http://www.sciencedirect.com/science/article/pii/S1674987111001319

The microbial diversity in Wuli Area,Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses.A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold springs.The bacterial clones could be classified into Pwteobacteria,Acidobacteria, Deinococci,Sphingobacteria,Flavobacteria.Nitrospirae,Actinobacteria,Gemmatimonadetes, and unclassified-bacteria;and the archaeal clones could be classified into Crenarchaeota and Thaumarchaeota.Among the major groups,Pwteobacteria and Crenarchaeota were dominant in the bacterial and archaeal 16S rRNA gene clone libraries,respectively.The clone sequences obtained in Wuli cold springs were closely related to those from cold habitats,such as snow/ice/soils on high mountains or at high latitude.Especially,the microbial community composition of Wuli Area was more similar to that in Tibetan glaciers than cold environments of other locations.The data presented in this study have implications for a better understanding of microbial diversity in cold springs on the Qinghai-Tibetan Plateau.     

Anaerobic Metabolism in Tidal Freshwater Wetlands: I. Plant Removal Effects on Iron Reduction and Methanogenesis

For energetic reasons, iron reduction suppresses methanogenesis in tidal freshwater wetlands; however, when iron reduction is limited by iron oxide availability, methanogenesis dominates anaerobic carbon mineralization. Plants can mediate this microbial competition by releasing oxygen into the rhizosphere and supplying oxidized iron for iron reducers. We utilized a plant removal experiment in two wetland sites to test the hypothesis that, in the absence of plants, rates of iron reduction would be diminished, allowing methanogenesis to dominate anaerobic metabolism. In both sites, methanogenesis was the primary anaerobic mineralization pathway, with iron reduction dominating only early and late in the growing season in the site with a less organic soil. These patterns were not influenced by the presence of plants, demonstrating that plants were not a key control of microbial metabolism. Instead, we suggest that site conditions, including soil chemistry, and temperature are important controls of the pathways of anaerobic metabolism.     

Increased Variability of Microbial Communities in Restored Salt Marshes nearly 30?Years After Tidal Flow Restoration

We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40?C50?years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season. Community composition and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) and sequence analysis of 16S ribosomal RNA (rRNA) genes. Our results indicated diverse communities, with sequences representing 14 different bacterial divisions. Proteobacteria, Bacteroidetes, and Planctomycetes dominated clone libraries from both restored and unimpounded sites. Multivariate analysis of the TRFLP data suggest significant site, sample date, and restoration status effects, but the exact causes of these effects are not clear. Composition of clone libraries and abundance of bacterial 16S rRNA genes were not significantly different between restored sites and unimpounded sites, but restored sites showed greater temporal and spatial variability of bacterial communities based on TRFLP profiles compared with unimpounded sites, and variability was greatest at sites more recently restored. In summary, our study suggests there may be long-lasting effects on stability of bacterial communities in restored salt marshes and raises questions about the resilience and ultimate recovery of the communities after chronic disturbance.     

Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan

Assessing the impacts of methane released from hydrate-bearing environments on global carbon cycling would require detailed insights into the distributions and capacities of microbial communities at different horizons of sediment column. In this study, we conducted geochemical, gene abundance and diversity analyses for a sediment core retrieved from a potential hydrate-bearing region off southwestern Taiwan. Geochemical profiles were characterized by a sulfate-to-methane transition with decreasing total organic carbon and nitrogen in sediments, and increasing dissolved inorganic carbon, ammonium and total sulfur in sediments. Bacterial and archaeal 16S rRNA and amoA gene abundances decreased with depth. In contrast, ANME-1 and -2 16S rRNA gene abundances increased significantly across the sulfate-to-methane transition and peaked at different horizons below this interface. A total of 124,379 bacterial and 130,351 archaeal reads were recovered through tag-pyrosequencing of 16S rRNA genes and categorized into 9014 bacterial and 6394 archaeal operational taxonomic units on the basis of 97% sequence similarity, respectively. Major bacterial phyla/divisions and archaeal groups (>5% of the total reads) detected included Chloroflexi, Planctomycetes, OP9, Deltaproteobacteria, BHI80-139, MBG-B, Halobacteria, MCG, Thermoplasmata, ANME-1 and MG-I. The abundance variations of most major OTUs (>0.5% of the total reads) were statistically correlated with those of geochemical parameters. These lines of evidence suggest that the populations represented by the major OTUs or detected by group-specific primers were compartmentalized into different horizons and involved directly or indirectly in the cycling of methane, sulfate, organic carbon and nitrogen. Overall, this study demonstrates that the deep sequencing coverage combined with the quantification of gene abundance and geochemical characterization would enable to uncover the detailed distributions and potential metabolic capabilities of specific groups from complexly structured microbial communities in methane-rich marine sediments.     

Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico

At the Chapopote Knoll in the Southern Gulf of Mexico, deposits of asphalt provide the substrate for a prolific cold seep ecosystem extensively colonized by chemosynthetic communities. This study investigates microbial life and associated biological processes within the asphalts and surrounding oil-impregnated sediments by analysis of intact polar membrane lipids (IPLs), petroleum hydrocarbons and stable carbon isotopic compositions (δ¹³C) of hydrocarbon gases. Asphalt samples are lightly to heavily biodegraded suggesting that petroleum-derived hydrocarbons serve as substrates for the chemosynthetic communities. Accordingly, detection of bacterial diester and diether phospholipids in asphalt samples containing finely dispersed gas hydrate suggests the presence of hydrocarbon-degrading bacteria. Biological methanogenesis contributes a substantial fraction to the methane captured as hydrate in the shallow asphalt deposits evidenced by significant depletion in ¹³C relative to background thermogenic methane. In sediments, petroleum migrating from the subsurface stimulates both methanogenesis and methanotrophy at a sulfate-methane transition zone 6-7 m below the seafloor. In this zone, microbial IPLs are dominated by archaeal phosphohydroxyarchaeols and archaeal diglycosidic diethers and tetraethers. Bacterial IPLs dominate surface sediments that are impregnated by severely biodegraded oil. In the sulfate-reduction zone, diagnostic IPLs indicate that sulfate-reducing bacteria (SRB) play an important role in petroleum degradation. A diverse mixture of phosphohydroxyarchaeols and mixed phospho- and diglycosidic archaeal tetraethers in shallow oil-impregnated sediments point to the presence of anaerobic methane-oxidizing ANME-2 and ANME-1 archaea, respectively, or methanogens. Archaeal IPLs increase in relative abundance with increasing sediment depth and decreasing sulfate concentrations, accompanied by a shift of archaeol-based to tetraether-based archaeal IPLs. The latter shift is suggested to be indicative of a community shift from ANME-2 and/or methanogenic archaea in shallower sediments to ANME-1/methanogenic archaea and possibly benthic archaea in deeper sediments.     

http://www.sciencedirect.com/science/article/pii/S1674987114000668

Microbial diversity in the hydrate-containing (sites SH3B and SH7B) and-free (sites SH1B, SH5B, SH5C) sediments collected from the Shenhu area of the South China Sea (SCS) was investigated using 16S rR...     

西太平洋暖池核心区Ontong Java 海台古菌多样性研究

为了研究西太平洋暖池核心区表层古菌群落结构及多样性,应用16S rDNA文库技术对KX08-973-22站位(取名为CWP)水体样构建基因文库,得到了561个克隆,经分析处理后得到50个OUT(Operational Taxonimic Units).通过对16S rRNA基因序列的同源性比较,构建系统发育树分析及统计...     

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。      

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.     

冀中地热区深部热水微生物群落组成及其功能预测

了解深部微生物群落组成和功能对探索早期生命起源和利用其独特功能均有重要意义.地热区深部碳酸盐岩岩溶-裂隙热储环境中微生物群落组成和功能特性仍然不清.为了探测冀中地热区深部热水微生物群落组成与功能特性,以浅层水和土壤为参照,利用冀中地热区地热科学钻探孔抽水试验,采集深部热水样,同时采集每个钻孔上方附近的大田农灌井浅层水和...     

