DOCSLIB.ORG

Massilia Yuzhufengensis Sp. Nov., Isolated from an Ice Core

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Massilia Yuzhufengensis Sp. Nov., Isolated from an Ice Core International Journal of Systematic and Evolutionary Microbiology (2013), 63, 1285–1290 DOI 10.1099/ijs.0.042101-0 Massilia yuzhufengensis sp. nov., isolated from an ice core Liang Shen,1 Yongqin Liu,1 Ninglian Wang,2 Tandong Yao,1 Nianzhi Jiao,3 Hongcan Liu,4 Yuguang Zhou,4 Baiqing Xu1 and Xiaobo Liu1 Correspondence 1Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, PR China Yongqin Liu 2Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of [email protected] Sciences, Lanzhou 730000, PR China 3State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China 4Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing 100101, PR China A Gram-negative, rod-shaped, aerobic, motile bacterium, strain Y1243-1T, was isolated from an ice core drilled from Yuzhufeng Glacier, Tibetan Plateau, China. Cells had polar flagella. The novel strain shared 94.7–97.6 % 16S rRNA gene sequence similarity with the type strains of species of the genus Massilia. The novel isolate is thus classified in the genus Massilia. The major fatty acids T of strain Y1243-1 were summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH) (43.98 %), C16 : 0 (27.86 %), C10 : 0 3-OH (7.10 %), C18 : 0 (6.95 %) and C18 : 1v7c (5.01 %). The predominant T isoprenoid quinone was Q-8. The DNA G+C content of strain Y1243-1 was 65.7 mol% (Tm). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphati- dylglycerol. A number of phenotypic characteristics distinguished the novel isolate from the type strains of recognized Massilia species. Furthermore, in DNA–DNA hybridization tests, strain Y1243-1T shared 45 % relatedness with its closest phylogenetic relative, Massilia consociata CCUG 58010T. From the genotypic and phenotypic data, it is evident that strain Y1243-1T represents a novel species of the genus Massilia, for which the name Massilia yuzhufengensis sp. nov. is proposed. The type strain is Y1243-1T (5KACC 16569T5CGMCC 1.12041T). The genus Massilia was first proposed by La Scola et al. (La Scola et al., 1998; Gallego et al., 2006; Zhang et al., (1998) for an isolate from the blood of an immunocom- 2006; Zul et al., 2008; Weon et al., 2008, 2009, 2010; promised patient with a cerebrellar lesion. Members of the Ka¨mpfer et al., 2011, 2012a; Wang et al., 2012). genus are characterized as aerobic, Gram-negative, motile, Ice core samples were drilled from Yuzhufeng Glacier on non-spore-forming rods, which contain several typical fatty the Qinghai–Tibetan Plateau of China (94u 14.779 E35u acids, such as C ,C 3-OH, iso-C 2-OH and/or 12 : 0 10 : 0 15 : 0 39.649 N). Temperatures on the glacier are extremely low. C v7c,C and C v7c. Q-8 is the predominant 16 : 1 16 : 0 18 : 1 Thawed water from sections of the ice core with depth was isoprenoid quinone. Phosphatidylethanolamine, phospha- used for cultivation. After incubation at 4 uC for 30 days tidylglycerol and diphosphatidylglycerol are the major with R2A agar medium (Reasoner & Geldreich, 1985), polar lipids of these bacteria. The DNA G+C content several bacterial colonies were recovered. ranges from 62.4 to 68.9 mol%. It was recently shown that four species of the genus Naxibacter were grouped together The genomic DNA of these strains was extracted according with the majority of species of the genus Massilia and no to the methods of Marmur (1961) from cells grown on significant differences could be detected when comparing R2A agar for 2 days at 28 uC. Purity was assessed using a the chemotaxonomic makers described for species of the NanoDrop spectrophotometer (2000c; Thermo). The 16S genera Naxibacter and Massilia. Therefore, Ka¨mpfer et al. rRNA gene was amplified