DOCSLIB.ORG

Cellulomonas Carbonis Sp. Nov., Isolated from Coal Mine Soil

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

%paper no. ije034934 charlesworth ref: ije034934& New Taxa - Actinobacteria International Journal of Systematic and Evolutionary Microbiology (2012), 62, 000–000 DOI 10.1099/ijs.0.034934-0 Cellulomonas carbonis sp. nov., isolated from coal mine soil Zunji Shi, Guosheng Luo and Gejiao Wang Correspondence State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Gejiao Wang Huazhong Agricultural University, Wuhan, Hubei 430070, PR China [email protected] or [email protected] A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain T26T, was isolated from subsurface soil of Tianjin coal mine, China. Colonies were yellow–white, convex, circular, smooth and non-transparent on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain T26T was closely related to members of the genus Cellulomonas and a member of the genus Actinotalea with 96.8–94.7 % and 96.7 % gene sequence similarities, T respectively. The peptidoglycan type of strain T26 was A4b, containing L-ornithine–D-glutamic acid as the interpeptide bridge. The cell-wall sugars were rhamnose, galactose, xylose and inositol. The major fatty acids (.10 %) were anteiso-C15 : 0 (33.6 %), anteiso-C15 : 1 A (22.1 %), C16 : 0 (14.4 %) and C14 : 0 (12.1 %). The predominant respiratory quinone was MK-9(H4) and the genomic DNA G+C content was 74.4 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol-mannosides and phosphatidylinositol. Comparison of phenotypic and phylogenetic characteristics between strain T26T and related organisms revealed that the new isolate represented a novel species of the genus Cellulomonas, for which the name Cellulomonas carbonis sp. nov. is proposed. The type strain is T26T (5CGMCC 1.10786T5KCTC 19824T5CCTCC AB2010450T). The family Cellulomonadaceae was originally defined by 2008), blood (Brown et al., 2005), cerebrospinal fluid Stackebrandt & Prauser (1991) and included the genera (Funke et al., 1995), a decayed elm tree (Rivas et al., 2004), Cellulomonas (18 species), Oerskovia (4 species) and sediment (Jones et al., 2005), air (Lee et al., 2008) and reed Actinotalea (1 species). The genus Cellulomonas was first periphyton (Rusznya´k et al., 2011), respectively. The described by Bergey et al. (1923) and later emended by typical characteristics of members of the genus Clark (1952) and Stackebrandt et al. (2006). At the time of Cellulomonas are Gram-positive, slender irregular rods writing, the 18 recognized species of the genus with cellulolytic activity, containing menaquinone MK- Cellulomonas were Cellulomonas flavigena (type species), 9(H4) as the predominant respiratory quinone, having C. biazotea, C. cellasea, C. fimi, C. gelida, C. uda (Bergey et anteiso-C15 : 0 and C16 : 0 as the major fatty acids al., 1923), C. hominis (Funke et al., 1995), C. humilata (Stackebrandt et al., 2006) and with a high DNA G+C (Collins & Pascual, 2000), C. iranensis, C. persica (Elberson content (68.5–76.0 mol%). Other diagnostic characteristics et al., 2000), C. xylanilytica (Rivas et al., 2004), C. terrae for the genus Cellulomonas include rhamnose (Rha) as the (An et al., 2005), C. denverensis (Brown et al., 2005), C. major cell-wall sugar in most of the strains, except for C. bogoriensis (Jones et al., 2005), C. composti (Kang et al., gelida, C. uda, C. composti (Kang et al., 2007) and C. 2007), C. aerilata (Lee et al., 2008), C. chitinilytica (Yoon et aerilata (Lee et al., 2008) (data are not available for C. al., 2008) and C. phragmiteti (Rusznya´k et al., 2011). These hominis, C. bogoriensis and C. phragmiteti). The diagnostic species were mostly isolated from soil (Collins & Pascual, diamino acid in position 3 of the peptide subunit of the 2000; Elberson et al., 2000; An et al., 2005). Others were peptidoglycan is ornithine (Orn) with the interpeptide isolated from compost (Kang et al., 2007; Yoon et al., bridge containing either D-aspartic acid (D-Asp) (for C. flavigena, C. persica, C. bogoriensis, C. iranensis and C. phragmiteti)orD-glutamic acid (D-Glu) (for all the other Abbreviations: DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PI, 13 species) (Stackebrandt et al., 2006). The polar lipids phosphatidylinositol; PIM, phosphatidylinositol mannosides; PL, have been reported for six species of the genus phospholipid; PGL, phosphoglycolipid. Cellulomonas and included diphosphatidylglycerol (DPG) The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene and phosphatidylglycerol (PG) (for C. aerilata and C. sequence of strain T26T is HQ702749. chitinilytica), PG (for C. bogoriensis), DPG, phosphatidy- Four supplementary figures are available with the online version of this linositol (PI) and phosphatidylethanolamine (PE) (for C. paper. composti), DPG and PI (for C. flavigena) and DPG, PG, PI, 034934 G 2012 IUMS Printed in Great Britain 1 %paper no. ije034934 charlesworth ref: ije034934& Cellulomonas carbonis sp. nov. Cells of strain T26T were Gram-staining-positive, aerobic, in this