Structural diversity and fate of intact polar lipids in marine sediments

Marine sediments harbor an enormous quantity of microorganisms, including a multitude of novel species. The habitable zone of the marine sediment column begins at the sediment-water interface and probably extends to depths of several thousands of meters. Studies of the microbial diversity in this ecosystem have mostly relied on molecular biological techniques. We used a complementary method - analysis of intact polar membrane lipids - to characterize the in-situ microbial community in sediments covering a wide range of environmental conditions from Peru Margin, Equatorial Pacific, Hydrate Ridge, and Juan de Fuca Ridge. Bacterial and eukaryotic phospholipids were only detected in surface sediments from the Peru Margin. In contrast, deeply buried sediments, independent of their geographic location, were dominated by archaeal diether and tetraether lipids with various polar head groups and core lipids. We compared ring distributions of archaeal tetraether lipids derived from polar glycosidic precursors with those that are present as core lipids. The distributions of these related compound pools were distinct, suggestive of different archaeal sources, i.e., the polar compounds derive from sedimentary communities and the core lipids are fossil remnants from planktonic communities with possible admixtures of decayed sedimentary archaea. This in-situ production of distinct archaeal lipid populations potentially affects applications of the TEX86 paleotemperature proxy as demonstrated by offsets in reconstructed temperatures between both pools. We evaluated how varying cell and lipid stabilities will influence the sedimentary pool by using a box-model. The results are consistent with (i) a requirement of continuous inputs of freshly synthesized lipids in subsurface sediments for explaining the observed distribution of intact polar lipids, and (ii) decreasing lipid inputs with increasing burial depth.     

通辽科尔沁地区土壤微生物群落结构和功能及其影响因素

农业作为通辽科尔沁地区的传统产业,是当地重要经济产业之一.了解土壤微生物群落结构和功能及其影响因素对农作物种植、污染土地修复等具有重要意义.采用Illumina Miseq高通量测序技术、FAPROTAX.1.1功能预测平台等方法,在该区采集71个土壤样品,分析其地球化学特征和微生物群落特征并对微生物群落进行功能预测,同时探讨不同环境因子和空间因子对微生物群落的影响.结果显示:微生物群落由变形菌门（Proteobacteria）（19.77%）、奇古菌门（Thaumarchaeota）（17.85%）、酸杆菌门（Acidobacteria）（17.14%）和放线菌门（Actinobacteria）（15.58%）等构成;功能预测表明该区存在大量活跃的参与氮循环过程的微生物功能群,其中有氧氨氧化功能群为该区的优势微生物功能群.方差分解分析显示,在对微生物群落结构差异的可解释范围内环境因子比空间因子的解释量更大.Mantel检验结果显示,整体微生物群落与土壤pH、EC、TN、C/N及Mg、Na、Sr元素含量显著相关（p < 0.05）.综合分析表明,pH、EC和Sr元素含量是影响通辽科尔沁地区土壤微生物群落结构和功能及多样性的主要环境因素.      

Distribution characteristics and factors influencing microbial communities in the core soils of a seawater intrusion area in Longkou City,China

Microbes live throughout the soil profile. Microbial communities in subsurface horizons are impacted by a saltwater–freshwater transition zone formed by seawater intrusion (SWI) in coastal regions. The main purpose of this study is to explore the changes in microbial communities within the soil profile because of SWI. The study characterizes the depth-dependent distributions of bacterial and archaeal communities through high-throughput sequencing of 16S rRNA gene amplicons by collecting surface soil and deep core samples at nine soil depths in Longkou City, China. The results showed that although microbial communities were considerably impacted by SWI in both horizontal and vertical domains, the extent of these effects was variable. The soil depth strongly influenced the microbial communities, and the microbial diversity and community structure were significantly different (p < 0.05) at various depths. Compared with SWI, soil depth was a greater influencing factor for microbial diversity and community structure. Furthermore, soil microbial community structure was closely related to the environmental conditions, among which the most significant environmental factors were soil depth, pH, organic carbon, and total nitrogen.

