relative paucity of polymorphic fragments, with generally homogeneous banding patterns both within and between populations. DNA sequence analysis of 515 bases of the 5′ portion of the mitochondrial COI gene showed haplotype diversity in the Chesapeake Bay sample to be significantly higher than in the Delaware Bay sample, despite the larger size of the latter. Haplotype analysis indicates minimal contemporary gene flow between Delaware Bay and Chesapeake Bay crab populations, and further suggests that the Delaware Bay population is recovering from a recent population decline.     

A revised evolutionary history of armadillos (Dasypus) in North America based on ancient mitochondrial DNA

The large, beautiful armadillo, Dasypus bellus, first appeared in North America about 2.5 million years ago, and was extinct across its southeastern US range by 11 thousand years ago (ka). Within the last 150 years, the much smaller nine‐banded armadillo, D. novemcinctus, has expanded rapidly out of Mexico and colonized much of the former range of the beautiful armadillo. The high degree of morphological similarity between these two species has led to speculation that they might be a single, highly adaptable species with phenotypical responses and geographical range fluctuations resulting from environmental changes. If this is correct, then the biology and tolerance limits for D. novemcinctus could be directly applied to the Pleistocene species, D. bellus. To investigate this, we isolated ancient mitochondrial DNA from late Pleistocene‐age specimens of Dasypus from Missouri and Florida. We identified two genetically distinct mitochondrial lineages, which most likely correspond to D. bellus (Missouri) and D. novemcinctus (Florida). Surprisingly, both lineages were isolated from large specimens that were identified previously as D. bellus. Our results suggest that D. novemcinctus, which is currently classified as an invasive species, was already present in central Florida around 10 ka, significantly earlier than previously believed.     

贵州喀斯特地区碳酸盐岩表生古菌群落结构及多样性研究——以南江大峡谷为例

为了研究贵州喀斯特地区碳酸盐岩表生古菌群落结构的多样性,应用16S rDNA文库技术,对采集于贵州南江大峡谷的白云岩和石灰岩样品进行基因文库的构建和限制性片段长度多态性(RFLP)分析。用限制性核酸内切酶MspⅠ对两个文库中分别随机挑选的300个阳性克隆子进行酶切分型,白云岩和石灰岩16S rDNA基因文库各得到14和13个基因型,其覆盖率分别为95.4%和91.3%,香农指数分别为2.14和1.93。系统发育分析表明白云岩和石灰岩表生古菌克隆子全部归属于泉古菌门（Crenarchaeota）,代表性克隆与GenBank数据库已有16S rRNA序列的相似性为96%～100%,且最高相似性序列均来源于土壤及岩石环境的未可培养古菌序列。