with universal primers 27F (59- (2011) transferred all Naxibacter species to the genus AGAGTTTGATCCTGGCTCAG-39) and 1492R (59-CG- Massilia. At the time of writing, a total of 18 Massilia GTTACCTTGTTACGACTT-39) (Embley, 1991). Nearly species with validly published names have been described full-length 16S rRNA gene sequences were compared with those in GenBank using the BLAST program (NCBI) and the The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene EzTaxon server 2.1 (Chun et al., 2007) to determine their sequence of strain Y1243-1T is JQ409016. approximate phylogenetic affiliation. The 16S rRNA gene Downloaded from www.microbiologyresearch.org by 042101 G 2013 IUMS Printed in Great Britain 1285 IP: 137.108.70.7 On: Mon, 04 Jul 2016 05:59:08 L. Shen and others T 66 Y1243-1 (JQ409016) Massilia consociata CCUG 58010 T (FN814307) Massilia niastensis 5516S-1T (EU808005) 95 Massilia aerilata 5516S-11T (EF688526) Massilia oculi CCUG 43427AT (FR773700) Massilia haematophila CCUG 38318T (AM774589) T 52 Massilia varians CCUG 35299 (AM774587) 73 96 Massilia alkalitolerans YIM 31775T (AY679161) Massilia suwonensis 5414S-25T (FJ969487) Massilia timonae UR/MT95T (U54470) Massilia niabensis 5420S-26T (EU808006) AP13T (AM231588) 64 Massilia aurea T 80 Massilia jejuensis 5317J-18 (FJ969486) 99 Massilia brevitalea byr23-80T (EF546777) Massilia flava Y9T (HM777013) T 94 Massilia albidiflava 45 (AY965999) 84 Massilia lutea 101T (AY966001) 63 Massilia dura 16T (AY965998) Massilia plicata 76T (AY966000) Pseudoduganella violaceinigra YIM 31327T (AY376163) T 100 Duganella zoogloeoides IAM 12670 (D14256) Duganella phyllosphaerae T54T (FR852575) T 72 Aquaspirillum arcticum IAM 14963 (AB074523) ‘Actimicrobium antarcticum’ KOPRI 25157T (HQ699437) 75 P6-12T (AF543312) 64 Herbaspirillum lusitanum Oxalicibacterium horti OD1T (AB469786) Herminiimonas saxobsidens NS11T (AM493906) Telluria chitinolytica ACM 3522T (X65590) 100 Telluria mixta ACM 1762T (X65598) 0.005 Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of strain Y1243-1T. Numbers at nodes are bootstrap percentages (based on 1000 replications); only values .50 % are shown. Bar, 0.005 accumulated changes per nucleotide. sequences were then analysed with the software package tree to be different for Telluria species (not shown). Therefore, MEGA 5.05 (Tamura et al., 2011). A phylogenetic tree was further extensive taxonomic studies are required to determine constructed using the neighbour-joining and maximum- whether to transfer members of the genus Telluria to the genus likelihood methods with bootstrap values based on 1000 Massilia. Although the distinct phylogenetic positions and replications (Fig. 1). One bacterial strain recovered from differences in chemotaxonomic markers such as polar lipids 119.6 m of the ice core, designated Y1243-1T, was shown to and fatty acids are usually used to distinguish bacteria at the be phylogenetically related to members of the genus genus level, assigning any novel isolate to Massilia–Duganella– Massilia (97.6–94.7 % 16S rRNA gene sequence similarity) Telluria species needs particular care because of the absence of with the closest relative being Massilia consociata CCUG 58010T. We therefore considered that strain Y1243-1T may represent a novel species of the genus Massilia. It was recently shown that Telluria species fell together with Massilia albidiflava, Massilia dura, Massilia lutea and Massilia plicata,andDuganella violaceinigra was reclassified within a novel genus as Pseudoduganella violaceinigra (Ka¨mpfer et al., 2012b). The phylogenetic tree based on the neighbour-joining method in this study supports the reclassification of D. violaceinigra. Telluria species form the basal group in the tree. Furthermore, we found the topology Fig. 2. Transmission electron micrograph