Marine cyanolichens from different littoral zones are associated with distinct bacterial communities

The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen species Lichina pygmaea and Lichina confinis, and the maritime chlorolichen species Xanthoria aureola which occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. The L. confinis and L. pygmaea communities were significantly different from those of the maritime Xanthoria aureola lichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notably Sphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the two Lichina species were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes genera Rubricoccus, Tunicatimonas and Lewinella, suggesting an important role of these species in the marine Lichina lichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Distinct bacterial groups contribute to carbon cycling during a naturally iron fertilized phytoplankton bloom in the Southern Ocean

We investigated the contribution of distinct bacterial groups to bulk abundance and leucine incorporation during a spring phytoplankton bloom induced by natural iron fertilization in the Southern Ocean (Kerguelen Ocean and Plateau Compared Study, January-February 2005). Oligonucleotide probes were designed to target five operational taxonomic units (OTUs) at a narrow phylogenetic level (>= 99% identity of the 16S ribosomal ribonucleic acid [rRNA] gene). During the peak of the phytoplankton bloom, the Roseobacter groups NAC11-7 and RCA, the OTUs SAR92 belonging to Gammaproteobacteria, and the Bacteroidetes OTU Agg58 dominated bulk abundance and leucine incorporation. These four OTUs disappeared with the decline of the bloom, when the cosmopolitan groups SAR11 and SAR86 became dominant. In high-nutrient, low-chlorophyll waters and at a site characterized by transient high phytoplankton biomass, the SAR11 and SAR86 clusters and a Polaribacter OTU dominated abundance and leucine incorporation in the upper 100 m. Our results demonstrate that a few distinct bacterial groups identified on a relatively narrow phylogenetic level account for 47% to 82% of bulk abundance and leucine incorporation during the spring phytoplankton bloom in the naturally fertilized region off Kerguelen. The major role of these bacterial groups in carbon cycling in response to natural iron fertilization in the Southern Ocean suggests they could play an important role in the coupling of the biogeochemical cycles of carbon and iron

A Study on transport of Inorganic Solute in Clay

近年來國內對於廢棄物之處理，常用之方式有焚化後掩埋或衛生掩埋等兩種，不論那一種方式，均須進行掩埋作業。由於不當的掩埋將造成土地污染問題；且社會大眾環保意識普遍提昇，對環境品質之要求日漸升高。因此，對於多孔介質內污染物質傳輸之研究，將有助於土壤污染之控制與管理。 由於污染物傳輸特性相當複雜，將因土壤種類、孔隙流速高低、溶液內陰、陽離子吸附行為之差異等，而有不同之傳輸結果；因此本研究以四種壓密黏土進行不同流速與不同無機溶質之土柱試驗，以瞭解無機溶質於黏土中傳輸特性之變化。 經由敏感度分析結果，推估低敏感度時間因子(Tpe=0)之位置，並配合遲滯因子(Rd)與Pe(Column Peclet Number)對相對流出濃度(Ce/Co)敏感度之個別影響情形，建立一種試驗規劃與迴歸步驟，期望能更準確求Rd、Pe與延散係數(dispersion coefficient)。 由孔隙流速對Pe 值之影響研究結果顯示，流速愈高則Pe 值隨之變大，而孔隙流速降低則遲滯現象愈顯著，即傳輸參數Rd變大。氯化鈣與氯化鈉溶液於高嶺土或高嶺土加皂土之混合土之滲透結果中，由於陽離子交換造成H+離子釋放，流出液（effluent）之pH值呈現下降趨勢；並且因為低pH值之條件，造成陰離子（Cl-）傳輸產生些微之遲滯現象，即遲滯因子Rd大於1。 由敏感度分析結果，所建立之改良式傳輸參數推求法，研究結果發現該法所得陰、陽離子D/Rd 比值之差異，較傳統分析方式小，顯示改良式推求法在分析傳輸參數上，確為較佳、且可靠度較高之分析方式。Landfill, even in the modern age, has been an indispensable procedure in the waste treatment process. Pollution and environmental concerns are constantly arisen if the landfill was not operated properly. Therefore, studies on the pollutant transport in porous media would be very important in the aspect of preventing soil pollution from landfill. The pollutant transportation is controlled by many factors, e.g. soil type, pore velocity, ion adsorption etc., and each of them will contribute to the transport parameters. Thus, in this study, the transportation of inorganic solutes in soil was evaluated through the column tests, with various pore velocities and inorganic solutes, on four kinds of clay to achieve better understanding. In order to determine the retardation factor (Rd), column peclet number (Pe) and dispersion coefficient more accurately and effectively, an enhanced analysis and regression procedures on the data of column test were proposed by estimating the dimensionless time factor at minimum sensitivity of Pe, and then incorporating with the individual effects of Rd and Pe on relative effluent concentration (Ce/Co), through the probabilistic sensitivity analysis. The results show that the Pe increases with higher pore velocity and the retardation is more significant when the pore velocity decreases, which indicates a higher Rd. During the column tests of CaCl2 and NaCl solutions in Kaolinite and mixture of Kaolinite and Bentonite, the pH value of the effluent decreases due to the higher H+ concentration as a result of cation exchange. And because of this low pH, the transportation of anions (Cl-) is therefore retarded and consequently yields a Rd that is greater than 1. The differences between D/Rd ratios of anion and cation obtained through this enhanced analysis were much smaller, as compared to that through traditional analysis. It is clear that the enhanced analysis, proposed in this study, is indeed a better and more reliable method of analyzing the solute transportation.封面 頁次 摘要 Abstract 誌謝 目錄 表目錄 圖目錄 符號說明 第一章 前言 1-1 研究動機 1-2 研究目的 1-3 研究內容 第二章 文獻回顧與溶質傳輸理論 2-1 影響土壤滲透性之因素 2-2 溶質傳輸理論 2-2-1 溶質於土壤中之傳輸現象 2-2-2 一維土柱試驗與貫穿曲線、濃度剖面 2-2-3 溶質傳輸之機制與理論模式 2-3 一維-移流-延散方程式解析解 2-3-1 濃度之形成 2-3-2 解析解 2-3-3 無因次化之解析解 2-4 一維-移流-延散方程式之傳輸參數推求 2-4-1 利用近似解切線斜率推求參數P與D 2-4-2 利用貫穿曲線之Log-Normal圖推求P 2-4-3 利用批次實驗推求Rd值 2-4-4 最小平方和法之傳輸參數推求 第三章 一維溶質傳輸之敏感度分析 3-1 背景 3-2 敏感度分析 3-2-1 Rd與Pe大小對Ce/Co之影響 3-2-2 Rd與Pe之機率分佈函數假設對Ce/Co之影響 3-2-3 Rd與Pe之不確定對Ce/Co之影響 3-3 T之時間因子位置探討 3-4 試驗規劃與迴歸步驟之建議 第四章 試驗設計與試驗方法 4-1 試驗設計與項目 4-2 試驗設備 4-2-1 土壤基本性質試驗 4-2-2 試體製作與三軸柔性壁滲透試驗 4-2-3 pH值、電導度及離子濃度之測定 4-3 試驗材料 4-4 試驗方法 4-4-1 土壤基本性質試驗 4-4-2 三軸柔性壁滲透暨土柱試驗 4-5 滲透暨土柱試驗統計 第五章 結果與討論 5-1 土壤基本性質試驗 5-2 試體性質 5-3 入滲無機溶質之性質 5-4 三軸柔性壁滲透暨土柱試驗 5-4-1 滲透性係數之變化 5-4-2 pH值之變化 5-4-3 相對導電度(EC/ECo)之變化 5-4-4 相對濃度(Ce/Co)之變化 5-5 傳輸參數之探討 5-5-1 孔隙流速對傳輸參數之影響 5-5-2 不同種類土樣與溶質對傳輸特性之影響 5-5-3 溶質濃度差異對遲滯因子之影響 5-6 傳輸參數推求方法之比較 第六章 結論與建議 6-1 結論 6-2 建議 參考文