study and showed very similar polar lipids to strain motile and rod-shaped. Colonies were yellow–white, T26T (Fig. S4). The polar lipid data and 16S rRNA gene convex, circular, smooth and non-transparent after 3 days sequence phylogenies of both strain T26T and C. bogoriensis incubation on R2A agar at 28 uC. The strain grew on R2A DSM 16987T were consistent with their assignment to the agar, nutrient agar, full-strength TSA and LB agar, but did genus Cellulomonas. The DNA G+C content of strain not grow on MacConkey agar. Detailed results of the T26T was 74.4 mol%. The cell-wall peptidoglycan type was morphological, physiological and biochemical character- A4b, containing L-Orn–D-Glu. The cell-wall sugars were istics are given in the species description. A scanning rhamnose (80.9 %), galactose (3.3 %), xylose (5.3 %) and electron and transmission electron micrographs showing inositol (6.3 %). All of these results for strain T26T were the general morphology of cells of strain T26T are available very similar to those of the type species of the genus as Fig. S1a and b, respectively. The main phenotypic Cellulomonas, C. flavigena DSM 20109T, and to other differences between strain T26T and closely related type species of the genus. Strain T26T could be differentiated strains are shown in Table 1. from members of the genera Actinotalea and Oerskovia on T the basis of differences in the respiratory quinone [MK- The 1442 bp 16S rRNA gene sequence of strain T26 was ] analysed to determine the phylogenetic position of the 9(H4) vs MK-10(H4) and peptidoglycan type (L-Orn–D- novel strain. Strain T26T shared gene sequence similarities Glu vs L-Lys–L-ThrrD-Asp or L-Lys–L-ThrrD-Glu), of 96.8–94.7 % with other species of the genus respectively. Cellulomonas and a member of the genus Actinotalea. On the basis of the close relationship and distinctive T Strain T26 showed the highest 16S rRNA gene sequence phenotypic and phylogenetic differences between strain T similarities with C. cellasea DSM 20118 (96.8 %), A. T26T and other closely related species, it is proposed that T T fermentans DSM 3133 (96.7 %), C. hominis DMMZ CE40 strain T26T represents a novel species of Cellulomonas, with T (96.6 %), C. denverensis W6929 (96.5 %) and C. the name Cellulomonas carbonis sp. nov. bogoriensis 69B4T (96.4 %). A phylogenetic tree constructed using the neighbour-joining algorithm showed that strain Description of Cellulomonas carbonis sp. nov. T26T was always very closely associated with C. bogoriensis 69B4T; other species of the genus Cellulomonas fell into Cellulomonas carbonis (car.bo9nis. L. gen. n. carbonis of other nearby clusters, but all in a large cluster (Fig. 1). This coal, of charcoal). cluster also included four strains of the genus Oerskovia T T Cells are Gram-positive-staining, aerobic, motile and rod- and Paraoerskovia marina CTT-37 , however, strain T26 shaped (0.5–0.862.0–2.4 mm). Colonies are yellow–white, was distinct from members of the genus Oerskovia based convex, circular, smooth and non-transparent after on the peptidoglycan structure (see below). In addition, P. u T T incubation on R2A agar at 28 C for 3 days. Grows on marina CTT-37 could be distinguised from strain T26 on R2A agar, nutrient agar, full-strength TSA and LB agar, but the basis of the cellular fatty acid content and peptidogly- does not grow on MacConkey agar. Temperature range for can structure (Khan et al., 2009). The maximum- growth is 4–45 uC, and optimal temperature for growth is parsimony and the maximum-likelihood trees (Fig. S2a, 28 uC. Growth occurs with NaCl concentrations in the b) also supported the phylogenetic position obtained with range 0–7 % and with pH 6–10 (optimum, pH 7.0). the neighbour-joining algorithm. Catalase-positive and oxidase-negative. Positive in tests Strain T26T gave a negative result in tests for urease activity for b-galactosidase activity but negative result for arginine but a positive result for the hydrolysis of carboxymethyl dihydrolase and urease. Hydrolyses carboxymethyl cel- cellulose and aesculin. The major cellular fatty acids lulose, starch, gelatin, aesculin, but not DNA, casein, (.10 %) were anteiso-C15 : 0 (33.6 %), anteiso-C15 : 1 A tyrosine or Tween 80. Does not produce indole from (22.1 %), C16 : 0 (14.4 %) and C14 : 0 (12.1 %) on R2A tryptophan, but H2S is produced from cysteine and NH3 is medium (details are shown in Table 2). The fatty acid produced from peptone. Positive in tests for nitrate profile of the novel strain was very similar to that of the reduction but negative result in methyl-red and Voges– type species of the genus Cellulomonas, C. flavigena DSM Proskauer tests. Assimilates D-glucose, L-arabinose, man- T 20109 . The major respiratory quinone was MK-9(H4) nose, N-acetylglucosamine, maltose, gluconate, sucrose, (Fig. S3), which was the same as that of members of the glycogen, salicin, melibiose, D-sorbitol, xylose, lactose, D- genus Cellulomonas and was different from A.
Recommended publications
  • Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico

    Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico

    bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga ,​ Annie Espinal-Centeno ,​ Shamayim Martinez-Sanchez ,​ Juan ​ ​ 1 2 ​ 1,3 ​ Caballero-Pérez ,​ Luis D. Alcaraz *​ & Alfredo Cruz-Ramirez *.​ ​ ​ ​ 1 Molecular​ & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio​ de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela​ de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ​ ​ ​ ● ​Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. ​ During colonial times they were renamed with the antillan word maguey. This was changed ​ ​ again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several ​ Mexican prehispanic cultures, Agave species were not only considered as crops, but also part ​ of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli.
  • Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample

    Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample

    geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated.
  • A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production

    A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production

    Downloaded from orbit.dtu.dk on: Dec 20, 2017 A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production Baggesen, Claus; Gjermansen, Claes; Brandt, Anders Bøving Publication date: 2014 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Baggesen, C., Gjermansen, C., & Brandt, A. B. (2014). A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production. Technical University of Denmark, Department of Chemical and Biochemical Engineering. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production Claus Baggesen Ph.D. Thesis June 2014 A Study of Microalgal Symbiotic Communities with the Aim to Increase Biomass and Biodiesel Production Claus Baggesen Ph.D. Thesis June 2014 1 Copyright©: Claus Baggesen June 2014 Address: CAPEC-PROCESS Computer Aided Process Engineering/ Process Engineering and Technology center Department of Chemical and Biochemical Engineering Technical University of Denmark Building 229 DK-2800 Kgs.
  • Actinotalea Ferrariae Sp. Nov., Isolated from an Iron Mine, and Emended Description of the Genus Actinotalea

    Actinotalea Ferrariae Sp. Nov., Isolated from an Iron Mine, and Emended Description of the Genus Actinotalea

    %paper no. ije048512 charlesworth ref: ije048512& New Taxa - Actinobacteria International Journal of Systematic and Evolutionary Microbiology (2013), 63, 000–000 DOI 10.1099/ijs.0.048512-0 Actinotalea ferrariae sp. nov., isolated from an iron mine, and emended description of the genus Actinotalea Yanzhi Li, Fang Chen, Kun Dong and Gejiao Wang Correspondence State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Gejiao Wang Huazhong Agricultural University, Wuhan, Hubei 430070, PR China [email protected] or [email protected] ; A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, designated strain CF5-4T, was isolated from iron mining powder. 16S rRNA gene sequence analysis grouped strain CF5-4T in a single cluster with Actinotalea fermentans DSM 3133T (97.6 % similarity). The major fatty acids T (.5 %) of strain CF5-4 were anteiso-C15 : 0, anteiso-C15 : 1 A, C16 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The predominant respiratory quinone was MK-10(H4) and the genomic DNA G+C content was 74.7 mol%. The major polar lipids were diphosphatidylglycerol and one unidentified phosphoglycolipid. The peptidoglycan type of strain CF5-4T was A4b, containing L-Orn–D-Ser–D-Asp. The cell-wall sugars were rhamnose, fucose, mannose and galactose. The results of DNA–DNA hybridization in combination with the comparison of phenotypic and phylogenetic characteristics among strain CF5-4T and related micro-organisms revealed that the isolate represents a novel species of the genus Actinotalea, for which the name Actinotalea ferrariae sp. nov. is proposed. The type strain is CF5-4T (5KCTC 29134T5CCTCC AB2012198T).
  • Data of Read Analyses for All 20 Fecal Samples of the Egyptian Mongoose

