DOCSLIB.ORG

Complete Genome Sequence of Flavisolibacter Ginsenosidimutans T Gsoil 636 , a Ginsenoside-Converting Bacterium, Isolated from Soil Used for Cultivating Ginseng

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Korean Journal of Microbiology (2019) Vol. 55, No. 4, pp. 459-461 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2019.9131 eISSN 2383-9902 Copyright ⓒ 2019, The Microbiological Society of Korea Complete genome sequence of Flavisolibacter ginsenosidimutans T Gsoil 636 , a ginsenoside-converting bacterium, isolated from soil used for cultivating ginseng 1 2 2 1 1,3 Dong-Ho Keum , Byoung Hee Lee , Ki-Eun Lee , Soon Youl Lee , and Wan-Taek Im * 1 Department of Biotechnology, Hankyong National University, Gyeonggi-do 17579, Republic of Korea 2 Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea 3 AceEMzyme Co., Ltd., Academic Industry Cooperation, Gyeonggi-do 17579, Republic of Korea 인삼 재배 토양에서 분리한 진세노사이드 전환능력이 있는 T Flavisolibacter ginsenosidimutans Gsoil 636 의 유전체 서열 분석 금동호1 ･ 이병희2 ･ 이기은2 ･ 이순열1 ･ 임완택1,3* 1 2 3 국립한경대학교 농업생명과학대학 생명공학과, 국림생물자원관 미생물자원과, (주)에이스엠자임 (Received October 30, 2019; Revised December 9, 2019; Accepted December 9, 2019) T A yellow-colored, circular, convex, rod-shaped baterial strain Im, 2007). Strain Gsoil 636 is Gram-negative-bacterium, rod- T designated Flavisolibacter ginsenosidimutans Gsoil 636 was shaped, non-motile, non-spore-forming, yellow-pigmented and isolated from soil of a ginseng cultivation field in Pocheon T is allocated to the family Chitinophagaceae. Within the genus Province, South Korea. Gsoil 636 showed the ability to con- Flavisolibacter, the genomic DNA G + C content range is from vert Rb1 (one of the dominant active components of ginseng) to 42.7 to 46.4 mol%. Based on recent studies, this genus consists F2, and its whole genome was sequenced. The whole genome T of Flavisolibacter ginsenosidimutans Gsoil 636 consist of a of four species with validly published names and isolated from single circular chromosome of 5,079,621 bp, with 48.9% G + C various sources such as soil and water: Flavisolibacter gin- content. Of the 4,338 predicted genes, 4,251 were protein- sengiterrae, Flavisolibacter ginsengisoli (Yoon and Im, 2007), cording genes, 46 were RNAs, and 41 were pseudogenes. Using Flavisolibacter rigui (Baik et al., 2014), and Flavisolibacter T the complete genome sequence of the strain Gsoil 636 , we tropicus (Lee et al., 2016). identified several glycoside hydrolase-encoding genes that A ginsenoside transforming-positive, Gram-negative bacte- may be involved in the conversion of major ginsenosides into T rium, Flavisolibacter ginsenosidimutans Gsoil 636 , were minor ginsenosides and unexpectedly found antibiotic bio- synthesis-encoding genes and excinuclease genes. isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea. Based on the transform from major Keywords: Flavisolibacter ginsenosidimutans, complete genome, ginsenosides to minor ginsenosides (Zhao et al., 2015), F. ginseng soil, glycoside hydrolase, PacBio RS II T ginsenosidimutans Gsoil 636 was chosed for a whole genome study to identify the target functional genes. Whole genome The genus Flavisolibacter was first proposed by (Yoon and sequence analysis showed more than 70 glycoside hydrolases that could be involved in the conversion of ginsenosides. This *For correspondence. E-mail: [email protected]; strain is available from the host institute and from three culture Tel.: +82-31-670-5335; Fax: +82-31-670-5339 460 ∙ Keum et al. T T T collections (= KCTC 22818 = JCM 18197 = KACC14277 ). with antibiotic biosynthesis, and multiple antibiotic resistance T Genomic DNA of F. ginsenosidimutans Gsoil 636 was proteins, excision endonuclease such as UvrABC subunits. extracted using a MagAttract HMW DNA kit (Qiagen) and was purified using the chloroform wash method (shared protocol; Nucleotide sequence accession number Pacific Biosciences). Genome