Evolution of a Σ–(C-Di-GMP)–Anti-Σ Switch
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
ABSTRACT Title of Document: MECHANISMS of RESISTANCE to IONIZING RADIATION in EXTREMOPHILES Kimberly Michelle Webb, Master of S
ABSTRACT Title of Document: MECHANISMS OF RESISTANCE TO IONIZING RADIATION IN EXTREMOPHILES Kimberly Michelle Webb, Master of Science, 2012 Directed by: Dr. Frank T. Robb, Marine Estuarine Environmental Sciences Extremophiles display an astonishing array of adaptations to harsh environmental conditions. We analyzed the mechanisms of ionizing radiation resistance from a diverse group of extremophilic archaea and bacteria. In Halobacterium salinarum IR resistance is conferred by antioxidant Mn2+-complexes, and protein-free cell extracts (ultrafiltrates, UFs) of super-resistant (IR+) isolates of H. salinarum had increased concentrations of Mn, PO4 and amino acids compared to the founder strain. Proteomic analysis determined that IR+ isolates with increased Mn had elevated protein expression for central carbon metabolism, suggesting a Mn-stimulated metabolic route to increased IR resistance. We examined the role of mannosylglycerate, di-myo-inositol phosphate, and trehalose in the IR resistance of various thermophiles; aerobic thermophiles had UFs which were radioprotective of enzyme activity under aerobic conditions, which is attributed to Mn, PO4 and trehalose accumulation. In contrast, anaerobic thermophile UFs did not contain significant amounts of Mn, and were radioprotective only under anaerobic conditions; we conclude the anaerobic environment confers their IR resistance. MECHANISMS OF RESISTANCE TO IONIZING RADIATION IN EXTREMOPHILES By Kimberly Michelle Webb Thesis submitted to the Faculty of the Graduate School of the University of Maryland, College Park in partial fulfillment of the requirements for the degree of Master of Science 2012 Advisory Committee: Dr. Frank T. Robb, Chair Dr. Michael Daly Dr. Jocelyne DiRuggiero Dr. Kevin R. Sowers © Copyright by Kimberly Michelle Webb 2012 Dedication This work is dedicated to my entire family, especially my husband Nathan, and my parents Kevyn and Peter, for all your love and support. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively). -
The Bacterial Communities of Sand-Like Surface Soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang
The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang To cite this version: Yang Wang. The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA). Agricultural sciences. Université Paris-Saclay, 2015. English. NNT : 2015SACLS120. tel-01261518 HAL Id: tel-01261518 https://tel.archives-ouvertes.fr/tel-01261518 Submitted on 25 Jan 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT : 2015SACLS120 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N°577 Structure et Dynamique des Systèmes Vivants Spécialité de doctorat : Sciences de la Vie et de la Santé Par Mme Yang WANG The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Thèse présentée et soutenue à Orsay, le 23 Novembre 2015 Composition du Jury : Mme. Marie-Claire Lett , Professeure, Université Strasbourg, Rapporteur Mme. Corinne Cassier-Chauvat , Directeur de Recherche, CEA, Rapporteur M. Armel Guyonvarch, Professeur, Université Paris-Sud, Président du Jury M. -
Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota -
Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans Gen
etics & E en vo g lu t lo i y o h n a P r f y Journal of Phylogenetics & Sathyanarayana Reddy, J Phylogen Evolution Biol 2013, 1:4 o B l i a o n l r o DOI: 10.4172/2329-9002.1000122 u g o y J Evolutionary Biology ISSN: 2329-9002 Research Article Open Access Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans gen. nov., and Parahymenobacter gen. nov Gundlapally Sathyanarayana Reddy* CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500 007, India Abstract Phylogenetic analyses of 26 species of the genus Hymenobacter based on the 16S rRNA gene sequences, resulted in polyphyletic clustering with three major groups, arbitrarily named as Clade1, Clade2 and Clade3. Delineation of Clade1 and Clade3 from Clade2 was supported by robust clustering and high bootstrap values of more than 90% and 100% in all the phylogenetic methods. 