DOCSLIB.ORG

A Report of 34 Unrecorded Bacterial Species in Korea, Belonging to the Actinobacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Report of 34 Unrecorded Bacterial Species in Korea, Belonging to the Actinobacteria Journal of Species Research 6(1):1-14, 2017 A report of 34 unrecorded bacterial species in Korea, belonging to the Actinobacteria Kwan Su Ko1, Chang-Jun Cha2, Wan-Taek Im3, Seung-Bum Kim4, Chi-Nam Seong5, Jin-Woo Bae6, Kwangyeop Jahng7, Jang-Cheon Cho8, Ki-seong Joh9 and Soon Dong Lee1,* 1Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea 2Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 3Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea 4Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Republic of Korea 5Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 6Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea 7Department of Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea 8Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea 9Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea *Correspondent: [email protected] As a subset study to discover indigenous prokaryotic species in Korea in 2014, a total of 34 bacterial strains assigned to the phylum Actinobacteria were isolated from various environmental samples col- lected from activate sludge, biotite, freshwater, gut of marine organisms, mud flat, sediment, soil, spent mushroom compost and sea water. On the basis of high 16S rRNA gene sequence similarity and a tight phylogenetic association with the closest species, it was revealed that each strain was assigned to in- dependent and previously described bacterial species, with the exception of one isolate. There is no offi­ cial report that these 34 species included in the phylum Actinobacteria have been described in Korea: 6 species of 5 genera in the order Corynebacteriales, 1 species of 1 genus in the order Frankiales, 2 spe- cies of 2 genera in the Micromonosporales, 14 species of 10 genera in Micrococcales, 2 species of 2 genera in the Propionibacteriales, 1 species of 1 genus in the Pseudonocardiales, 4 species of 2 genera in the Streptomycetales, 2 species of 2 genera in the Streptosporangiales and 1 species of 1 genus in the Solirubrobacterales. Gram reaction, cell and colony morphology, pigmentation, physiological charac- teristics, isolation sources and strain IDs are described in the section of species description. Keywords: 16S rRNA gene, Actinobacteria, indigenous prokaryotic species, unrecorded species Ⓒ 2017 National Institute of Biological Resources DOI:10.12651/JSR.2017.6.1.001 INTRODUCTION insertions and deletions in certain proteins, and charac- teristic gene rearrangements (Goodfellow and Fiedler, The recently proposed phylum Actinobacteria (Lud- 2010) and encompasses six classes Actinobacteria, wig et al., 2012) is composed of aerobic, Gram-stain- Acidimicrobiia, Coriobacteriia, Nitriliruptoria, ing-positive bacteria that have high-G+C contents in Rubrobacteria and Thermoleophilia (Ludwig et al., their genomic DNAs. They exhibit a very wide range 2012). of morphology and form cocci, rods or fragmented or The class Actinobacteria is composed of 15 orders branched hyphae depending on species. Some of them Actinomycetales, Actinopolysporales, Bifidobacteriales, produce resting structure such as spores and sporangium Catenulisporales, Corynebacteriales, Frankiales, on permanent, well-developed mycelium (Goodfellow Glycomycetales, Jiangellales, Kineosporiales, and Cross, 1984; Ensign, 1992). Micromonosporales, Micrococcales, Propionibacteriales, The phylum Actinobacteria is well supported by anal- Pseudonocardiales, Streptomycetales and Streptosporangiales. yses of the 16S and 23S rRNA, presence of conserved Members of this class have been received considerable 2 JOURNAL OF SPECIES RESEARCH Vol. 6, No. 1 concerns as the source of antibiotics since the discov- sequencing of the 16S rRNA gene were performed us- ery of actinomycin from actinomyctes (Waksman and ing the standard procedures described elsewhere. The Woodruff, 1940) and widely distributed in natural en- 