    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.
  • International Journal of Advanced Research in Biological Sciences

    International Journal of Advanced Research in Biological Sciences

    Int. J. Adv. Res. Biol. Sci. (2017). 4(12): 292-299 International Journal of Advanced Research in Biological Sciences ISSN: 2348-8069 www.ijarbs.com DOI: 10.22192/ijarbs Coden: IJARQG(USA) Volume 4, Issue 12 - 2017 Research Article DOI: http://dx.doi.org/10.22192/ijarbs.2017.04.12.032 Taxonomic characterization of the chitinolytic actinomycete Cellulomonas chitinilytica strain HwAC11 Gamal M. El-Sherbiny1, Osama M. Darwesh2*, Ahmad S. El-Hawary1 1Botany and Microbiology Department, Faculty of Science (Boys); Al-Azhar University, Nasr City, Cairo, Egypt. 2Agricultural Microbiology Department, National Research Centre, Cairo, Egypt. *Corresponding author: E-mail: [email protected] Mobile: +201155265558, Fax: +20237601036 Abstract Chitinases apply in several useful fields such as agriculture, food industries and environmental applications. Because it helps degradation of fungal cell walls containing chitin and thus accelerates protoplast formation. The alkaliphilic action-bacterial strain HwAC11 was isolated from compost after examine 99 different samples. This isolate exhibited good growth on medium containing chitin as sole carbon source. Macro- and micro–morphological characteristics, enzyme activities, physiological and biochemical properties of the isolate were investigated. It was concluded that the strain HwAC11 is a member of the genus Cellulomonas. The results were compared with the taxonomic characteristics of Cellulomonas members and it was found to be similar to those of Cellulomonas chitinilytica. The phylogenetic analysis based on 16s ribosomal RNA gene sequence confirmed the phenotypic results and the sequences were deposited in gene bank under Cellulomonas chitinilytica strain HwAC11with accession number MH050787. The strain HwAC11 displayed intensive chitinase activity under alkaline conditions. It leads to apply this strain in agriculture field, especially as biological control agent for pathogenic fungi and harmful nematodes.
  • Proposed Minimal Standards for Describing New Genera and Species of the Suborder Micrococcineae

    Proposed Minimal Standards for Describing New Genera and Species of the Suborder Micrococcineae

    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1823–1849 DOI 10.1099/ijs.0.012971-0 Proposed minimal standards for describing new genera and species of the suborder Micrococcineae Peter Schumann,1 Peter Ka¨mpfer,2 Hans-Ju¨rgen Busse 3 and Lyudmila I. Evtushenko4 for the Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, P. Schumann 38124 Braunschweig, Germany [email protected] 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t, 35392 Giessen, Germany 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria 4All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Moscow Region 142290, Russia The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names. INTRODUCTION Aureobacterium and Rothia/Stomatococcus) and one pair of homotypic synonyms (Pseudoclavibacter/Zimmer- The suborder Micrococcineae was established by mannella) (Table 1 and http://www.the-icsp.org/taxa/ Stackebrandt et al.
  • Abstract Tracing Hydrocarbon

    Abstract Tracing Hydrocarbon

    ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.
  • Cellulomonas Gilvus Sp. Nov

    Cellulomonas Gilvus Sp. Nov

    The Genome Sequences of Cellulomonas fimi and ‘‘Cellvibrio gilvus’’ Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of ‘‘Cellvibrio gilvus’’ to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp. nov Melissa R. Christopherson1., Garret Suen1., Shanti Bramhacharya1, Kelsea A. Jewell1, Frank O. Aylward1,2, David Mead2,3, Phillip J. Brumm2,4* 1 Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America, 2 Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America, 3 Lucigen, Middleton, Wisconsin, United States of America, 4 C5-6 Technologies, Middleton, Wisconsin, United States of America Abstract Actinobacteria in the genus Cellulomonas are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the Cellulomonas fimi ATCC 484T. For comparative purposes, we also sequenced the genome of the aerobic cellulolytic ‘‘Cellvibrio gilvus’’ ATCC 13127T. An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that ‘‘Cellvibrio gilvus’’ belongs to the genus Cellulomonas. We thus propose to assign ‘‘Cellvibrio gilvus’’ to the genus Cellulomonas. A comparative genomics analysis between these two Cellulomonas genome sequences and the recently completed genome for Cellulomonas flavigena ATCC 482T showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose.
  • The Gastric Caeca of Pentatomids As a House for Actinomycetes Tiago D Zucchi1,2*, Simone S Prado2,3 and Fernando L Cônsoli2*