     

苏禄海深海沉积物古菌群落结构多样性研究

为了研究热带西太平洋深海沉积物中古菌群落结构的多样性,应用16S rDNA文库技术,对IMAGES ⅪⅤ航次采集的岩芯MD3 059进行基因文库的构建和分析,选取得到543个克隆,处理获得137个OTUs(Operational Taxonomic Units).基于16s rRNA序列的同源性比较,绘制系统进化树,进行统计学分析.研究结果显示,热带西太平洋苏禄海沉积物中有丰富多样的古菌群落,在不足5 m的沉积物中垂直分布着11种古菌类群.古菌序列归属于泉古菌(Crenarchaeota)和广古菌(Euryarchaeota),其中,前者主要由Miscellaneous Crenarchaeotic Group(MCG)构成(占总古菌克隆序列的50%以上),而后者主要由Marine Benthic Group D(MBG-D)、South Africa Gold Mine Euryarchaeotic Group(SAGMEG)和Marine Benthic Group B(MBG-B)等种属构成(占总古菌克隆序列的30%以上).研究结果对于理解热带西太平洋深海沉积物中微生物多样性和未来开发利用微生物资源具有重要意义.     

A comparison of isotope fractionation of carbon and hydrogen from paddy field rice roots and soil bacterial enrichments during CO2/H2 methanogenesis

To better understand the isotope biogeochemistry of paddy field CH₄, we investigated carbon and hydrogen isotope fractionation during CO₂ reduction by a methanogenic community enriched from California paddy field soil and rice plants. Results from analyses of terminal restriction fragment length polymorphism (T-RFLP) and sequences of the archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) showed a difference in methanogenic community structure between the soil (dominated by Methanobacteriaceae) and roots (dominated by Methanospirillaceae) which was essentially the same for sampling dates 15 and 99 days after flooding (DAF). CO₂/H₂ methanogenesis by these microbial communities produced CH₄ with different isotope ratios and fractionation factors (α factors). The carbon isotope α factors in an open system with a continuous supply of 0.5% H₂ were 1.050 ± 0.002 and 1.057 ± 0.001 for soil and root enrichment cultures at 15 DAF, and 1.052 ± 0.0.002 and 1.059 ± 0.002 for soil and root enrichment cultures at 99 DAF, respectively. These α factors are similar to, but distinct from values previously obtained from cultures of mesophilic methanogens and are larger than calculated values (1.045) for paddy soil. Fractionation of hydrogen isotopes was also studied in a closed system under 80% H₂. The difference in α factors between soil and root enrichment cultures remained clear. The hydrogen isotope fractionations between culture water and the product CH₄ were −327 ± 14‰ and −319 ± 18‰ for soil enrichments, and −389 ± 17‰ and −382 ± 21‰ for root enrichments at 15 DAF and 99 DAF, respectively.     

祁连山水合物分布区不同高寒生态类型冬季表层土壤中古菌群落及变化特征

祁连山冻土区是我国青藏高原重要永久冻土区之一,也是我国陆域天然气水合物分布的重要地区。前期调查表明祁连山木里天然气水合物钻井区一带具 有丰富多样的高寒冻土生态类型。为了解该地区高寒草甸和高寒沼泽草甸表层土壤中古菌群落的多样性及分布特征,对2014年初冬在该区采集的表层土壤样品利用16S rRNA分子生物学技术和 地球化学等方法进行了分析和研究。结果显示,高寒草甸区土壤呈中性,而高寒沼泽草甸区土壤呈弱酸性。钻井区土壤中的TOC和顶空气甲烷含量均显著高于背景区,而在背景区内的两种生态 类型土壤中的TOC和顶空气甲烷含量差别较小。钻井区(除1个点)微生物细胞丰度高于背景区2~5倍。冬季表层土壤中的古菌多样性较低,含泉古菌的3个类群和广古菌的3个类群。不同植被类型 古菌群落的优势种群显著不同,在高寒草甸区为泉古菌门的Group Ⅰ.1b,而高寒沼泽草甸区为广古菌门的甲烷八叠球菌目(Methanosarcinales)。根据研究结果推测,土壤水分可能是导致高 寒草甸区和高寒沼泽草甸区细胞丰度和古菌群落差异的一个主要原因,高寒沼泽草甸区内产甲烷菌占优势可能与土壤高TOC含量有关。高寒沼泽草甸土壤中存在较丰富的产甲烷古菌,它们在厌 氧条件下的甲烷氧化作用也是土壤中甲烷来源之一。     