16S rRNA gene sequences of the strains assigned to the vironment such as soil, fresh or sea water, manure and phylum Actinobacteria were compared with the corre- compost where contribute significantly to turnover of sponding sequences collected from and the EzTaxon-e complex biopolymers as the decomposer (Williams et server (Kim et al., 2012) and public database. Multiple al., 1984). alignments of the sequences were performed using the The class Thermoleophila contains two orders Clustal_X program (Thompson et al., 1997) and opti- Solirubrobacterales and Thermoleophilales; the for- mized manually according to the secondary structure of mer consists of the families Solirubrobacteraceae, Escheichia coli. Evolutionary distances were calculated Conexibacteraceae and Patulibacteraceae, while the using the correction of Jukes & Cantor (1969). Phylo- latter comprises the family Thermoleophilaceae (Reddy genetic analyses were performed by using the neigh- and Garcia-Pichel, 2009; Ludwig et al., 2012). bor-joining (Saitou and Nei, 1987), maximum-parsimo- We collected diverse environmental samples for bac- ny (Fitch, 1971) and maximum-likelihood (Felsenstein, terial isolation and recovered a great number of indige- 1981) treeing algorithms contained in the PHYLIP pack- nous bacterial species in Korea by the research program age (Felsenstein, 2008). A neighbour-joining tree was supported by NIBR (National Institute of Biological drawn with bootstrap values based on 1,000 replications Resources) in 2014. The aim of present study is to deal (Felsenstein, 1985). with the classification and identification of bacterial strains assigned to the phylum Actinobacteria which have not been previously reported in Korea and to describe RESULTS AND DISCUSSION 34 unrecorded bacterial species belonging to 9 orders of the two classes Actinobacteria and Thermoleophilia. The 34 strains were found to belong to the two class- es Actinobacteria (33 strains) and Thermoleophila (1 strains) in the phylum Actinobacteria. Among them, 33 MATERIALS AND METHODS strains were distributed in 8 orders of the Actinobacteria; 6 strains for the order Corynebacteriales, 1 strain for A total of 34 bacterial strains which were assigned to the Frankiales, 2 strains for the Micromonosporales, the phylum Actinobacteria were isolated from various 14 strains for the Micrococcales, 2 strain for the environmental samples collected from activate sludge, Propionibacteriales, 1 strain for the Pseudonocardiales, biotite, freshwater, gut of marine organisms, mud flat, 5 strains for the Streptomycetales and 2 strains for the sediment, soil, spent mushroom compost and sea water Streptosporangiales. One strain which belonged to the class (Table 1). Treatment of environmental samples and Thermoleophila was assigned to the Solirubrobacterales bacterial isolation was done independently in several (Table 1). These strains were Gram-staining-positive and laboratories. The pure cultures of isolated bacteria were chemoheterotrophic and were morphologically charac- grown on diverse culture media including R2A agar terized by the formation of cocci, rods or mycelia (Fig. 1). (BD), marine agar 2216 (MA; BD), tryptic soy agar The strains of the order Corynebacteriales (Fig. 2) were (TSA; BD), nutrient agar (NA; BD), ISP (International assigned to 5 genera of 3 families: Dietzia (1 species) Streptomyces Project) 2 and 4 media (Shirling & Got- the family Dietziaceae, Mycobacterium (2 species) of tlieb, 1966) at 15-30°C for 2-7 day, depending on the the Mycobacteriaceae, Gordonia (1 species), Nocardia (1 strains. The designated strain IDs, isolation sources, cul- species) and Rhodococcus (1 species) of the Nocardiaceae. ture media, and incubation conditions are summarized in In general, members of the genus Nocardia are morpho- Table 1. The pure cultures were maintained as 10-20% logically characterized by fragmentation of mycelium, glycerol suspensions at -80°C and lyophilized ampoules. in contrast to other genera of the family Nocardiaceae Cell morphology was observed by either transmission having coccoid- or