Conexibacter Woesei Type Strain (ID131577T)
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. -
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). -
Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils Daniel Mummey 1, William Holben1, Johan Six 2 and Peter Stahl3
Microbial Ecology Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils Daniel Mummey 1, William Holben1, Johan Six 2 and Peter Stahl3 (1) Division of Biological Sciences, University of Montana, Missoula, MO, USA (2) Department of Plant Sciences, University of California-Davis, Davis, CA, USA (3) Department of Renewable Resources, University of Wyoming, Laramie, WY, USA Received: 23 December 2004 / Accepted: 1 January 2005 / Online publication: 6 April 2006 Abstract influenced by, the environment. Such an understanding can only be attained by analysis at scales relevant to those Most soil microbial community studies to date have at which processes influencing microbial diversity actu- focused on homogenized bulk soil samples. However, it ally operate [29]. However, because of the biotic and is likely that many important microbial processes occur abiotic complexity exhibited by most soils at nearly all in spatially segregated microenvironments in the soil scales, determining soil microbial diversity patterns leading to a microscale biogeography. This study at- remains a formidable challenge for soil microbiologists tempts to localize specific microbial populations to dif- [54]. ferent fractions or compartments within the soil matrix. The vast majority of soil microbial analyses are Microbial populations associated with macroaggregates conducted on bulk soil samples, and often composited and inner- versus total-microaggregates of three diverse bulk soil samples, which averages localized heterogeneity soils were -
Identifying Stress-Tolerance Genes in Hyperarid Desert Soils Using Functional Metagenomics
Identifying stress-tolerance genes in hyperarid desert soils using functional metagenomics by Gideon Jacobus de Jager Submitted in partial fulfilment of the requirements for the degree Magister Scientiae In the Faculty of Natural & Agricultural Sciences Department of Genetics University of Pretoria Pretoria 12 February 2015 Supervisor: Prof. Don A. Cowan Co-supervisor: Dr René Sutherland Declaration I, Gideon Jacobus de Jager declare that the thesis, which I hereby submit for the degree Magister Scientiae at the University of Pretoria, is my own work and has not previously been submitted by me for a degree at this or any other tertiary institution. Signature: DdeJager Date: 12 February 2015 ii Dedication This thesis is dedicated to my mom, dad and Mari. Without your support and belief I would not have been able to reach this point. iii Acknowledgements I would like to thank the National Research Foundation (NRF) for providing me with a bursary so I could pursue this degree. The financial assistance of the NRF towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. Prof Don Cowan, thank you for your supervision and guidance during this research project and for always expecting the best from me and believing in my abilities. You are an inspiration in both science and life. Dr René Sutherland, thank you for your hands-on supervision and for your continuing support after your departure, despite having so much else on your plate! Dr Eloy Ferreras and Dr Eldie Berger, thank you for taking over from René as my go-to people when I needed advice about which experimental approaches to use and for your guidance in carrying these out. -
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. -
Colonization Patterns of Soil Microbial Communities in the Atacama Desert
Crits-Christoph et al. Microbiome 2013, 1:28 http://www.microbiomejournal.com/content/1/1/28 RESEARCH Open Access Colonization patterns of soil microbial communities in the Atacama Desert Alexander Crits-Christoph1, Courtney K Robinson1, Tyler Barnum1, W Florian Fricke2, Alfonso F Davila3, Bruno Jedynak4, Christopher P McKay3 and Jocelyne DiRuggiero1* Abstract Background: The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. Results: Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P <0.001) and that commu- nities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicro- biales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes indicated that most bacteria in the soil were in the form of vegetative cells. Integrating molecular data with climate and soil geo- chemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial com- munities’ diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P <0.001; UniFrac PCoA Spearman’s correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. -
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. -
Metagenomic SMRT Sequencing-Based Exploration Of
J. Microbiol. Biotechnol. (2017), 27(9), 1670–1680 https://doi.org/10.4014/jmb.1705.05008 Research Article Review jmb Metagenomic SMRT Sequencing-Based Exploration of Novel Lignocellulose-Degrading Capability in Wood Detritus from Torreya nucifera in Bija Forest on Jeju Island Han Na Oh1, Tae Kwon Lee2, Jae Wan Park1, Jee Hyun No2, Dockyu Kim3, and Woo Jun Sul1* 1Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 2Department of Environmental Engineering, Yonsei University, Wonju 26493, Republic of Korea 3Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea Received: May 4, 2017 Revised: June 12, 2017 Lignocellulose, composed mostly of cellulose, hemicellulose, and lignin generated through Accepted: June 19, 2017 secondary growth of woody plant, is considered as promising resources for biofuel. In order to First published online use lignocellulose as a biofuel, biodegradation besides high-cost chemical treatments were June 21, 2017 applied, but knowledge on the decomposition of lignocellulose occurring in a natural *Corresponding author environment is insufficient. We analyzed the 16S rRNA gene and metagenome to understand Phone: +82-31-670-4707; how the lignocellulose is decomposed naturally in decayed Torreya nucifera (L) of Bija forest Fax: +82-31-670-3108; E-mail: [email protected] (Bijarim) in Gotjawal, an ecologically distinct environment. A total of 464,360 reads were obtained from 16S rRNA gene sequencing, representing diverse phyla; Proteobacteria (51%), Bacteroidetes (11%) and Actinobacteria (10%). The metagenome analysis using single molecules real-time sequencing revealed that the assembled contigs determined originated from Proteobacteria (58%) and Actinobacteria (10.3%). -
Comparative Genomic Analysis of The
de Crécy-Lagard et al. Biology Direct 2012, 7:32 http://www.biology-direct.com/content/7/1/32 RESEARCH Open Access Comparative genomic analysis of the DUF71/ COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage Valérie de Crécy-Lagard1*, Farhad Forouhar2, Céline Brochier-Armanet3, Liang Tong2 and John F Hunt2 Abstract Background: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. Results: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. -
Studying the Microbiome of Cyanobacterial Biocrusts from Drylands and Its Functional Infuence on Biogeochemical Cycles
Studying the Microbiome of Cyanobacterial Biocrusts From Drylands and Its Functional Inuence on Biogeochemical Cycles Isabel Miralles ( [email protected] ) University of Almería Raúl Ortega University of Almería Maria Carmen Montero-Calasanz Newcastle University Research Article Keywords: desert biome, soil bacterial taxa, shotgun, bacterial functions, MG-RAST, MicrobiomeAnalyst Posted Date: February 24th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-252045/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/51 Abstract Background: Drylands are areas under continuous degradation and desertication largely covered by cyanobacterial biocrusts. Several studies have already shown that soil microorganisms play a fundamental role in the correct soil functioning. Nevertheless, little is known about the relationship taxonomy-function in arid soils and, in particular, in cyanobacterial biocrusts. An in-depth study of the taxonomic composition and the functions carried out by soil microorganisms in biogeochemical cycles was here carried out by using a shotgun metagenomic approach. Results: Metagenomic analysis carried out in this study showed a high taxonomic and functional similarity in both incipient and mature cyanobacterial biocrusts types with a dominance of Proteobacteria, Actinobacteria and Cyanobacteria. The predominant functional categories related to soil biogeochemical cycles were “carbon metabolism” followed by “phosphorus, nitrogen, sulfur, potassium and iron metabolism”. Reads involved in the metabolism of carbohydrates and respiration were the most abundant functional classes. In the N cycle dominated “ammonia assimilation” and “Nitrate and nitrite ammonication”. The major taxonomic groups also seemed to drive phosphorus and potassium cycling by the production of organic acids and the presence of extracellular enzymes and specialised transporters.