Transition from Seed to Root and Effect of Compost Amendment Stefan J
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Microbial Community Dynamics in the Recirculating Nutrient Solution of Tomato Plug Seedlings Cultivated Under Ebb-And-Fow System
Microbial community dynamics in the recirculating nutrient solution of tomato plug seedlings cultivated under ebb-and-ow system Chun-Juan Dong ( [email protected] ) Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers https://orcid.org/0000- 0002-8740-6649 Qian Li Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Ling-Ling Wang Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Qing-Mao Shang Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Research article Keywords: Tomato, Bacterial, Fungal, Ebb-and-ow system, Nutrient solution, Illumina sequencing Posted Date: December 2nd, 2019 DOI: https://doi.org/10.21203/rs.2.17978/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/27 Abstract Background: The ebb-and-ow system has ability to recirculate water and nutrients, and offers a good method to control nutrient leaching from greenhouses into the environment. However, the potential for the rapid spread of bacterial and fungal pathogens is the main hindrance for its adoption in vegetable seedlings production. Natural microora has often shown a certain ability to suppress diseases. Results: Here, through 16S rRNA- and ITS1-targeted Illumina sequencing, the dynamic changes in bacterial and fungal communities in the recirculating nutrient solution were characterized for tomato plug seedlings cultivated in an ebb-and-ow system in summer and winter. Both bacterial number and microbial diversity in the nutrient solution increased with recirculating irrigation, and these changes differed between summer and winter. Pseudomonas was among the most predominant bacterial genera in the nutrient solution; its relative abundance gradually increased with recycling in summer but decreased dramatically in winter. -
Pseudomonas Gessardii Sp. Nov. and Pseudornonas Migulae Sp. Nov., Two New Species Isolated from Natural Mineral Waters
International Journal of Systematic Bacteriology (1 999), 49, 1 559-1 572 Printed in Great Britain Pseudomonas gessardii sp. nov. and Pseudornonas migulae sp. nov., two new species isolated from natural mineral waters Sophie Verhille,l Nader Batda,' Fouad Dabboussi,' Monzer Hamze,* Daniel Izard' and Henri Leclerc' Author for correspondence: Henri Leclerc. Tel: + 33 3 20 52 94 28. Fax: + 33 3 20 52 93 61. e-mail : leclerc(@univ-lille2.fr Service de Bact6riologie- Twenty-f ive non-identif ied fluorescent Pseudomonas strains isolated from Hygihne, Facult6 de natural mineral waters were previously clustered into three phenotypic Medecine Henri Warembourg (p81e subclusters, Xlllb, XVa and XVc. These strains were characterized genotypically recherche), 1 place de in the present study. DNA-DNA hybridization results and DNA base Verdun, 59045 Lille Cedex, composition analysis revealed that these strains were members of two new France species, for which the names Pseudomonas gessardii sp. nov. (type strain CIP * Facult6 de Sant6 Publique, 1054693 and Pseudomonas migulae sp. nov. (type strain CIP 1054703 are U n iversite Liba na ise, Tripoli, Lebanon and CNRS proposed. P. gessardii included 13 strains from phenotypic subclusters XVa and Liban, Beirut, Lebanon XVc. P. migulae included 10 strains from phenotypic subcluster Xlllb. The levels of DNA-DNA relatedness ranged from 71 to 100% for P. gessardii and from 74 to 100% for P. migulae. The G+C content of the DNA of each type strain was 58 mol%. DNA similarity levels, measured with 67 reference strains of Pseudomonas species, were below 55%, with ATm values of 13 "C or more. -
The Case of the Red Pigment Miltos
Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome: The case of the red pigment miltos E. Photos-Jones a,b, C.W.Knapp c, D. Venieri d, G.E.Christidis f, C.Elgy e, E. Valsami-Jones e, I. Gounaki c and N.C.Andriopoulou f. a Analytical Services for Art and Archaeology (Ltd), Glasgow G12 8JD, UK b Archaeology, School of Humanities, University of Glasgow, Glasgow G12 8QQ, UK c Civil and Environmental Engineering, University of Strathclyde, Glasgow G1 1XQ, UK d School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece e School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK f School of Mineral Resources Engineering, Technical University of Crete, 73100 Chania, Greece Journal of Archaeological Science: Reports. Volume 22, December 2018, Pages 179-192 https://doi.org/10.1016/j.jasrep.2018.07.017 corresponding author address: [email protected] Abstract This paper introduces a holistic approach to the study of Greco-Roman (G-R) lithotherapeutics. These are the minerals or mineral combinations that appear in the medical and scientific literature of the G-R world. It argues that they can best be described not simply in terms of their bulk chemistry/mineralogy but also their ecological microbiology and nanofraction component. It suggests that each individual attribute may have underpinned the bioactivity of the lithotherapeutic as an antibacterial, antifungal or other. We focus on miltos, the highly prized, naturally fine, red iron oxide-based mineral used as a pigment, in boat maintenance, agriculture and medicine. -
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. -
Massilia Tieshanensis Sp. Nov., Isolated from Mining Soil
%paper no. ije034306 charlesworth ref: ije034306& New Taxa - Proteobacteria International Journal of Systematic and Evolutionary Microbiology (2012), 62, 000–000 DOI 10.1099/ijs.0.034306-0 Massilia tieshanensis sp. nov., isolated from mining soil Yan Du, Xiang Yu and Gejiao Wang Correspondence State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Gejiao Wang Huazhong Agricultural University, Wuhan, Hubei 430070, PR China [email protected] or [email protected] A bacterial isolate, designated strain TS3T, was isolated from soil collected from a metal mine in Tieshan District, Daye City, Hubei Province, in central China. Cells of this strain were Gram- negative, motile and rod-shaped. The strain had ubiquinone Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1v7c as the major fatty acids. The G+C content was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TS3T was most closely related to Massilia niastensis 5516S-1T (98.5 %), Massilia consociata CCUG 58010T (97.6 %), Massilia aerilata 5516S-11T (97.4 %) and Massilia varians CCUG 35299T (97.2 %). DNA–DNA hybridization revealed low relatedness between strain TS3T and M. niastensis KACC 12599T (36.5 %), M. consociata CCUG 58010T (27.1 %), M. aerilata KACC 12505T (22.7 %) and M. varians CCUG 35299T (46.5 %). On the basis of phenotypic and phylogenetic characteristics, strain TS3T belongs to the genus Massilia, but is clearly differentiated from other members of the genus. -
Massilia Norwichensis Sp. Nov., Isolated from an Air Sample
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by ZENODO International Journal of Systematic and Evolutionary Microbiology (2015), 65, 56–64 DOI 10.1099/ijs.0.068296-0 Massilia norwichensis sp. nov., isolated from an air sample Ivana Orthova´,1 Peter Ka¨mpfer,2 Stefanie P. Glaeser,2 Rene´ Kaden3 and Hans-Ju¨rgen Busse1 Correspondence 1Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Hans-Ju¨rgen Busse Austria hans-juergen.busse@vetmeduni. 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, ac.at Germany 3Department of Medical Sciences, Clinical Bacteriology, University of Uppsala, SE-75185 Uppsala, Sweden A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2- hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia. -
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. -
Fertilization Shapes a Well-Organized Community of Bacterial
www.nature.com/scientificreports OPEN Fertilization shapes a well- organized community of bacterial decomposers for accelerated paddy Received: 14 February 2018 Accepted: 2 May 2018 straw degradation Published: xx xx xxxx Yushan Zhan1, Wenjing Liu1, Yuanyuan Bao1, Jianwei Zhang1, Evangelos Petropoulos2, Zhongpei Li1, Xiangui Lin1 & Youzhi Feng1 Straw, mainly dry stalks of crops, is an agricultural byproduct. Its incorporation to soils via microbial redistribution is an environment-friendly way to increase fertility. Fertilization infuences soil microorganisms and straw degradation. However, our up to date knowledge on the responses of the straw decomposers to fertilization remains elusive. To this end, inoculated with paddy soils