rod-shaped morphology (Good- or scanning electron microscopy. Gram staining was fellow and Maldonado, 2012). The Frankiales strain performed using a Gram-staining kit according to the in- (Fig. 2) was affiliated to the genus Geodermatophilus structions of the manufacturer. Colony morphology and (1 species) of the family Geodermatophilaceae. The 2 pigmentation were observed on agar plates with cells Micromonosporales strains were distributed to two gen- grown to stationary phase. Utilization of carbon sourc- era Actinocatenispora (1 species) and Micromonospora es and some biochemical properties were examined by (1 species) of the family Micromonosporaceae, which using API 20NE galleries (bioMérieux) according to the were morphologically characterized by the formation of manufacturer’s instructions. mycelia (Fig. 1). The phylogenetic relationships between Bacterial DNA extraction, PCR amplification and the Micrococcales strains and their closest relatives are February 2017 Table 1. Summary of the isolated strains belonging to the Actinobacteria and their taxonomic affiliations. Most closely related species Similarity Isolation Incubation Order Family Genus Strain ID NIBR ID Medium (Name of type strain) (%) source conditions Class Actinobacteria Corynebacteriales Dietziaceae Dietzia IMCC 12370
Load more

Recommended publications
  • Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
    TAXONOMIC DESCRIPTION Zhang et al., Int J Syst Evol Microbiol 2018;68:47–51 DOI 10.1099/ijsem.0.002426 Arthrobacter paludis sp. nov., isolated from a marsh Qi Zhang,1 Mihee Oh,1 Jong-Hwa Kim,1 Rungravee Kanjanasuntree,1 Maytiya Konkit,1 Ampaitip Sukhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % T similarity). Strain CAU 9143 contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (L-Lys–D-Glu2) and the major cellular fatty T acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143 and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T).
    [Show full text]
  • S41598-018-29442-2 1
    www.nature.com/scientificreports OPEN Actinobacteria associated with Chinaberry tree are diverse and show antimicrobial activity Received: 28 February 2018 Ke Zhao1, Jing Li1, Meiling Shen1, Qiang Chen1, Maoke Liu2, Xiaolin Ao1, Decong Liao1, Accepted: 10 July 2018 Yunfu Gu1, Kaiwei Xu1, Menggen Ma1, Xiumei Yu1, Quanju Xiang1, Ji Chen1, Xiaoping Zhang1 & Published: xx xx xxxx Petri Penttinen 3,4 Many actinobacteria produce secondary metabolites that include antimicrobial compounds. Since most of the actinobacteria cannot be cultivated, their antimicrobial potential awaits to be revealed. We hypothesized that the actinobacterial endophyte communities inside Melia toosendan (Chinaberry) tree are diverse, include strains with antimicrobial activity, and that antimicrobial activity can be detected using a cultivation independent approach and co-occurrence analysis. We isolated and identifed actinobacteria from Chinaberry, tested their antimicrobial activities, and characterized the communities using amplicon sequencing and denaturing gradient gel electrophoresis as cultivation independent methods. Most of the isolates were identifed as Streptomyces spp., whereas based on amplicon sequencing the most abundant OTU was assigned to Rhodococcus, and Tomitella was the most diverse genus. Out of the 135 isolates, 113 inhibited the growth of at least one indicator organism. Six out of the 7577 operational taxonomic units (OTUs) matched 46 cultivated isolates. Only three OTUs, Streptomyces OTU4, OTU11, and OTU26, and their corresponding isolate groups were available for comparing co-occurrences and antimicrobial activity. Streptomyces OTU4 correlated negatively with a high number of OTUs, and the isolates corresponding to Streptomyces OTU4 had high antimicrobial activity. However, for the other two OTUs and their corresponding isolate groups there was no clear relation between the numbers of negative correlations and antimicrobial activity.
    [Show full text]
  • Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
    A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp.