Dynamics of community structure and phosphate status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea. Limnol Oceanogr 50: 363–375

We monitored the genetic diversity and phosphate (P) status of Prochlorococcus and Synechococcus populations during an annual cycle (1999–2000) in the Gulf of Aqaba, Red Sea, using DNA probes and antibodies against the protein PstS, a molecular marker of P stress. The usual spring Synechococcus bloom was not observed in this year, and the picophytoplankton was dominated by Prochlorococcus from April to December. A single high light (HL)– adapted ecotype of Prochlorococcus, HLII, dominated, and this dominance extended even to the base of the euphotic zone for much of the year. Low light (LL)–adapted ecotypes only appeared between July and October and were confined to waters deeper than 50 m. The Synechococcus population was also dominated by a single clade (clade II), with the exception of a peak of clade III genotypes in June. Highest PstS expression from the collective Synechococcus and Prochlorococcus populations, indicative of P stress, was observed during the acutely oligotrophic summer, whereas low expression occurred during the winter and spring. Prochlorococcus abundance appeared unaffected by P stress and only decreased with the beginning of winter mixing, whereas P stress might have caused the decline of the Synechococcus population in May 1999. Unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus are known to be widespread and abundan

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water

Chemosynthetic mats involved in cycling sulfur compounds are often found in hydrothermal vents, cold seeps and whale falls. However, there are only few records of wood fall mats, even though the presence of hydrogen sulfide at the wood surface should create a perfect niche for sulfide-oxidizing bacteria. Here we report the growth of microbial mats on wood incubated under conditions that simulate the Mediterranean deep-sea temperature and darkness. We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features. We show that the wood surface was first colonized by sulfide-oxidizing bacteria belonging to the Arcobacter genus after only 30 days of immersion. Subsequently, the number of sulfate reducers increased and the dominant Arcobacter phylotype changed. The ecological succession was reflected by a change in the metabolic potential of the community from chemolithoheterotrophs to potential chemolithoautotrophs. Our work provides clear evidence for the chemosynthetic nature of wood fall ecosystems and demonstrates the utility to develop experimental incubation in the laboratory to study deep-sea chemosynthetic mats

Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides

International audienceAn in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Prochlorococcus using horseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)-adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992 R8 , Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow water in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea

Author Correction: Surface properties of SAR11 bacteria facilitate grazing avoidance

International audienc