of cells of strain Y1243- of the maximum-likelihood tree and the neighbour-joining 1T after 24 h growth on R2A agar. Bar, 1 mm. Downloaded from www.microbiologyresearch.org by 1286 International Journal of Systematic and Evolutionary Microbiology 63 IP: 137.108.70.7 On: Mon, 04 Jul 2016 05:59:08 http://ijs.sgmjournals.org Table 1. Differential properties between strain Y1243-1T and the type strains of recognized species of the genus Massilia Strains: 1, Y1243-1T;2,M. consociata CCUG 58010T;3,M. niabensis KACC 12632T;4,M. niastensis KACC 12599T;5,M. jejuensis 5317J-18T;6,M. brevitalea DSM 18925T;7,M. suwonensis 5414S- 25T;8,M. varians KACC 13770T;9,M. haematophila CCUG 38318T; 10, M. aurea DSM 18055T; 11, M. aerilata KACC 12505T; 12, M. alkalitolerans KACC 12188T; 13, M. timonae DSM 16850T; 14, M. flava KCTC 23585T; 15, M. albidiflava KCTC 12343T; 16, M. lutea KCTC 12345T; 17, M. plicata KCTC 12344T; 18, M. dura KCTC 12342T; 19, Massilia oculi CCUG 43427AT. Data for taxa 3 and 6 are from Weon et al. (2009); for 9 and 12 from Weon et al. (2010); for 10, 11, 13 and 15–18 from Weon et al. (2008); for 14 from Wang et al. (2012); for 19 from Ka¨mpfer et al. (2012a). Data for taxa 1, 2, 4, 5, 7 and 8 are from this study, except where indicated. +, Positive; (+), weakly positive; 2, negative; ND, not determined. Characteristic 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 a b c d c e e f g h i i i i Catalase/oxidase +/2 ND/2 +/++/+ ND/+ (+)/2 ND/+ ND/+ ND/+ +/(+) +/+ ND/2 +/+ ND/++/+ +/+ +/2 +/+ ND/2 Temperature range 2–35 15–37a 5–35 5–35b 5–35c 4–30d 5–40c 15–37e 15–37e 4–30f 5–35 4–55g 25–35j 10–40 10–45i 10–45i 10–45i 10–45i 15–37 (uC) Isolation source Ice core Blooda Air Airb Airc Soild Airc Eyee Bloode Waterf Air Soilg Bloodj Soil Soili Soili Soili Soili Eye Nitrate reduction 22+ 22+d 22c 22+ 2g 2 ++ 2222 Urease 2 2222222c 22++g 2222222 Hydrolysis of: c g Aesculin ++2 +++2
Load more

Recommended publications
  • Plant-Derived Benzoxazinoids Act As Antibiotics and Shape Bacterial Communities
    Supplemental Material for: Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities Niklas Schandry, Katharina Jandrasits, Ruben Garrido-Oter, Claude Becker Contents Supplemental Tables 2 Supplemental Table 1. Phylogenetic signal lambda . .2 Supplemental Table 2. Syncom strains . .3 Supplemental Table 3. PERMANOVA . .6 Supplemental Table 4. PERMANOVA comparing only two treatments . .7 Supplemental Table 5. ANOVA: Observed taxa . .8 Supplemental Table 6. Observed diversity means and pairwise comparisons . .9 Supplemental Table 7. ANOVA: Shannon Diversity . 11 Supplemental Table 8. Shannon diversity means and pairwise comparisons . 12 Supplemental Table 9. Correlation between change in relative abundance and change in growth . 14 Figures 15 Supplemental Figure 1 . 15 Supplemental Figure 2 . 16 Supplemental Figure 3 . 17 Supplemental Figure 4 . 18 1 Supplemental Tables Supplemental Table 1. Phylogenetic signal lambda Class Order Family lambda p.value All - All All All All 0.763 0.0004 * * Gram Negative - Proteobacteria All All All 0.817 0.0017 * * Alpha All All 0 0.9998 Alpha Rhizobiales All 0 1.0000 Alpha Rhizobiales Phyllobacteriacae 0 1.0000 Alpha Rhizobiales Rhizobiacaea 0.275 0.8837 Beta All All 1.034 0.0036 * * Beta Burkholderiales All 0.147 0.6171 Beta Burkholderiales Comamonadaceae 0 1.0000 Gamma All All 1 0.0000 * * Gamma Xanthomonadales All 1 0.0001 * * Gram Positive - Actinobacteria Actinomycetia Actinomycetales All 0 1.0000 Actinomycetia Actinomycetales Intrasporangiaceae 0.98 0.2730 Actinomycetia Actinomycetales Microbacteriaceae 1.054 0.3751 Actinomycetia Actinomycetales Nocardioidaceae 0 1.0000 Actinomycetia All All 0 1.0000 Gram Positive - All All All All 0.421 0.0325 * Gram Positive - Firmicutes Bacilli All All 0 1.0000 2 Supplemental Table 2.
