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Assemblage and Functioning of Bacterial Communities in Soil and Rhizosphere Issue Date: 2016-06-08
Cover Page The handle http://hdl.handle.net/1887/40026 holds various files of this Leiden University dissertation. Author: Yan Y. Title: Assemblage and functioning of bacterial communities in soil and rhizosphere Issue Date: 2016-06-08 Assemblage and functioning of bacterial communities in soil and rhizosphere Yan Yan 闫 燕 503396-L-bw-Yan Assemblage and functioning of bacterial communities in soil and rhizosphere PhD thesis, Leiden University, The Netherlands. The research described in this thesis was performed at the Netherlands Institute of Ecology, NIOO-KNAW and at the Institute of Biology of Leiden University. 2016 闫燕 Yan Yan. No part of this thesis may be reoroduced or transmitted without prior written permission of the author. Cover (封面): Tree Roots (树根), Vincent van Gogh (梵⾼), 1890. Inspiration to rhizosphere. Lay-out by Yan Yan Printed by Ipskamp Printing ISBN: 978-94-028-0205-4 503396-L-bw-Yan Assemblage and functioning of bacterial communities in soil and rhizosphere Proefschrift ter verkrijging van de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof.mr.C.J.J.M.Stolker, volgens besluit van het College voor Promoties te verdedigen op woensdag 8 juni 2016 klokke 16.15 uur door Yan Yan geboren te Shijiazhuang, Hebei, China in 1986 503396-L-bw-Yan Promotiecommissie Promotor: Prof. dr. J. A. van Veen Promotor: Prof. dr. P. G. L. Klinkhamer Co-promotor: Dr. E. E. Kuramae, Nederlands Instituut voor Ecologie-KNAW Overige leden Prof. dr. H.P.Spaink Prof. dr. G.A.Kowalchuk, Universiteit Utrecht Prof. dr. Jos Raaijmakers Prof. -
Validation of the Asaim Framework and Its Workflows on HMP Mock Community Samples
Validation of the ASaiM framework and its workflows on HMP mock community samples The ASaiM framework and its workflows have been tested and validated on two mock metagenomic data of an artificial community (with 22 known microbial strains). The datasets are available on EBI metagenomics database (project accession number: SRP004311). First we checked that the targeted abundances (based on number of PCR product) from both mock datasets were similar to the effective abundance (by mapping reads on reference genomes). Second, taxonomic and functional results produced by the ASaiM framework have been extensively analyzed and compared to expectations and to results obtained with the EBI metagenomics pipeline (S. Hunter et al. 2014). For these datasets, the ASaiM framework produces accurate and precise taxonomic assignations, different functional results (gene families, pathways, GO slim terms) and results combining taxonomic and functional information. Despite almost 1.4 million of raw metagenomic sequences, these analyses were executed in less than 6h on a commodity computer. Hence, the ASaiM framework and its workflows are proven to be relevant for the analysis of microbiota datasets. 1Data On EBI metagenomics database, two mock community samples for Human Microbiome Project (HMP) are available. Both samples contain a genomic mixture of 22 known microbial strains. Relative abundance of each strain has been targeted using the number of PCR product of their respective 16S sequences (Table 1). In first sample (SRR072232), the targeted 16S copies of the strains vary by up to four orders of magnitude between the strains (Table 1), whereas in second sample (SRR072233) the same 16S copy number is targeted for each strain (Table 1). -
Quantitative and Qualitative Evaluation of the Impact of the G2 Enhancer
bioRxiv preprint doi: https://doi.org/10.1101/365395; this version posted July 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Quantitative and qualitative evaluation of the impact of the G2 2 enhancer, bead sizes and lysing tubes on the bacterial community 3 composition during DNA extraction from recalcitrant soil core 4 samples based on community sequencing and qPCR 5 6 Alex Gobbi1¶, Rui G. Santini2¶, Elisa Filippi1, Lea Ellegaard-Jensen1, Carsten S. 7 Jacobsen1, Lars H. Hansen1* 8 9 1 Department of Environmental Science, Aarhus University, Roskilde, Denmark 10 2 Natural History Museum, Centre for GeoGenetics, University of Copenhagen, Copenhagen, 11 Denmark 12 13 14 * Corresponding author 15 E-mail: [email protected] (LHH) 16 17 18 ¶ These authors contributed equally to this work. 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/365395; this version posted July 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 21 Abstract 22 Soil DNA extraction encounters numerous challenges that can affect both yield and 23 purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, 24 and PCR inhibitors from the soil matrix can negatively affect downstream analyses 25 when applying DNA sequencing. -
And Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments
Mathematisch-Naturwissenschaftliche Fakultät Steffi Genderjahn | Mashal Alawi | Kai Mangelsdorf | Fabian Horn | Dirk Wagner Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments Suggested citation referring to the original publication: Frontiers in Microbiology 9 (2018) 2082 DOI https://doi.org/10.3389/fmicb.2018.02082 ISSN (online) 1664-302X Postprint archived at the Institutional Repository of the Potsdam University in: Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe ; 993 ISSN 1866-8372 https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-459154 DOI https://doi.org/10.25932/publishup-45915 fmicb-09-02082 September 19, 2018 Time: 14:22 # 1 ORIGINAL RESEARCH published: 20 September 2018 doi: 10.3389/fmicb.2018.02082 Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments Steffi Genderjahn1,2*, Mashal Alawi1, Kai Mangelsdorf2, Fabian Horn1 and Dirk Wagner1,3 1 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany, 2 GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany, 3 Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. -