    [Show full text]
  • Successful Drug Discovery Informed by Actinobacterial Systematics
    Successful Drug Discovery Informed by Actinobacterial Systematics Verrucosispora HPLC-DAD analysis of culture filtrate Structures of Abyssomicins Biological activity T DAD1, 7.382 (196 mAU,Up2) of 002-0101.D V. maris AB-18-032 mAU CH3 CH3 T extract H3C H3C Antibacterial activity (MIC): S. leeuwenhoekii C34 maris AB-18-032 175 mAU DAD1 A, Sig=210,10 150 C DAD1 B, Sig=230,10 O O DAD1 C, Sig=260,20 125 7 7 500 Rt 7.4 min DAD1 D, Sig=280,20 O O O O Growth inhibition of Gram-positive bacteria DAD1 , Sig=310,20 100 Abyssomicins DAD1 F, Sig=360,40 C 75 DAD1 G, Sig=435,40 Staphylococcus aureus (MRSA) 4 µg/ml DAD1 H, Sig=500,40 50 400 O O 25 O O Staphylococcus aureus (iVRSA) 13 µg/ml 0 CH CH3 300 400 500 nm 3 DAD1, 7.446 (300 mAU,Dn1) of 002-0101.D 300 mAU Mode of action: C HO atrop-C HO 250 atrop-C CH3 CH3 CH3 CH3 200 H C H C H C inhibitior of pABA biosynthesis 200 Rt 7.5 min H3C 3 3 3 Proximicin A Proximicin 150 HO O HO O O O O O O O O O A 100 O covalent binding to Cys263 of PabB 100 N 50 O O HO O O Sea of Japan B O O N O O (4-amino-4-deoxychorismate synthase) by 0 CH CH3 CH3 CH3 3 300 400 500 nm HO HO HO HO Michael addition -289 m 0 B D G H 2 4 6 8 10 12 14 16 min Newcastle Michael Goodfellow, School of Biology, University Newcastle University, Newcastle upon Tyne Atacama Desert In This Talk I will Consider: • Actinobacteria as a key group in the search for new therapeutic drugs.
    [Show full text]
  • Genome-Based Classification of The
    Antonie van Leeuwenhoek https://doi.org/10.1007/s10482-021-01564-0 (0123456789().,-volV)( 0123456789().,-volV) ORIGINAL PAPER Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune Ali B. Kusuma . Imen Nouioui . Michael Goodfellow Received: 26 January 2021 / Accepted: 18 March 2021 Ó The Author(s) 2021 Abstract A polyphasic study was designed to fatty acids. Whole-genome sequences generated for determine the taxonomic provenance of a strain, the isolate and Streptomyces albiflaviniger DSM isolate PRKS01-29T, recovered from an Indonesian 41598T and Streptomyces javensis DSM 41764T were sand dune and provisionally assigned to the Strepto- compared with phylogenetically closely related myces violaceusniger clade. Genomic, genotypic and strains, the isolate formed a branch within the S. phenotypic data confirmed this classification. The violaceusniger clade in the resultant phylogenomic isolate formed an extensively branched substrate tree. Whole-genome sequences data showed that mycelium which carried aerial hyphae that differen- isolate PRKS01-29T was most closely related to the tiated into spiral chains of rugose ornamented spores, S. albiflaviniger strain but was distinguished from the contained LL-as the wall diaminopimelic acid, MK-9 latter and from other members of the clade using (H6,H8) as predominant isoprenologues, phos- combinations of phenotypic properties and average phatidylethanolamine as the diagnostic phospholipid nucleotide identity and digital DNA:DNA hybridiza- and major proportions of saturated, iso- and anteiso- tion scores. Consequently, it is proposed that isolate PRKS01-29T (= CCMM B1303T = ICEBB-02T- = NCIMB 15210T) should be classified in the genus Supplementary Information The online version contains Streptomyces as Streptomyces sabulosicollis sp.
    [Show full text]
  • Corynebacterium Sp.|NML98-0116
    1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album
    [Show full text]
  • 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.