    [Show full text]
  • Reduction by Soil Isolates of Heterotrophic Aerobic Bacteria: Formation of Extracellular Sete Nanospheres Mini Bajaj* and Josef Winter
    Bajaj and Winter Microbial Cell Factories (2014) 13:168 DOI 10.1186/s12934-014-0168-2 RESEARCH Open Access Se (IV) triggers faster Te (IV) reduction by soil isolates of heterotrophic aerobic bacteria: formation of extracellular SeTe nanospheres Mini Bajaj* and Josef Winter Abstract Background: Selenium and Tellurium have many common chemical properties as both belong to group 16 of the periodic table. High toxicities of Se and Te oxyanions cause environmental problems in contaminated soils and waters. Three strains (C4, C6 and C7) of selenite reducing and nanoparticle forming aerobic bacteria which were isolated from agricultural soils of India containing high concentrations of Se were investigated after 3.5 months of freeze-storage for their resistance against the toxic oxyanion tellurite and its reduction to non toxic elemental form Te0 as well as nanoparticles formation. Results: Strains C4, C6 and C7 reduced tellurite at maximum reduction rates of 2.3, 1.5 and 2.1 mg Te (IV)/L/d, respectively and produced extracellular Te0 nanospheres as revealed from SEM-EDX analysis. Production of extracellular Te nanospheres has been described seldom. Further, concurrent reduction of both selenite and tellurite by bacteria was examined as these toxic oxyanions are often present together in natural environments, mine tailings or wastewater from copper refining. Interestingly, bioreduction of 100 mg/L selenite in shake flasks was not much affected by the presence of 10 mg/L tellurite but tellurite reduction rate increased 13 fold with selenite in the medium. The concurrent reduction of these oxyanions resulted in rarely described bioformation of extracellular nanoparticles composed of both Se and Te, reported first time for aerobically growing heterotrophic non-halophilic bacterial cultures.
    [Show full text]
  • Herbaspirillum Huttiense Synonym Pseudomonas Huttiense Briefly Describe the Biological Characteristics of the Organism
    APPLICATION FORM Section 26 Determination To obtain a determination of whether an organism is a new organism Send to Environmental Protection Authority preferably by email ([email protected]) or alternatively by post (Private Bag 63002, Wellington 6140) Payment must accompany final application; see our fees and charges schedule for details. Application Number APP202506 Date April 2015 www.epa.govt.nz 2 Application Form To obtain a determination of whether an organism is a new organism Completing this application form 1. This form is used when you wish to apply for a statutory determination under section 26 of the Hazardous Substances and New Organisms (HSNO) Act 1996 as to whether or not an organism is a new organism (i.e. whether the organism is regulated under the HSNO Act or not). 2. If you wish to make an application for approval of for use of a new organism, a different form will have to be used. All forms are available on our website. 3. It is recommended that you contact an Advisor at the Environmental Protection Authority (EPA) as early in the application process as possible. An Advisor can assist you with any questions you have during the preparation of your application. 4. Unless otherwise indicated, all sections of this form must be completed for the application to be formally received and assessed. If a section is not relevant to your application, please provide a comprehensive explanation why this does not apply. If you choose not to provide the specific information, you will need to apply for a waiver under section 59(3)(a)(ii) of the HSNO Act.
    [Show full text]
  • Massilia Umbonata Sp. Nov., Able to Accumulate Poly-B-Hydroxybutyrate, Isolated from a Sewage Sludge Compost–Soil Microcosm
    International Journal of Systematic and Evolutionary Microbiology (2014), 64, 131–137 DOI 10.1099/ijs.0.049874-0 Massilia umbonata sp. nov., able to accumulate poly-b-hydroxybutyrate, isolated from a sewage sludge compost–soil microcosm Marina Rodrı´guez-Dı´az,1,23 Federico Cerrone,33 Mar Sa´nchez-Peinado,3 Lucı´a SantaCruz-Calvo,3 Clementina Pozo1,3 and Jesu´s Gonza´lez Lo´pez1,3 Correspondence 1Department of Microbiology, University of Granada, Granada, Spain Clementina Pozo 2Max-Planck-Institut fu¨r Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany [email protected] 3Water Research Institute, University of Granada, Granada, Spain A bacterial strain, designated strain LP01T, was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain- negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472T and M. lutea DSM 17473T. DNA–DNA hybridization showed low relatedness of strain LP01T to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia.