16S rRNA gene sequence similarity shared by Clade1 and Clade2 was 88 to 93%, Clade1 and Clade3 was 88 to 91% and Clade2 and Clade3 was 89 to 92%. Based on robust phylogenetic clustering, less than 93.0% sequence similarity, unique in silico restriction patterns, presence of distinct signature nucleotides and signature motifs in their 16S rRNA gene sequences, two more genera were carved to accommodate species of Clade1 and Clade3. The name Hymenobacter, sensu stricto, was retained to represent 17 species of Clade2. For members of Clade1 and Clade3, the names Siccationidurans gen. nov. and Parahymenobacter gen. nov. were proposed, respectively, and species belonging to Clade1 and Clade3 were transferred to their respective genera. -
Data of Read Analyses for All 20 Fecal Samples of the Egyptian Mongoose
Supplementary Table S1 – Data of read analyses for all 20 fecal samples of the Egyptian mongoose Number of Good's No-target Chimeric reads ID at ID Total reads Low-quality amplicons Min length Average length Max length Valid reads coverage of amplicons amplicons the species library (%) level 383 2083 33 0 281 1302 1407.0 1442 1769 1722 99.72 466 2373 50 1 212 1310 1409.2 1478 2110 1882 99.53 467 1856 53 3 187 1308 1404.2 1453 1613 1555 99.19 516 2397 36 0 147 1316 1412.2 1476 2214 2161 99.10 460 2657 297 0 246 1302 1416.4 1485 2114 1169 98.77 463 2023 34 0 189 1339 1411.4 1561 1800 1677 99.44 471 2290 41 0 359 1325 1430.1 1490 1890 1833 97.57 502 2565 31 0 227 1315 1411.4 1481 2307 2240 99.31 509 2664 62 0 325 1316 1414.5 1463 2277 2073 99.56 674 2130 34 0 197 1311 1436.3 1463 1899 1095 99.21 396 2246 38 0 106 1332 1407.0 1462 2102 1953 99.05 399 2317 45 1 47 1323 1420.0 1465 2224 2120 98.65 462 2349 47 0 394 1312 1417.5 1478 1908 1794 99.27 501 2246 22 0 253 1328 1442.9 1491 1971 1949 99.04 519 2062 51 0 297 1323 1414.5 1534 1714 1632 99.71 636 2402 35 0 100 1313 1409.7 1478 2267 2206 99.07 388 2454 78 1 78 1326 1406.6 1464 2297 1929 99.26 504 2312 29 0 284 1335 1409.3 1446 1999 1945 99.60 505 2702 45 0 48 1331 1415.2 1475 2609 2497 99.46 508 2380 30 1 210 1329 1436.5 1478 2139 2133 99.02 1 Supplementary Table S2 – PERMANOVA test results of the microbial community of Egyptian mongoose comparison between female and male and between non-adult and adult. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
A Meta-Analysis of the Publicly Available Bacterial and Archaeal Sequence Diversity in Saline Soils
World J Microbiol Biotechnol (2013) 29:2325–2334 DOI 10.1007/s11274-013-1399-9 ORIGINAL PAPER A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils Bin Ma • Jun Gong Received: 19 April 2013 / Accepted: 3 June 2013 / Published online: 12 June 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract An integrated view of bacterial and archaeal Halorubrum and Thermofilum were the dominant archaeal diversity in saline soil habitats is essential for understanding genera in saline soils. Rarefaction analysis indicated that less the biological and ecological processes and exploiting than 25 % of bacterial diversity, and approximately 50 % of potential of microbial resources from such environments. archaeal diversity, in saline soil habitats has been sampled. This study examined the collective bacterial and archaeal This analysis of the global bacterial and archaeal diversity in diversity in saline soils using a meta-analysis approach. All saline soil habitats can guide future studies to further available 16S rDNA sequences recovered from saline soils examine the microbial diversity of saline soils. were retrieved from publicly available databases and sub- jected to phylogenetic and statistical analyses. A total of Keywords Archaea Á Bacteria Á Halophilic Á Microbial 9,043 bacterial and 1,039 archaeal sequences, each longer diversity Á Saline soil than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known Introduction bacterial phyla, with Proteobacteria (44.9 %), Actinobacte- ria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Saline soils are increasingly abundant as a consequence of Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being pre- irrigation and desertification processes (Rengasamy 2006). -