with 26-year applications of chemical fertilizers, organic amendments or controls without fertilization, microcosms were anoxically incubated with 13C-labelled rice straw amendment. DNA-based stable isotope probing and molecular ecological network analysis were conducted to unravel how straw degrading bacterial species shift in responses to fertilizations, as well as evaluate what their roles/links in the microbiome are. It was found that only a small percentage of the community ecotypes was participating into straw degradation under both fertilizations. Fertilization, especially with organic amendments decreased the predominance of Firmicutes- and Acidobacteria-like straw decomposers but increased those of the copiotrophs, such as β-Proteobacteria and Bacteroidetes due to increased soil fertility. For the same reason, fertilization shifted the hub species towards those of high degrading potential and created a more stable and efcient microbial consortium. These fndings indicate that fertilization shapes a well- organized community of decomposers for accelerated straw degradation. Rice production is expected to signifcantly increase in the near future to meet the demand of the rising human population. -
Betaproteobacteria Are Predominant in Drinking Water: Are There Reasons for Concern?
1 Betaproteobacteria are predominant in drinking water: are there reasons 2 for concern? 3 4 Abstract 5 Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that 6 can be found in drinking water, including mineral water. The combination of physiology and 7 ecology traits place some Betaproteobacteria in the list of potential, yet sometimes neglected, 8 opportunistic pathogens that can be transmitted by water or aqueous solutions. Indeed, some 9 drinking water Betaproteobacteria with intrinsic and sometimes acquired antibiotic 10 resistance, harboring virulence factors and often found in biofilm structures, can persist after 11 water disinfection and reach the consumer. 12 This literature review summarizes and discusses the current knowledge about the occurrence 13 and implications of Betaproteobacteria in drinking water. Although the sparse knowledge 14 on the ecology and physiology of Betaproteobacteria thriving in tap or bottled natural 15 mineral/spring drinking water (DW) is an evidence of this review, it is demonstrated that DW 16 holds a high diversity of Betaproteobacteria, whose presence may not be innocuous. 17 Frequently belonging to genera also found in humans, DW Betaproteobacteria are ubiquitous 18 in different habitats, have the potential to resist antibiotics either due to intrinsic or acquired 19 mechanisms, and hold different virulence factors. The combination of these factors place DW 20 Betaproteobacteria in the list of candidates of emerging opportunistic pathogens. Improved 21 bacterial -
Microbial Degradation of Furanic Compounds: Biochemistry, Genetics, and Impact
Appl Microbiol Biotechnol (2011) 92:1095–1105 DOI 10.1007/s00253-011-3632-5 MINI-REVIEW Microbial degradation of furanic compounds: biochemistry, genetics, and impact Nick Wierckx & Frank Koopman & Harald J. Ruijssenaars & Johannes H. de Winde Received: 21 July 2011 /Revised: 29 September 2011 /Accepted: 6 October 2011 /Published online: 28 October 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Microbial metabolism of furanic compounds, lized to the primary intermediate 2-oxoglutarate. HMF is especially furfural and 5-hydroxymethylfurfural (HMF), is converted, via 2,5-furandicarboxylic acid, into 2-furoic rapidly gaining interest in the scientific community. This acid. The enzymes in these HMF/furfural degradation interest can largely be attributed to the occurrence of toxic pathways are encoded by eight hmf genes, organized in furanic aldehydes in lignocellulosic hydrolysates. However, two distinct clusters in Cupriavidus basilensis HMF14. The these compounds are also widespread in nature and in organization of the five genes of the furfural degradation human processed foods, and are produced in industry. cluster is highly conserved among microorganisms capable Although several microorganisms are known to degrade of degrading furfural, while the three genes constituting the furanic compounds, the variety of species is limited mostly initial HMF degradation route are organized in a highly to Gram-negative aerobic bacteria, with a few notable diverse manner. The genetic and biochemical characteriza- exceptions. Furanic aldehydes are highly toxic to micro- tion of the microbial metabolism of furanic compounds organisms, which have evolved a wide variety of defense holds great promises for industrial applications such as the mechanisms, such as the oxidation and/or reduction to the biodetoxifcation of lignocellulosic hydrolysates and the furanic alcohol and acid forms. -