    [Show full text]
  • Burkholderiales Participating in Pentachlorophenol Biodegradation in Iron-Reducing
    Electronic Supplementary Material (ESI) for Environmental Science: Processes & Impacts. This journal is © The Royal Society of Chemistry 2015 Burkholderiales participating in pentachlorophenol biodegradation in iron-reducing paddy soil as identified by stable isotope probing Hui Tong a,b,c,1, Min Hu b,1, Fangbai Li *b, Manjia Chen b, Yahui Lv b,d a Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China b Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China c Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China d School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, PR China * Corresponding author. Tel.: +86 20 87024721; fax: +86 20 87024123. E-mail address: [email protected] (F.B., Li). 1These authors contributed equally to this work. Number of pages: 5 Number of figures: 1 Number of tables: 2 Figure S1 The relative abundance of T-RFs in the 13C-DNA heavy fractions. The solid line is the model-fitted relative abundance using the pseudo-first-order kinetic model. Table S1. Phylogenetic affiliation of two (A and B) 16S rRNA clone in PCP degrading microcosms. A 12C-Heavy fraction of clones Phylum Class Order Family Genus 8 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia/Shigella 7 Proteobacteria Betaproteobacteria Unclassified 4 Planctomycetes Planctomycetacia Planctomycetales Planctomycetaceae
    [Show full text]
  • And Endophytic Bacterial Communities of [I]Senecio Vulgaris[I] L
    A peer-reviewed version of this preprint was published in PeerJ on 7 January 2019. View the peer-reviewed version (peerj.com/articles/6162), which is the preferred citable publication unless you specifically need to cite this preprint. Cheng D, Tian Z, Feng L, Xu L, Wang H. 2019. Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 6:e6162 https://doi.org/10.7717/peerj.6162 Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range Dandan Cheng Corresp., 1 , Zhongsai Tian 2 , Liang Feng 2 , Lin Xu 2 , Hongmei Wang 1 1 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China 2 School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China Corresponding Author: Dandan Cheng Email address: [email protected] Because increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, it is believed that interactions between bacteria and alien plants play an important role in plant invasions. However, the diversity of bacterial communities associated with invasive plants is poorly understood. Therefore, we investigated the diversity of rhizo- and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L (Asteraceae) based on bacterial 16S rRNA gene data obtained from 57 samples of four S. vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Rhizosphere harbored much more bacterial OTUs and showed higher alpha diversity than the leaf and root endosphere.
    [Show full text]
  • As Duganella Zoogloeoides Gen. Nov., Sp. Nov
    INTERNATIONAL JOURNALOF SYSTEMATIC BACTERIOLOGY,OCt. 1997, p. 1249-1252 Vol. 47, No. 4 0020-7713/97/$04.00 +0 Copyright 0 1997, International Union of Microbiological Societies Proposal To Reclassify Zoogloea ramigera IAM 12670 (P. R. Dugan 115) as Duganella zoogloeoides gen. nov., sp. nov. AKIRA HIRAISHI,132*YONG KOOK SHIN,’? AND JUNTA SUGIYAMA’ Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113,’ and Department of Ecological Engneering Toyohashi University of Technology, Tenpaku, Toyohashi 441, Japan The taxonomic position of a misclassified strain, Zoogloea ramigera IAM 12670T (= ATCC 25925T = P. R. Dugan lUT),was reevaluated. A phylogenetic analysis based on 16s ribosomal rDNA sequences revealed that this organism was located in the beta subclass of the class Proteobacteria with members of the genus TeZZuria as its closest relatives. On the basis of phenotypic and phylogenetic information, we propose that this organism should be reclassified in a new taxon with the name Duganella zoogloeoides gen. nov., sp. nov. Zoogloea ramigera, which is at this time the only species of ical groups of colonies appeared and were designated strains the genus Zoogloea Itzigsohn 1868, is an aerobic, chemoor- 12670A and 12670B. The colonies of strain 12670A, which ganotrophic, gram-negative, rod-shaped bacterium that forms accounted for more than 70% of the colonies recovered, were characteristic cell aggregates surrounded by gelatinous matri- glistening, convex with entire margins, viscous, and cream to ces, the so-called zoogloeal matrices. This organism has been straw colored. The viscous appearance of this strain became isolated from wastewater environments, such as activated more pronounced with time of incubation.