sequencing was performed using The complete genome sequence of Flavisolibacter ginseno- a Pacific Biosciences RSII sequencing platform, with a 20 kb T sidimutans Gsoil 636 has been deposited in DDBJ/EMBL/ SMRTbellTM templates library, at DNA Link, Inc. Sequences NCBI GenBank under the accession number CP042433. were assembled using the HGAP3 (Pacific Biosciences) pro- tocol and the sequencing depth was 194.66×. The genome sequence was annotated using the NCBI Prokaryotic Genome 적 요 Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/ books/NBK174280/) (DiCuccio et al., 2016). rRNAs and tRNAs 인삼 재배 토양으로부터 분리한 Flavisolibacter ginseno- T were predicted using rRNAmmer and tRNAscan-SE, respec- sidimutans Gsoil 636 균주의 유전체서열을 분석하였다. 균주 T tively. Gsoil 636 는 진세노사이드 Rb1을 F2로 전환하는 능력을 보 T T The complete genome of F. ginsenosidimutans Gsoil 636 여주었다. Gsoil 636 의 유전체는 G + C 비율이 48.9%이며, consisted of one circular chromosome of 5,079,621 bp, with 4,338개의 유전자와 4,251개의 단백질 코딩 유전자, 46개의 48.9% G + C content. Of the 4,338 predicted genes, 4,251 were RNA 유전자 그리고 41개의 위유전자를 포함한 단일 원형 염 protein-cording genes (CDSs), and 46 were RNA genes, and 41 색체로 구성되었으며 그 크기는 5,079,612 bp였다. 전체 DNA T pseudogenes. The majority of the protein coding genes (99.04%) 시컨싱을 통해 균주 Gsoil 636 이여러 타입의 글라이코시다 was assigned function, while the remaining predicted in Table 제 유전자를 가지고 있어 메이저 진세노사이드를 마이너진세 1. Analysis of the complete genome sequence showed many 노사이드로 전환하는 것을 확인하였다. 그 외에 항생제 생합 glycoside hydrolase-encoding genes, including 10 β-glucosidases, 성 유전자와 UV 관련 유전자도 가지고 있었다. 8 α-glucosidases, 23 β-xylosidases, 3 α-arabinofuranosidases, and 32 β-galactosidases, which may be related for its ability to convert ginsenosides. In addition, genome annotation revealed Acknowledgements other genes of interest, including nitrite reductase large sub- units, vitamin B12-dependent ribonucleotide reductase, multiple This work was supported by grants from the National biosynthesis genes such as quinone biosynthesis C-methlylase Institute of Biological Resources, funded by the Ministry of (UbiE), the cellulose synthase (CesA), and bacillithiol bio- Environment (No.NIBR201801106). synthesis deacetylase (BshB1), antibiotic related genes such as bleomycin resistance proteins, monooxygenase genes associated References T Table 1. General features of Flavisolibacter ginsenosidimutans Gsoil 636 Baik KS, Kim MS, Lee JH, Im WT, and Seong CN. 2014. Flavi- Features Chromosome solibacter rigui sp. nov., isolated from freshwater of an artificial Genome size (bp) 5,079,621 reservoir and emended description of the genus Flavisolibacter. DNA coding region (bp) 4,977,748 Int. J. Syst. Evol. Microbiol. 64, 4038–4042. G + C content (%) 48.9 DiCuccio M, Zaslavsky L, Chetvernin V, Ostell J, Badretdin A, Total genes 4,338 Tatusova T, Lomsadze A, Borodovsky M, Nawrocki EP, and Pruitt KD. 2016. NCBI prokaryotic genome annotation pipeline. Pseudo genes 41 Nucleic Acids Res. 44, 6614–6624. Protein-cording genes 4,251 Lee JJ, Kang MS, Kim GS, Lee CS, Lim SY, Lee JD, Roh SH, Kang Number of rRNA genes (5S, 16S, 23S) 3 (1, 1, 1) HR, Ha JM, Bae SJ, et al. 2016. Flavisolibacter tropicus sp. Number of tRNA genes 40 nov., isolated from tropical soil. Int. J. Syst. Evol. Microbiol. 66, Number of ncRNA genes 3 3413–3419. 미생물학회지 제55권 제4호 T Complete genome sequence of F. ginsenosidimutans Gsoil 636 ∙ 461 Yoon MH and Im WT. 2007. Flavisolibacter ginsengiterrae gen. nov., Zhao Y, Liu Q, Kang MS, Jin FX, Yu HS, and Im WT. 2015. sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from Flavisolibacter ginsenosidimutans sp. nov., with ginsenoside- ginseng cultivating soil. Int. J. Syst. Evol. Microbiol. 57, 1834– converting activity isolated from soil used for cultivating 1839. ginseng. Int. J. Syst. Evol. Microbiol. 65, 4868–4872. Korean Journal of Microbiology, Vol. 55, No. 4.
Recommended publications
  • Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil

    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.
  • The Nasal Microbiome Mirrors and Potentially Shapes Olfactory Function Received: 10 August 2017 Kaisa Koskinen 1,2, Johanna L

    The Nasal Microbiome Mirrors and Potentially Shapes Olfactory Function Received: 10 August 2017 Kaisa Koskinen 1,2, Johanna L

    www.nature.com/scientificreports OPEN The nasal microbiome mirrors and potentially shapes olfactory function Received: 10 August 2017 Kaisa Koskinen 1,2, Johanna L. Reichert2,3, Stefan Hoier4, Jochen Schachenreiter5, Accepted: 29 December 2017 Stefanie Duller1, Christine Moissl-Eichinger1,2 & Veronika Schöpf 2,3 Published: xx xx xxxx Olfactory function is a key sense for human well-being and health, with olfactory dysfunction having been linked to serious diseases. As the microbiome is involved in normal olfactory epithelium development, we explored the relationship between olfactory function (odor threshold, discrimination, identifcation) and nasal microbiome in 67 healthy volunteers. Twenty-eight subjects were found to have normal olfactory function, 29 had a particularly good sense of smell (“good normosmics”) and 10 were hyposmic. Microbial community composition difered signifcantly between the three olfactory groups. In particular, butyric acid-producing microorganisms were found to be associated with impaired olfactory function. We describe the frst insights of the potential interplay between the olfactory epithelium microbial community and olfactory function, and suggest that the microbiome composition is able to mirror and potentially shape olfactory function by producing strong odor compounds. Te human olfactory system is able to discriminate a vast number of odors1. Tis function is mediated by olfac- tory receptors situated within the olfactory epithelium. Te sense of smell shapes our perception of our external environment and is essential in decision-making and in guiding behavior, including eating behavior, and detec- tion of danger, as well as contributing signifcantly to the hedonic component of everyday life (e.g. favor and fragrance perception2,3). Anosmia (complete loss of olfactory function) and hyposmia (decreased olfactory function) together afect approximately 20% of the population3.
  • Culture Independent Analysis of Microbiota in the Gut of Pine Weevils

    Culture Independent Analysis of Microbiota in the Gut of Pine Weevils

    Culture independent analysis of microbiota in the gut of pine weevils KTH Biotechnology 2013-January-13 Diploma work by: Tobias B. Ölander Environmental Microbiology, KTH Supervisor: Associate prof. Gunaratna K. Rajarao Examinator: Prof. Stefan Ståhl 1 Abstract In Sweden, the pine weevil causes damages for several hundreds of millions kronor annually. The discouraged use of insecticides has resulted in that other methods to prevent pine weevil feeding needs to be found. Antifeedants found in the pine weevil own feces is one such alternative. The source of the most active antifeedants in the feces is probably from bacterial or fungal lignin degrading symbionts in the pine weevil gut. The aim of the project was to analyze the pine weevil gut microbiota with the help of culture independent methods. DNA (including bacterial DNA) was extracted from both midgut and egg cells. The extracted DNA was amplified with PCR. A clone library was created by cloning the amplified DNA into plasmid vectors and transforming the vector constructs with chemically competent cells. The clones were amplified again with either colony PCR or plasmid extraction followed by PCR, and used for RFLP (Restriction Fragment Length Polymorphism) and sequencing. Species found in the midgut sample included Acinetobacter sp., Ramlibacter sp., Chryseobacterium sp., Flavisolibacter sp. and Wolbachia sp. Species found in the egg sample included Wolbachia sp. and Halomonas sp. Wolbachia sp. and Halomonas sp. were found to be the dominant members of the midgut and egg cells respectively.
  • Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure

    Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure

    Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure Authors: Suzanne L. Ishaq, Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled The final publication is available at Springer via http://dx.doi.org/10.1007/s00248-016-0861-2. Ishaq, Suzanne L. , Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled. "Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure." Microbial Ecology 73, no. 2 (February 2017): 417-434. DOI: 10.1007/s00248-016-0861-2. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure 1,2 & 2 & 3 & 4 & Suzanne L. Ishaq Stephen P. Johnson Zach J. Miller Erik A. Lehnhoff 1 1 2 Sarah Olivo & Carl J. Yeoman & Fabian D. Menalled 1 Department of Animal and Range Sciences, Montana State University, P.O. Box 172900, Bozeman, MT 59717, USA 2 Department of Land Resources and Environmental Sciences, Montana State University, P.O. Box 173120, Bozeman, MT 59717, USA 3 Western Agriculture Research Center, Montana State University, Bozeman, MT, USA 4 Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, USA Abstract Farming practices affect the soil microbial commu- then individual farm. Living inoculum-treated soil had greater nity, which in turn impacts crop growth and crop-weed inter- species richness and was more diverse than sterile inoculum- actions.
  • Dinghuibacter Silviterrae Gen. Nov., Sp. Nov., Isolated from Forest Soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu

    Dinghuibacter Silviterrae Gen. Nov., Sp. Nov., Isolated from Forest Soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu

    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1785–1791 DOI 10.1099/ijsem.0.000940 Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu Correspondence State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Li-Hong Qiu Guangzhou, 510275, PR China [email protected] A novel Gram-stain negative, non-motile, rod-shaped, aerobic bacterial strain, designated DHOA34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. Comparative 16S rRNA gene sequence analysis showed that it exhibited highest similarity with Flavisolibacter ginsengiterrae Gsoil 492T and Flavitalea populi HY-50RT, at 90.89 and 90.83 %, respectively. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, DHOA34T formed an independent lineage within the family Chitinophagaceae but was distinct from all recognized species and genera of the family. T The major cellular fatty acids of DHOA34 included iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1v6c and/or C16 : 1v7c). The DNA G+C content was 51.6 mol% and the predominant quinone was menaquinone 7 (MK-7). Flexirubin pigments were produced. The phenotypic, chemotaxonomic and phylogenetic data demonstrate consistently that strain DHOA34T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Dinghuibacter silviterrae gen. nov., sp. nov. is proposed. The type strain of Dinghuibacter silviterrae is DHOA34T (5CGMCC 1.15023T5KCTC 42632T). The family Chitinophagaceae, belonging to the class Sphingo- For isolation of DHOA34T, the soil sample was thoroughly bacteriia of the phylum Bacteroidetes, was proposed by suspended with 100 mM PBS (pH 7.0) and the suspension Ka¨mpfer et al.
  • The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol

    The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol

    Diversity 2012, 4, 375-395; doi:10.3390/d4040375 OPEN ACCESS diversity ISSN 1424-2818 www.mdpi.com/journal/diversity Article The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol Patricia Dorr de Quadros 1,2,*, Kateryna Zhalnina 2, Austin Davis-Richardson 2, Jennie R. Fagen 2, Jennifer Drew 2, Cimelio Bayer 1, Flavio A.O. Camargo 1 and Eric W. Triplett 2 1 Department of Soil Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil; E-Mails: [email protected] (C.B.); [email protected] (F.A.O.C.) 2 Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA; E-Mails: [email protected] (K.Z.), [email protected] (A.C.R.), [email protected] (J.D.), [email protected] (E.W.T.) *Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: (352)-575-5731. Received: 29 August 2012; in revised form: 11 October 2012 / Accepted: 19 October 2012 / Published: 31 October 2012 Abstract: Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in a subtropical Acrisol was studied in south Brazil. The plots at this site represent two tillage systems, two nitrogen fertilization regimes and three crop rotation systems. Using Illumina high-throughput sequencing of the 16S rRNA gene, the archaeal and bacterial composition was determined from phylum to species level in the different plot treatments.
  • Characterization of Black Patina from the Tiber River Embankments Using Next- Generation Sequencing