    The Gastric Caeca of Pentatomids As a House for Actinomycetes Tiago D Zucchi1,2*, Simone S Prado2,3 and Fernando L Cônsoli2*

    Zucchi et al. BMC Microbiology 2012, 12:101 http://www.biomedcentral.com/1471-2180/12/101 RESEARCH ARTICLE Open Access The gastric caeca of pentatomids as a house for actinomycetes Tiago D Zucchi1,2*, Simone S Prado2,3 and Fernando L Cônsoli2* Abstract Background: Microbes are extensively associated with insects, playing key roles in insect defense, nutrition and reproduction. Most of the associations reported involve Proteobacteria. Despite the fact that Actinobacteria associated with insects were shown to produce antibiotic barriers against pathogens to the hosts or to their food and nutrients, there are few studies focusing on their association with insects. Thus, we surveyed the Actinobacteria diversity on a specific region of the midgut of seven species of stinkbugs (Hemiptera: Pentatomidae) known to carry a diversity of symbiotically-associated Proteobacteria. Results: A total of 34 phylotypes were placed in 11 different Actinobacteria families. Dichelops melacanthus held the highest diversity with six actinobacteria families represented by nine phylotypes. Thyanta perditor (n =7),Edessa meditabunda (n =5),Loxa deducta (n =4)andPellaea stictica (n = 3) were all associated with three families. Piezodorus guildini (n =3)andNezara viridula (n = 3) had the lowest diversity, being associated with two (Propionibacteriaceae and Mycobacteriaceae) and one (Streptomyceataceae) families, respectively. Corynebacteriaceae and Mycobacteriaceae were the most common families with phylotypes from three different insect species each one. Conclusions: Many phylotypes shared a low 16S rRNA gene similarity with their closest type strains and formed new phyletic lines on the periphery of several genera. This is a strong indicative that stinkbug caeca can harbor new species of actinobacteria, which might be derived from specific associations with the species of stinkbugs studied.
  • Microbial Community Structure Analysis in Acer Palmatum Bark and Isolation of Novel Bacteria IAD-21 of the Phylum Abditibacteriota (Former Candidate Division FBP)

    Microbial Community Structure Analysis in Acer Palmatum Bark and Isolation of Novel Bacteria IAD-21 of the Phylum Abditibacteriota (Former Candidate Division FBP)

    Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the phylum Abditibacteriota (former candidate division FBP) Kazuki Kobayashi1 and Hideki Aoyagi1,2 1 Division of Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 2 Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan ABSTRACT Background: The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. Methods: In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. Results: At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and Submitted 2 February 2019 Abditibacteriota, which contain many uncultured microbial species, existed in the Accepted 12 September 2019 A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, Published 29 October 2019 some genera belonging to the phyla mentioned were detected. A total of 70 isolates Corresponding author could be isolated and cultured using the low-nutrient agar media DR2A and Hideki Aoyagi, PE03.
  • A Review on Bacterial Contribution to Lignocellulose Breakdown Into Useful Bio-Products

    A Review on Bacterial Contribution to Lignocellulose Breakdown Into Useful Bio-Products

    International Journal of Environmental Research and Public Health Review A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products Ogechukwu Bose Chukwuma , Mohd Rafatullah * , Husnul Azan Tajarudin and Norli Ismail Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; [email protected] (O.B.C.); [email protected] (H.A.T.); [email protected] (N.I.) * Correspondence: [email protected] or [email protected]; Tel.: +60-4-653-2111; Fax: +60-4-653-6375 Abstract: Discovering novel bacterial strains might be the link to unlocking the value in lignocel- lulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent Citation: Chukwuma, O.B.; scaling up industrially still pose challenges to their adoption. However, recent studies have seen Rafatullah, M.; Tajarudin, H.A.; the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using Ismail, N. A Review on Bacterial bacterial strains to breakdown lignocellulose into its major polymers and then to useful products Contribution to Lignocellulose Breakdown into Useful Bio-Products.