    [Show full text]
  • Changes in the Bacterioplankton Community of Oligotrophic Lake Stechlin (Northeastern Germany) After Humic Matter Addition
    Vol. 55: 155–168, 2009 AQUATIC MICROBIAL ECOLOGY Printed May 2009 doi: 10.3354/ame01288 Aquat Microb Ecol Published online April 23, 2009 Changes in the bacterioplankton community of oligotrophic Lake Stechlin (northeastern Germany) after humic matter addition Kristine Michelle L. Hutalle-Schmelzer1, 2, Hans-Peter Grossart1,* 1Department of Limnology of Stratified Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany 2Department of Biological Sciences, College of Science, University of Santo Tomas, España St., 1008 Manila, Philippines ABSTRACT: In an effort to better understand the dynamics of members of the bacterioplankton com- munity in relation to humic matter (HM) addition, and to provide insight into the ecology of common and persistent as well as transient freshwater bacteria, we designed a study with a batch and a dilu- tion approach. We used single vs. repeated HM additions in incubations with bacterial communities from the epilimnion (0–10 m) and hypolimnion (40 m) of oligotrophic Lake Stechlin (northeastern Germany). Molecular methods were applied for detailed phylogenetic characterization of bacterial community composition (BCC) every 2 wk over 8 wk of incubation at in situ temperature. Whereas no significant differences in the development of BCC in batch vs. dilution cultures were observed, the BCC of epilimnic and hypolimnic samples greatly differed. This indicates that HM addition led to the establishment of a highly specific but different BCC depending on the source community in combi- nation with the respective in situ temperature. Further, DGGE banding patterns revealed a high vari- ability in the BCC of epilimnic and hypolimnic samples.
    [Show full text]
  • Rhbio2 Rhbio1
    Figure S1. Overview of aggregate samples from Chivasso at family level, taxa > 0.6% are shown. 100% Others U. m. of Bacteria kingdom Verrucomicrobiaceae DA101 soil group Opitutaceae U. m. of OPB35 soil group class 90% U. m. of Proteobacteria phylum U. m. of Xanthomonadales order Xanthomonadaceae Solimonadaceae Pseudomonadaceae Enterobacteriaceae U. m. of Sh765B-TzT-29 order U. m. of Myxococcales order 80% Polyangiaceae Haliangiaceae U. m. of GR-WP33-30 order TRA3-20 order U. m. of SC-I-84 order Nitrosomonadaceae Methylophilaceae U. m. of Betaproteobacteria class 70% Oxalobacteraceae Comamonadaceae Burkholderiaceae Sphingomonadaceae U. m. of Rhodospirillales order Rhodospirillaceae DA111 Xanthobacteraceae 60% Rhodobiaceae U. m. of Rhizobiales order Hyphomicrobiaceae Brucellaceae Bradyrhizobiaceae Caulobacteraceae Planctomycetaceae Nitrospiraceae 50% 0319-6A21 Gemmatimonadaceae Clostridiaceae 1 Planococcaceae Paenibacillaceae Bacillaceae U. m. of Chloroflexi phylum U. m. of TK10 class 40% U. m. of JG30-KF-CM45 order U. m. of S085 class U. m. of KD4-96 class Roseiflexaceae Anaerolineaceae U. m. of Candidate division WS3 phylum Sphingobacteriaceae Chitinophagaceae 30% Flavobacteriaceae Cytophagaceae U. m. of Solirubrobacterales order Solirubrobacteraceae U. m. of Gaiellales order Gaiellaceae U. m. of MB-A2-108 class U. m. of Actinobacteria class 20% Nocardioidaceae Micromonosporaceae U. m. of Micrococcales order Microbacteriaceae Geodermatophilaceae U. m. of Corynebacteriales order Bifidobacteriaceae U. m. of Acidimicrobiales order 10% U. m. of Subgroup 7 order (Holophagae class) U. m. of Subgroup 6 order (Acidobacteria class) U. m. of Subgroup 5 order (Acidobacteria class) U. m. of Subgroup 4 order (Acidobacteria class) RB41 11-24 U. m. of Subgroup 3 order (Acidobacteria class) U. m. of Subgroup 17 order (Acidobacteria class) 0% Acidobacteriaceae (Subgroup 1) U.