    Characterization of Black Patina from the Tiber River Embankments Using Next- Generation Sequencing

    RESEARCH ARTICLE Characterization of black patina from the Tiber River embankments using Next- Generation Sequencing Federica Antonelli1*, Alfonso Esposito2, Ludovica Calvo3, Valerio Licursi4, Philippe Tisseyre5, Sandra Ricci6, Manuela Romagnoli1, Silvano Piazza2, 3,7 Francesca GuerrieriID * 1 Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy, 2 Department of Cellular, Computational and Integrative Biology±CIBIO, University of Trento, Trento, Italy, 3 Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, 4 Institute for a1111111111 Systems Analysis and Computer Science ªAntonio Rubertiº, National Research Council, Rome, Italy, a1111111111 5 Soprintendenza del Mare, Regione Sicilia, Palermo, Italy, 6 Biology Laboratory, Istituto Superiore per la a1111111111 Conservazione e per il Restauro (ISCR), Rome, Italy, 7 Epigenetics and epigenomic of hepatocellular a1111111111 carcinoma, U1052, Cancer Research Center of Lyon (CRCL), Lyon, France a1111111111 * [email protected] (FG); [email protected] (FA) Abstract OPEN ACCESS Black patinas are very common biological deterioration phenomena on lapideous artworks Citation: Antonelli F, Esposito A, Calvo L, Licursi V, Tisseyre P, Ricci S, et al. (2020) Characterization of in outdoor environments. These substrates, exposed to sunlight, and atmospheric and envi- black patina from the Tiber River embankments ronmental agents (i.e. wind and temperature changes), represent extreme environments using Next-Generation Sequencing. PLoS ONE 15 that can only be colonized by highly versatile and adaptable microorganisms. Black patinas (1): e0227639. https://doi.org/10.1371/journal. pone.0227639 comprise a wide variety of microorganisms, but the morphological plasticity of most of these microorganisms hinders their identification by optical microscopy. This study used Next- Editor: Ana R.
  • Microbial Communities in Dark Oligotrophic Volcanic Ice Cave Ecosystems of Mt

    Microbial Communities in Dark Oligotrophic Volcanic Ice Cave Ecosystems of Mt

    UC Davis UC Davis Previously Published Works Title Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica. Permalink https://escholarship.org/uc/item/2gr9z5d5 Journal Frontiers in microbiology, 6(MAR) ISSN 1664-302X Authors Tebo, Bradley M Davis, Richard E Anitori, Roberto P et al. Publication Date 2015 DOI 10.3389/fmicb.2015.00179 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 11 March 2015 doi: 10.3389/fmicb.2015.00179 Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica Edited by: Bradley M. Tebo 1*, Richard E. Davis 1 ‡, Roberto P. Anitori 1 † ‡, Laurie B. Connell 2, D’Arcy Renee Meyer-Dombard, Peter Schiffman 3 and Hubert Staudigel 4 University of Illinois at Chicago, USA 1 Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Reviewed by: Portland, OR, USA, 2 School of Marine Sciences, University of Maine, Orono, ME, USA, 3 Department of Geology, University Nathan Yee, of California, Davis, Davis, CA, USA, 4 Institute of Geophysics and Planetary Physics, Scripps Institution of Oceanography, Rutgers, The State University of La Jolla, CA, USA New Jersey, USA Jason Raymond, Arizona State University, USA The Earth’s crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly Dawn Cardace, University of Rhode Island, USA understood in terms of the energy supporting its biomass production and impact on *Correspondence: food webs at the Earth’s surface. Dark oligotrophic volcanic ecosystems (DOVEs) are Bradley M. Tebo, good environments for investigations of life in the absence of sunlight as they are poor Division of Environmental in organics, rich in chemical reactants and well known for chemical exchange with and Biomolecular Systems, Institute of Environmental Health, Earth’s surface systems.
  • Regional Fresh Snowfall Microbiology and Chemistry Are Driven by Geography in Storm-Tracked Events, Colorado, USA

    Regional Fresh Snowfall Microbiology and Chemistry Are Driven by Geography in Storm-Tracked Events, Colorado, USA

    Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA Alexander S. Honeyman, Maria L. Day and John R. Spear Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA ABSTRACT Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture- independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only Submitted 19 July 2018 common, but is capable of disseminating vast amounts of microbiota of different Accepted 16 October 2018 physiologies and genetics that then affect ecosystems globally.
  • Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and Without Tomato Bacterial Wilt Collected from Different Fields

    Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and Without Tomato Bacterial Wilt Collected from Different Fields

    Microbes Environ. Vol. 32, No. 4, 376-385, 2017 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME17131 Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields CHOL GYU LEE1*, TOSHIYA IIDA1, YOHEI UWAGAKI2,†, YOKO OTANI3, KAZUHIRO NAKAHO4, and MORIYA OHKUMA1 1Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, 305–0074, Japan; 2Ishikawa Agriculture and Forestry Research Center, Kanazawa, Ishikawa, 920–3198, Japan; 3Wakayama Agricultural Experiment Station, Koinokawa, Wakayama, 640–0423, Japan; and 4Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsu, Mie 514–2392, Japan (Received August 17, 2017—Accepted October 15, 2017—Published online November 28, 2017) Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms.
  • Hdl 120912.Pdf

    Hdl 120912.Pdf

    Environment International 129 (2019) 105–117 Contents lists available at ScienceDirect Environment International journal homepage: www.elsevier.com/locate/envint Can bacterial indicators of a grassy woodland restoration inform ecosystem T assessment and microbiota-mediated human health? ⁎ Craig Liddicoata, , Philip Weinsteina, Andrew Bissettb, Nicholas J.C. Gelliea, Jacob G. Millsa, Michelle Waycotta, Martin F. Breeda a School of Biological Sciences and the Environment Institute, The University of Adelaide, SA 5005, Australia b CSIRO Oceans and Atmosphere, Hobart, TAS, 7000, Australia ARTICLE INFO ABSTRACT Handling Editor: Yong-Guan Zhu Understanding how microbial communities change with environmental degradation and restoration may offer Keywords: new insights into the understudied ecology that connects humans, microbiota, and the natural world. Bacterial indicators Immunomodulatory microbial diversity and ‘Old Friends’ are thought to be supplemented from biodiverse Biodiversity hypothesis natural environments, yet deficient in anthropogenically disturbed or degraded environments. However, few Ecological restoration studies have compared the microbiomes of natural vs. human-altered environments and there is little knowledge Environmental health of which microbial taxa are representative of ecological restoration—i.e. the assisted recovery of degraded Merged-sample bootstrap ecosystems typically towards a more natural, biodiverse state. Here we use novel bootstrap-style resampling of Restoration genomics site-level soil bacterial 16S
  • Relationships of Decomposability and C/N Ratio in Different Types Of

    Relationships of Decomposability and C/N Ratio in Different Types Of

    Biological Control 101 (2016) 103–113 Contents lists available at ScienceDirect Biological Control journal homepage: www.elsevier.com/locate/ybcon Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation Liangliang Liu a, Jijie Kong a, Huiling Cui a, Jinbo Zhang a,b,d, Fenghe Wang a, Zucong Cai a,b,c,d,e, ⇑ Xinqi Huang a,b,c,d,e, a School of Geography Science, Nanjing Normal University, Nanjing 210023, China b Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing 210023, China c Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China d Key Laboratory of Virtual Geographical Environment (VGE), Ministry of Education, Nanjing Normal University, Nanjing 210023, China e State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing 210023, China highlights The decomposability of plant residuals was positively related to DE of RSD. C/N of plant residuals had a significant negative correlation with DE of RSD. Clarifying the changes of dominant bacteria during RSD and their main functions. article info abstract Article history: Although reductive soil disinfestation (RSD) is an effective method for suppressing Fusarium oxysporum, Received 29 February 2016 there is limited information on the relationships among types of organic matter, disinfestation efficiencies Revised 17 June 2016 (DEs), and changes in soil functional microorganisms during the RSD process. Hence, we performed Accepted 28 June 2016 laboratory experiments using nine different organic materials and used quantitative real-time PCR and Available online 29 June 2016 MiSeq pyrosequencing to investigate the suppression of F.