Phylogenomic and Comparative Analysis of the Distribution And
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Fungal Evolution: Major Ecological Adaptations and Evolutionary Transitions
Biol. Rev. (2019), pp. 000–000. 1 doi: 10.1111/brv.12510 Fungal evolution: major ecological adaptations and evolutionary transitions Miguel A. Naranjo-Ortiz1 and Toni Gabaldon´ 1,2,3∗ 1Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2 Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain ABSTRACT Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). -
Supporting Information
Supporting Information Bender et al. 10.1073/pnas.0802779105 Table S1. Species names and calculated numeric values pertaining to Fig. 1 Mitochondrially Nuclear encoded Nuclear encoded Species name encoded methionine, % methionine, % methionine, corrected, % Animals Primates Cebus albifrons 6.76 Cercopithecus aethiops 6.10 Colobus guereza 6.73 Gorilla gorilla 5.46 Homo sapiens 5.49 2.14 2.64 Hylobates lar 5.33 Lemur catta 6.50 Macaca mulatta 5.96 Macaca sylvanus 5.96 Nycticebus coucang 6.07 Pan paniscus 5.46 Pan troglodytes 5.38 Papio hamadryas 5.99 Pongo pygmaeus 5.04 Tarsius bancanus 6.74 Trachypithecus obscurus 6.18 Other mammals Acinonyx jubatus 6.86 Artibeus jamaicensis 6.43 Balaena mysticetus 6.04 Balaenoptera acutorostrata 6.17 Balaenoptera borealis 5.96 Balaenoptera musculus 5.78 Balaenoptera physalus 6.02 Berardius bairdii 6.01 Bos grunniens 7.04 Bos taurus 6.88 2.26 2.70 Canis familiaris 6.54 Capra hircus 6.84 Cavia porcellus 6.41 Ceratotherium simum 6.06 Choloepus didactylus 6.23 Crocidura russula 6.17 Dasypus novemcinctus 7.05 Didelphis virginiana 6.79 Dugong dugon 6.15 Echinops telfairi 6.32 Echinosorex gymnura 6.86 Elephas maximus 6.84 Equus asinus 6.01 Equus caballus 6.07 Erinaceus europaeus 7.34 Eschrichtius robustus 6.15 Eumetopias jubatus 6.77 Felis catus 6.62 Halichoerus grypus 6.46 Hemiechinus auritus 6.83 Herpestes javanicus 6.70 Hippopotamus amphibius 6.50 Hyperoodon ampullatus 6.04 Inia geoffrensis 6.20 Bender et al. www.pnas.org/cgi/content/short/0802779105 1of10 Mitochondrially Nuclear encoded Nuclear encoded Species -
Characterization of a Microbial Community Capable of Nitrification At
Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics. -
Alishewanella Jeotgali Sp. Nov., Isolated from Traditional Fermented Food, and Emended Description of the Genus Alishewanella
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2313–2316 DOI 10.1099/ijs.0.007260-0 Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Min-Soo Kim,1,2 Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,1 Kyoung-Ho Kim,1 Mi-Ja Jung,1 Jung-Hye Choi,1 Eun-Jin Park1 and Jin-Woo Bae1,2 Correspondence 1Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee Jin-Woo Bae University, Seoul 130-701, Republic of Korea [email protected] 2University of Science and Technology, Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 6C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values ,70 % (42.6 and 14.8 % with A. -
Pulmonary Mycobiome of Patients with Suspicion of Respiratory Fungal Infection – an Exploratory Study Mariana Oliveira 1,2 , Miguel Pinto 3, C
#138: Pulmonary mycobiome of patients with suspicion of respiratory fungal infection – an exploratory study Mariana Oliveira 1,2 , Miguel Pinto 3, C. Veríssimo 2, R. Sabino 2,* . 1Faculty of Sciences of the University of Lisbon, Portugal; 2Department of Infectious Diseases of the National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal; 3 Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Avenida Padre Cruz, 1600-560 Lisboa, Portugal. ABSTRACT INTRODUCTION This pilot study aimed to characterize the pulmonary mycobiome of patients with suspicion of fungal infection of the The possibility of knowing and comparing the mycobiome of healthy individuals with respiratory tract as well as to identify potentially pathogenic fungi infecting their lungs. the mycobiome of patients with different pathologies, as well as the capacity to quickly and DNA was extracted from the respiratory samples of a cohort of 10 patients with suspicion of respiratory fungal infection. The specifically detect and identify potentially pathogenic fungi present in the pulmonary internal transcribed spacer 1 (ITS1) region and the calmodulin (CMD) gene were amplified by PCR and the resulting amplicons were sequenced through next generation sequencing (NGS) techniques. The DNA sequences obtained were taxonomically mycobiome of patients makes NGS techniques useful for the laboratory diagnosis of identified using the PIPITS and bowtie2 platforms. fungal infections. Thus, the aim of this exploratory study was to optimize the procedure for Twenty-four different OTU (grouped in 17 phylotypes) were considered as part of the pulmonary mycobiome. Twelve genera the detection of fungi through NGS techniques. A metagenomic analysis was performed in of fungi were identified. -