互花米草入侵下福建漳江口红树林湿地土壤生态化学变化

采集了福建云霄漳江口米草入侵下红树林自然湿地保护区内红树林群落、米草群落、红树林—米草交互群落以及光滩的剖面土壤样品,分析了土壤的总养分库、有效养分库及微生物活性等指标。结果表明,不同植被群落下土壤理化性质均存在明显差异。土壤有机质、全氮、全磷、阳离子交换量和微生物生物量碳、氮在同一深度的含量变化为：红树林>红树林—米草混作>米草>光滩;土壤蔗糖酶、脲酶、磷酸酶、过氧化氢酶和多酚氧化酶等酶活性指标也表现出相似的变化趋势。从深度变化而言,上述各项土壤质量指标均随剖面深度而降低。米草入侵后土壤的各项养分指标均有明显下降,湿地土壤生态化学性质发生了明显的退化。土壤有机碳、土壤微生物生物量碳、氮含量以及土壤蔗糖酶与磷酸酶活性对滨海湿地土壤退化的反映最为强烈, 可以作为指示性指标。     

Relating groundwater to seasonal wetlands in southeastern Wisconsin, USA

Historically, drier types of wetlands have been difficult to characterize and are not well researched. Nonetheless, they are considered to reflect the precipitation history with little, if any, regard for possible relation to groundwater. Two seasonal coastal wetland types (wet prairie, sedge meadow) were investigated during three growing seasons at three sites in the Lake Michigan Basin, Wisconsin, USA. The six seasonal wetlands were characterized using standard soil and vegetation techniques and groundwater measurements from the shallow and deep systems. They all met wetland hydrology criteria (e.g., water within 30 cm of land surface for 5% of the growing season) during the early portion of the growing season despite the lack of appreciable regional groundwater discharge into the wetland root zones. Although root-zone duration analyses did not fit a lognormal distribution previously noted in groundwater-dominated wetlands, they were able to discriminate between the plant communities and showed that wet prairie communities had shorter durations of continuous soil saturation than sedge meadow communities. These results demonstrate that the relative rates of groundwater outflows can be important for wetland hydrology and resulting wetland type. Thus, regional stresses to the shallow groundwater system such as pumping or low Great Lake levels can be expected to affect even drier wetland types.     

Cryptogam covers on sepulchral monuments and re-colonization of a marble surface after cleaning

Re-colonization of freshly cleaned surfaces by aeroterrestrial microbial communities is up to now poorly understood. Here, we present a comparative study addressing the composition of algal and fungal communities on a marble sculpture, based upon the analysis of 18S rRNA gene clone libraries from environmental samples. The samples were taken from a blackish and greenish biofilm cover before surface cleaning and 1 year after cleaning treatment, when traces of re-colonization became visible to the naked eye. The composition of the fungal community indicated clear differences between the old grown biofilm and the treated surface. While the former was dominated by the ascomycetes Rhinocladiella, Glyphium and Capnodiales, the black yeast Sarcinomyces was clearly dominant 1 year after cleaning, but could not be retrieved from the old grown black biofilm. The green algal community was dominated by different phylotypes of the lichen algae Trebouxia, as well as the cosmopolitan green algae Apatococcus and Stichococcus. No essential differences in the green algal community before and after cleaning could be observed.     

东海内陆架泥质区沉积物古菌群落垂向分布特征

为研究东海内陆架闽浙沿岸泥质区不同深度沉积物中古菌群落垂向分布特征, 利用古菌16S rDNA基因文库得到473个有效克隆、50个OTUs(Operational Taxonomic Units).16S rDNA序列系统进化和统计分析发现古菌分别归属于泉古生菌(Crenarchaeota)和广古生菌(Euryarchaeota), 其中以Miscellaneous Crenarchaeotic Group(MCG)为主, 仅含少量的Marine Benthic Group B(MBG-B)、South African Gold Mine Euryarchaeotic Group(SAGMEG)、Anaerobic Methanotrophs 3(ANME-3)、Marine Crenarchaeotic Group I(MG-I)和Marine Benthic Group D(MBG-D).该泥质区沉积物可能存在由ANME-3催化的甲烷厌氧氧化作用, 同源序列分析表明其古菌群落分布与周边环境有较大联系.UniFrac与沉积物环境因子分析表明该泥质区古菌群落垂向分布与沉积物有机质含量和粒度变化密切相关.