Contrasting Patterns of Seed and Root Colonization by Bacteria from the Genus Chryseobacterium and from the Family Oxalobacteraceae
The ISME Journal (2007) 1, 291–299 & 2007 International Society for Microbial Ecology All rights reserved 1751-7362/07 $30.00 www.nature.com/ismej ORIGINAL ARTICLE Contrasting patterns of seed and root colonization by bacteria from the genus Chryseobacterium and from the family Oxalobacteraceae Stefan J Green1,2,4, Frederick C Michel Jr3, Yitzhak Hadar1 and Dror Minz2 1Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel; 2Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel and 3Department of Food, Agricultural, and Biological Engineering, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, USA Microbial colonization of plant seeds and roots is a highly complex process in which soil and plant type can influence the composition of the root-associated and rhizosphere microbial communities. Amendment of compost, a common agricultural technique, introduces exogenous nutrients and microorganisms to the soil–plant environment, and can further influence microbial community composition in the plant environment. Although compost amendments can strongly influence soil and rhizosphere microbial communities, there is evidence that with increasing proximity to the root, plant influences predominate over soil effects. We hypothesized that the ‘rhizosphere effect’ observed with proximity to plant surfaces does not act equally on all microorganisms. To explore this issue, we examined two bacterial taxa that reproducibly colonized seed and root surfaces in an experiment examining the influence of compost amendment on plant-associated bacterial communities. Population-specific analyses revealed striking differences in the ecology of bacteria from the genus Chryseobacterium and the family Oxalobacteraceae in potting mix and plant- associated environments. -
Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream
RESEARCH ARTICLE Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream Molli M. Newman*, Mark R. Liles, Jack W. Feminella Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America * [email protected] Abstract Microbial succession during leaf breakdown was investigated in a small forested stream in west-central Georgia, USA, using multiple culture-independent techniques. Red maple (Acer rubrum) and water oak (Quercus nigra) leaf litter were incubated in situ for 128 days, and litter breakdown was quantified by ash-free dry mass (AFDM) method and microbial OPEN ACCESS assemblage composition using phospholipid fatty acid analysis (PLFA), ribosomal inter- Citation: Newman MM, Liles MR, Feminella JW genic spacer analysis (RISA), denaturing gradient gel electrophoresis (DGGE), and bar- (2015) Litter Breakdown and Microbial Succession on coded next-generation sequencing of 16S rRNA gene amplicons. Leaf breakdown was Two Submerged Leaf Species in a Small Forested faster for red maple than water oak. PLFA revealed a significant time effect on microbial Stream. PLoS ONE 10(6): e0130801. doi:10.1371/ journal.pone.0130801 lipid profiles for both leaf species. Microbial assemblages on maple contained a higher rela- tive abundance of bacterial lipids than oak, and oak microbial assemblages contained Editor: Hauke Smidt, Wageningen University, NETHERLANDS higher relative abundance of fungal lipids than maple. RISA showed that incubation time was more important in structuring bacterial assemblages than leaf physicochemistry. Received: December 12, 2014 DGGE profiles revealed high variability in bacterial assemblages over time, and sequencing Accepted: May 25, 2015 of DGGE-resolved amplicons indicated several taxa present on degrading litter.