Digestive Diseases
Progress Report 進度報告 2019 Progress Report 進度報告 2019 DIGESTIVE Research Progress Summary Colorectal Cancer: DISEASES Gut microbiota: 1. The team led by Professor Jun Yu demonstrated tumour-associated neutrophils, which are that Peptostreptococcus anaerobius, an anaerobic associated with chronic infl ammation and tumour gut bacterium, could adhere to colon mucosa progression were observed in P. anaerobius- Min/+ and accelerates CRC development in mice. They treated Apc mice. Blockade of integrin α2/ϐ1 by further identifi ed that a P. anaerobius surface RGDS peptide, small interfering RNA or antibodies protein, putative cell wall binding repeat 2 all impaired P. anaerobius attachment and 01 (PCWBR2), directly interacts with colonic cell abolished P. anaerobius-mediated oncogenic Principal Investigator response in vitro and in vivo. They determined lines via α2/ϐ1 integrin. Interaction between PCWBR2 and integrin α /ϐ induced the activation that P. anaerobius drives CRC via a PCWBR2- Professor Jun Yu 2 1 of the PI3K–Akt pathway in CRC cells, leading to integrin α2/ϐ1-PI3K–Akt–NF-κB signalling axis increased cell proliferation and nuclear factor and that the PCWBR2-integrin α2/ϐ1 axis is a Team kappa-light-chain-enhancer of activated B potential therapeutic target for CRC (Nature cells (NF-κB) activation. Signifi cant expansion Communication 2019 ). Joseph Sung | Francis Chan | Henry Chan | Vincent Wong | of myeloid-derived suppressor cells, tumour- Dennis Wong | Jessie Liang | Olabisi Coker associated macrophages and granulocytic 84 85 Progress -
Microbial Diversity of Drilling Fluids from 3000 M Deep Koyna Pilot
Science Reports Sci. Dril., 27, 1–23, 2020 https://doi.org/10.5194/sd-27-1-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust Himadri Bose1, Avishek Dutta1, Ajoy Roy2, Abhishek Gupta1, Sourav Mukhopadhyay1, Balaram Mohapatra1, Jayeeta Sarkar1, Sukanta Roy3, Sufia K. Kazy2, and Pinaki Sar1 1Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India 2Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, 713209, West Bengal, India 3Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, 415114, Maharashtra, India Correspondence: Pinaki Sar ([email protected], [email protected]) Received: 24 June 2019 – Revised: 25 September 2019 – Accepted: 16 December 2019 – Published: 27 May 2020 Abstract. Scientific deep drilling of the Koyna pilot borehole into the continental crust up to a depth of 3000 m below the surface at the Deccan Traps, India, provided a unique opportunity to explore microbial life within the deep granitic bedrock of the Archaean Eon. Microbial communities of the returned drilling fluid (fluid re- turned to the mud tank from the underground during the drilling operation; designated here as DF) sampled during the drilling operation of the Koyna pilot borehole at a depth range of 1681–2908 metres below the surface (m b.s.) were explored to gain a glimpse of the deep biosphere underneath the continental crust. Change of pH 2− to alkalinity, reduced abundance of Si and Al, but enrichment of Fe, Ca and SO4 in the samples from deeper horizons suggested a gradual infusion of elements or ions from the crystalline bedrock, leading to an observed geochemical shift in the DF. -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
Genomes Outside SIGS October - November 2012 Burkholderia Thailandensis MSMB43, Sequence Hydrogenophaga Sp
Standards in Genomic Sciences (2012) 7:331-350 DOI:10.4056/sigs.3597227 Genome sequences published outside of Standards in Genomic Sciences, October - November 2012 Oranmiyan W. Nelson1 and George M. Garrity1 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the biblio- graphic data for such references to the SIGS editorial office. Domain Archaea Alcaligenes faecalis subsp. faecalis NCIB 8687, Phylum Crenarchaeota sequence accession AKMR01000001 through “Thermogladius cellulolyticus” 1633, AKMR01000186 [9] sequence accession CP003531 [1] Alishewanella aestuarii Strain B11T, sequence accession ALAB00000000 [10] Phylum Euryarchaeota Methanomassiliicoccus luminyensis, se- Alishewanella agri BL06T, sequence accession quence accession CAJE01000001 AKKU00000000 [11] through CAJE01000026 [2] Bartonella birtlesii strain IBS 135T, sequence Pyrococcus sp. Strain ST04, sequence accession AKIP00000000 [12] accession CP003534 [3] Brucella abortus A13334, sequence accession CP003176.1 (Chromosome I), CP003177.1 Domain Bacteria (Chromosome II) [13] Nitrospirae Phylum Brucella canis Strain HSK A52141, sequence Leptospirillum ferrooxidans Strain C2- accession CP003174.1 (chromosome I), and 3, sequence accession AP012342 [4] CP003175.1 (chromosome II) [14] Phylum Cyanobacteria Brucella melitensis 16M13w, sequence acces- Prochlorococcus marinus MED4, se- sion AHWE00000000 [15] quence accession BX548174 [5] Brucella melitensis 16M1w, sequence acces- sion AHWD00000000 [15] Phylum Proteobacteria Acinetobacter sp. -