    [Show full text]
  • Pdfفایلی 488.72 K
    طؤظاري زانكؤي طةرميان Journal of Garmian University جملة جامعة كرميان http://garmian.edu.krd https://doi.org/10.24271/garmian.164 Isolation and identification of some uncommon bacterial species isolated from different clinical sample Rahman K. Faraj1 and Muhamed N. Maarof 2 1Kalar general hospital/2College of education for pure science-Tikrit university Abstract There are many opportunistic bacterial species that are uncommon and infrequently exist in clinical specimen, most of them are difficult to routine identification, even some of them are poorly documented in clinical specimen. also had no less role in the coordinates of the disease than common bacterial species. Six hundred and fifty samples were collected from patients attending to some hospitals in Sulaimanya City and Kalar General Hospital during the period from October 2015 to November 2016. Samples were firstly cultured on different media in order to isolate and identify bacterial isolates according to cultural characteristics, morphological features and biochemical reactions in addition to Vitek 2 system for identifying uncommon and infrequent isolates. The identification and susceptibility test were performed in Kalar General Hospital. Isolated 286(44%) bacterial strains from different clinical samples, 125 of them were identified by Vitek 2 automated system, while 23(8%) of isolates were considered as uncommon bacterial species. The antimicrobial susceptibility of uncommon isolates, showed significant variation against twenty four antibiotics. Four isolates; Acinatobacter
    [Show full text]
  • Using Community Analysis to Explore Bacterial Indicators for Disease
    www.nature.com/scientificreports OPEN Using community analysis to explore bacterial indicators for disease suppression of tobacco Received: 08 February 2016 Accepted: 20 October 2016 bacterial wilt Published: 18 November 2016 Xiaojiao Liu, Shuting Zhang, Qipeng Jiang, Yani Bai, Guihua Shen, Shili Li & Wei Ding Although bacterial communities play important roles in the suppression of pathogenic diseases and crop production, little is known about the bacterial communities associated with bacterial wilt. Based on 16S rRNA gene sequencing, statistical analyses of microbial communities in disease-suppressive and disease-conducive soils from three districts during the vegetation period of tobacco showed that Proteobacteria was the dominant phylum, followed by Acidobacteria. Only samples from September were significantly correlated to disease factors. Fifteen indicators from taxa found in September (1 class, 2 orders, 3 families and 9 genera) were identified in the screen as being associated with disease suppression, and 10 of those were verified for potential disease suppression in March.Kaistobacter appeared to be the genus with the most potential for disease suppression. Elucidating microbially mediated natural disease suppression is fundamental to understanding microecosystem responses to sustainable farming and provides a possible approach for modeling disease-suppressive indicators. Here, using cluster analysis, MRPP testing, LEfSe and specific filters for a Venn diagram, we provide insight into identifying possible indicators of disease
    [Show full text]
  • Diversity and Taxonomic Novelty of Actinobacteria Isolated from The
    Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Alvaro S. Villalobos Kiel 2018 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: Prof. Dr. Ute Hentschel Humeida Tag der mündlichen Prüfung: Zum Druck genehmigt: 03.12.2018 gez. Prof. Dr. Frank Kempken, Dekan Table of contents Summary .......................................................................................................................................... 1 Zusammenfassung ............................................................................................................................ 2 Introduction ...................................................................................................................................... 3 Geological and climatic background of Atacama Desert ............................................................. 3 Microbiology of Atacama Desert ................................................................................................. 5 Natural products from Atacama Desert ........................................................................................ 9 References .................................................................................................................................. 12 Aim of the thesis ...........................................................................................................................
    [Show full text]
  • Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile
    ORIGINAL RESEARCH published: 19 July 2016 doi: 10.3389/fmicb.2016.01135 Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile Agustina Undabarrena 1, Fabrizio Beltrametti 2, Fernanda P. Claverías 1, Myriam González 1, Edward R. B. Moore 3, 4, Michael Seeger 1 and Beatriz Cámara 1* 1 Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile, 2 Actygea S.r.l., Gerenzano, Italy, 3 Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, 4 Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Edited by: Bioprospecting natural products in marine bacteria from fjord environments are attractive Learn-Han Lee, due to their unique geographical features. Although, Actinobacteria are well known Monash University Malaysia Campus, Malaysia for producing a myriad of bioactive compounds, investigations regarding fjord-derived Reviewed by: marine Actinobacteria are scarce. In this study, the diversity and biotechnological Atte Von Wright, potential of Actinobacteria isolated from marine sediments within the Comau University of Eastern Finland, Finland fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. Polpass Arul Jose, Central Salt and Marine Chemicals The 16S rRNA gene sequences revealed that members phylogenetically related Research Institute, India to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, *Correspondence: Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were Beatriz Cámara [email protected] present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media.
    [Show full text]
  • 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.
    [Show full text]