Gut Microbiota Composition Is Correlated to Host Hummingbird Protein Requirements
1 Gut Microbiota Composition is Correlated to Host Hummingbird Protein Requirements ABSTRACT: The gut microbiome shapes and is shaped by a host animal’s physiology. Avian taxa hold physiological characteristics unique from mammals and might inform novel pressures experienced by microbial communities. Further, the symbionts’ relative abundance and their abilities to adapt to available resources are of critical importance to a holobiont’s fitness in rapidly changing climates. Therefore, wild populations of hummingbirds Selasphorus rufus and Calypte anna were studied. The two systems differ in S. rufus’s annual migrations from wintering grounds to their breeding grounds in the Pacific Northwest, whereas C. anna are resident in the latter region. Previous findings have indicated host microbiome composition varied with hummingbird fat score and the month during which fecal sampling occurred. Although fat is an important resource, especially for S. rufus in their migrations, protein requirements are critical because other annual activities, pressuring the organism to access nitrogen. Three of these activities are producing an egg, replacing molted feathers, and carrying parasites. The hypothesis for this study was that birds performing these activities will have microbiota that will make nitrogen available to them. Analysis of OTUs from 16S rDNA V3-V5 amplicon sequencing showed Actinobacteria are more abundant in these hummingbird species than in mammals, replicating our lab’s previous findings. Notably, S. rufus adult females with evidence of recent or current egg production had significantly lower relative levels of Actinobacteria and significantly higher abundances of five of the other ten most abundant bacterial phyla than S. rufus males. The composition of major bacterial phyla in C. -
Distribution of Long Linear and Branched Polyamines in the Thermophiles Belonging to the Domain Bacteria
Journal of Japanese Society for Extremophiles (2008) Vol.7 (1) Journal of Japanese Society for Extremophiles (2008), Vol. 7, 10-20 ORIGINAL PAPER Hamana Ka,b,e, Hosoya Ra, Yokota Ac, Niitsu Md, Hayashi He and Itoh Tb Distribution of long linear and branched polyamines in the thermophiles belonging to the domain Bacteria a Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan. bJapan Collection of Microorganisms, RIKEN, BioResource Center, Wako, Saitama 351-0198, Japan. c Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan. d Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0290, Japan. e Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan. Corresponding author : Koei Hamana, [email protected] Phone : +81-27-220-8916, FAX : +81-27-220-8999 Received: April 3, 2008/ Reviced:May 26, 2008/ Acepted:June 3, 2008 Abstract Cellular polyamines of 44 newly validated have been published in eubacteria 15, 16). However, the eubacterial thermophiles growing at 45-80℃, belonging degree of thermophily is roughly estimated and not to eight orders (six phyla) of the domain Bacteria, were defined exactly. The cellular occurrence of long linear analyzed by HPLC and GC. A quaternary branched and/or branched polyamines in extremely thermophilic penta-amine, N4-bis(aminopropyl)norspermidine, was (or hyperthermophilic) eubacteria suggested that the found in Hydrogenivirga and Sulfurihydrogenibium extreme thermophiles (or hyperthermophiles) may have belonging to the order of Aquificales. Another some novel polyamine synthetic abilities possibly quaternary branched penta-amine, N4-bis(aminopropyl) associated with their thermophily 8-11, 13-15, 18, 23, 24).