Alishewanella Aestuarii Sp. Nov., Isolated from Tidal Flat Sediment, and Emended Description of the Genus Alishewanella
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 421–424 DOI 10.1099/ijs.0.65643-0 Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,2 Kyoung-Ho Kim,2 Min-Soo Kim,1,2 Hee-Mock Oh2 and Jin-Woo Bae1,2,3 Correspondence 1University of Science & Technology, 52, Eoeun-dong, Daejeon 305-333, Republic of Korea Jin-Woo Bae 2Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea [email protected] 3Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea A Gram-negative strain, B11T, was isolated from tidal flat sediment in Yeosu, Republic of Korea. Strain B11T did not require NaCl for growth and grew between 18 and 44 6C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B11T was associated with the genus Alishewanella and was closely related to the type strain of Alishewanella fetalis (98.3 % similarity). Within the phylogenetic tree, the novel isolate shared a branching point with A. fetalis. Analysis of 16S rRNA gene sequences and DNA–DNA relatedness, as well as physiological and biochemical tests, indicated genotypic and phenotypic differences between strain B11T and the type strain of A. fetalis. Thus, strain B11T is proposed as a representative of a novel species, Alishewanella aestuarii sp. nov.; the type strain is B11T (5KCTC 22051T 5DSM 19476T). The genus Alishewanella, proposed by Fonnesbech Vogel et description; Table 1 shows a comparison between the al. -
SYSTEMATICS of DIVISION ASCOMYCOTA 1 Group
References: Kirk PM, Cannon PF, Minter DW, Stalpers JA. 2008. Dictionary of the Fungi (10th ed.). Wallingford, UK: CABI. Webster, J., & Weber, R. (2007). Introduction to fungi. Cambridge, UK: Cambridge University Press. Url1.: https://en.wikipedia.org/wiki/Ascomycota SYSTEMATICS OF DIVISION ASCOMYCOTA 1 Group: Plectomycetes Plectomycetes is an artificial group of Ascomycota and it originally contained all Ascomycete fungi which produce their asci within a cleistothecium. Plectomycetes can be defined by the following set of characters; Cleistothecium or gymnothecium is usually present, ascogenous hyphae are usually not conspicuous, asci are scattered throughout the cleistothecium, asci are mostly globose and thin-walled, and the ascospores are released passively after disintegration of the ascus wall, not by active discharge, ascospores are small, unicellular and usually spherical or ovoid, conidia are commonly produced from phialides or as arthroconidia. Class: Eurotiomycetes Most members of the class produce an enclosed structure cleistothecium within which they produce their spores. It contains 10 order, 27 families 280 genus and about 3400 species. Order: Onygenales Onygenales members are able to digest keratin and because of this have become dominant organisms in environments where keratin is available. The most members have colorless cleistothecia and ascospores. The spherical to egg-shaped asci are always uniformly packed in the centrum and may be dispersed among hyphal elements. The ascospores are always single-celled (example: Chrysosporium, Microsporum and Trichophyton). Order: Eurotiales Most members of the order have phialidic asexual stages belonging to the genera Aspergillus and Penicillium or, less commonly, to Paecilomyces or even simpler types. Rarely there is no anamorph at all. -
Draft Genomic Sequence of a Chromate- and Sulfate-Reducing
Xia et al. Standards in Genomic Sciences (2016) 11:48 DOI 10.1186/s40793-016-0169-3 SHORT GENOME REPORT Open Access Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination Xian Xia1, Jiahong Li1, Shuijiao Liao1,2, Gaoting Zhou1,2, Hui Wang1, Liqiong Li1, Biao Xu1 and Gejiao Wang1* Abstract Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr6+) to the much 3+ 2− 2− 2− 2+ less toxic Cr . In addition, it reduces sulfate (SO4 )toS . The S could react with Cd to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified. Keywords: Alishewanella, Chromate-reducing bacterium, Sulfate-reducing bacterium, Cadmium, Chromium Abbreviation: PGAP, Prokaryotic Genome Annotation Pipeline Introduction Alishewanella sp. WH16-1 was isolated from mining The genus Alishewanella was established by Vogel et al., soil in 2009. This strain could resist to multiple heavy in 2000 with Alishewanella fetalis as the type species. It metals. During cultivation, it could efficiently reduce the belongs to the family Alteromonadaceae of the class toxic chromate (Cr6+) to the much less toxic and less 3+ 2− Gammaproteobacteria [1].