    [Show full text]
  • INTERACTIONS of CYANOBACTERIA and CO-OCCURRING MICROORGANISMS DURING CYANOBACTERIAL HARMFUL ALGAL BLOOMS a Dissertation Submitte
    INTERACTIONS OF CYANOBACTERIA AND CO-OCCURRING MICROORGANISMS DURING CYANOBACTERIAL HARMFUL ALGAL BLOOMS A dissertation submitted to Kent State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Kai Wang May 2021 © Copyright All rights reserved Except for previously published materials Dissertation written by Kai Wang B.S., Sichuan Agricultural University, 2012 M.S., Ocean University of China, 2015 Ph.D., Kent State University, 2021 Approved by Xiaozhen Mou, Ph.D. , Chair, Doctoral Dissertation Committee Helen Piontkivska, Ph.D. , Members, Doctoral Dissertation Committee David Costello, Ph.D. Hanbin Mao, Ph.D. Joseph Ortiz, Ph.D. Accepted by Laura G. Leff, Ph.D. , Chair, Department of Biological Sciences Mandy Munro-Stasiuk, Ph.D., Interim Dean, College of Arts and Sciences TABLE OF CONTENTS TABLE OF CONTENTS ......................................................................................................... iii LIST OF FIGURES ................................................................................................................... v LIST OF TABLES .................................................................................................................... ix ACKNOWLEDGEMENTS ....................................................................................................... x I. GENERAL INTRODUCTION ................................................................................ 1 REFERENCES ...........................................................................................
    [Show full text]
  • A Blue-Purple Pigment-Producing Bacterium Isolated from the Vezelka River in the City of Belgorod
    microorganisms Article A Blue-Purple Pigment-Producing Bacterium Isolated from the Vezelka River in the City of Belgorod Nikita S. Lyakhovchenko 1, Tatiana N. Abashina 2, Valentina N. Polivtseva 2 , Vladislav Yu. Senchenkov 1, Daniil A. Pribylov 1, Anna A. Chepurina 1, Ilja A. Nikishin 1, Alina A. Avakova 1, Michael A. Goyanov 1, Elizaveta D. Gubina 1, Daria A. Churikova 1, Alexander A. Sirotin 1, Nataliya E. Suzina 2 and Inna P. Solyanikova 1,2,* 1 Federal State Autonomous Educational Institution of Higher Education, Belgorod National Research University, 308015 Belgorod, Russia; [email protected] (N.S.L.); [email protected] (V.Y.S.); [email protected] (D.A.P.); [email protected] (A.A.C.); [email protected] (I.A.N.); [email protected] (A.A.A.);[email protected] (M.A.G.); [email protected] (E.D.G.); [email protected] (D.A.C.); [email protected] (A.A.S.) 2 G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; [email protected] (T.N.A.); [email protected] (V.N.P.); [email protected] (N.E.S.) * Correspondence: [email protected] Abstract: Violacein is a biotechnologically significant secondary metabolite due to its antibacterial, antifungal, and other properties. Isolation, research, and identification of violacein producing strains are of interest for the development of biotechnological processes, in order to enhance the biosynthesis of this compound. The purpose of the present work was to study the properties of a newly isolated bacterium capable of synthesizing blue-purple pigment.
    [Show full text]
  • Isolation and Identification of Potential Bioinoculants Based on Phosphate Solubilizing and Plant Growth Promoting Benefits Rachel Raths South Dakota State University
    South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2019 Isolation and Identification of Potential Bioinoculants based on Phosphate Solubilizing and Plant Growth Promoting Benefits Rachel Raths South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Agronomy and Crop Sciences Commons, Microbiology Commons, Plant Biology Commons, and the Soil Science Commons Recommended Citation Raths, Rachel, "Isolation and Identification of Potential Bioinoculants based on Phosphate Solubilizing and Plant Growth Promoting Benefits" (2019). Electronic Theses and Dissertations. 3359. https://openprairie.sdstate.edu/etd/3359 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. ISOLATION AND IDENTIFICATION OF POTENTIAL BIOINOCULANTS BASED ON PHOSPHATE SOLUBILIZING AND PLANT GROWTH PROMOTING BENEFITS BY RACHEL RATHS A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2019 iii I would like to dedicate this to my husband who encouraged me and made me laugh every day of the last two years and helping keep Elam alive during this crazy time of life. iv ACKNOWLEDGMENTS I would like to thank Heike Bücking for all her help and guidance in my research as my PI, as well as my committee members.
    [Show full text]