High Quality Draft Genome of Nakamurella Lactea Type Strain, a Rock Actinobacterium, and Emended Description of Nakamurella Lactea
Nouioui et al. Standards in Genomic Sciences (2017) 12:4 DOI 10.1186/s40793-016-0216-0 SHORTGENOMEREPORT Open Access High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea Imen Nouioui1, Markus Göker2, Lorena Carro1, Maria del Carmen Montero-Calasanz1*, Manfred Rohde3, Tanja Woyke4, Nikos C. Kyrpides4,5 and Hans-Peter Klenk1 Abstract Nakamurella lactea DLS-10T, isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed. Keywords: Frankineae, Rare actinobacteria, Nakamurellaceae, Bioactive natural product, Next generation sequencing Introduction The availability of the genome of one more species in The genus Nakamurella, belong to the order Nakamur- the genus will provide vital baseline information for bet- ellales [1] and is one of the rare genera in the class ter understanding of the ecology of these rare actinobac- Actinobacteria [2]. The genus Nakamurella is the sole teria and their potential as source of bioactive natural and type genus of the family Nakamurellaceae,which products. In the present study, we summarise the replaced the family Microsphaeraceae [2] in 2004 [3]. phenotypic, physiological and chemotaxonomic, features The genus and family names were assigned in honour of N. -
Bioprospecting from Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity
Mar. Drugs 2014, 12, 899-925; doi:10.3390/md12020899 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Bioprospecting from Marine Sediments of New Brunswick, Canada: Exploring the Relationship between Total Bacterial Diversity and Actinobacteria Diversity Katherine Duncan 1, Bradley Haltli 2, Krista A. Gill 2 and Russell G. Kerr 1,2,* 1 Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada; E-Mail: [email protected] 2 Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada; E-Mails: [email protected] (B.H.); [email protected] (K.A.G.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-902-566-0565; Fax: +1-902-566-7445. Received: 13 November 2013; in revised form: 7 January 2014 / Accepted: 21 January 2014 / Published: 13 February 2014 Abstract: Actinomycetes are an important resource for the discovery of natural products with therapeutic properties. Bioprospecting for actinomycetes typically proceeds without a priori knowledge of the bacterial diversity present in sampled habitats. In this study, we endeavored to determine if overall bacterial diversity in marine sediments, as determined by 16S rDNA amplicon pyrosequencing, could be correlated with culturable actinomycete diversity, and thus serve as a powerful tool in guiding future bioprospecting efforts. Overall bacterial diversity was investigated in eight marine sediments from four sites in New Brunswick, Canada, resulting in over 44,000 high quality sequences (x̄ = 5610 per sample). Analysis revealed all sites exhibited significant diversity (H’ = 5.4 to 6.7). -
Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils
microorganisms Article Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils Nazareth Torres † , Runze Yu and S. Kaan Kurtural * Department of Viticulture and Enology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA; [email protected] (N.T.); [email protected] (R.Y.) * Correspondence: [email protected] † Current address: Advanced Fruit and Grape Growing Group, Public University of Navarra, 31006 Pamplona, Spain. Abstract: Vineyard-living microbiota affect grapevine health and adaptation to changing environ- ments and determine the biological quality of soils that strongly influence wine quality. However, their abundance and interactions may be affected by vineyard management. The present study was conducted to assess whether the vineyard soil microbiome was altered by the use of biostimulants (arbuscular mycorrhizal fungi (AMF) inoculation vs. non-inoculated) and/or irrigation management (fully irrigated vs. half irrigated). Bacterial and fungal communities in vineyard soils were shaped by both time course and soil management (i.e., the use of biostimulants and irrigation). Regarding alpha diversity, fungal communities were more responsive to treatments, whereas changes in beta diversity were mainly recorded in the bacterial communities. Edaphic factors rarely influence bacte- rial and fungal communities. Microbial network analyses suggested that the bacterial associations Citation: Torres, N.; Yu, R.; Kurtural, were weaker than the fungal ones under half irrigation and that the inoculation with AMF led to S.K. Inoculation with Mycorrhizal the increase in positive associations between vineyard-soil-living microbes. Altogether, the results Fungi and Irrigation Management highlight the need for more studies on the effect of management practices, especially the addition Shape the Bacterial and Fungal of AMF on cropping systems, to fully understand the factors that drive their variability, strengthen Communities and Networks in Vineyard Soils. -
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. -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
The Shiga Toxin Producing Escherichia Coli
microorganisms Review An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli Panagiotis Sapountzis 1,* , Audrey Segura 1,2 , Mickaël Desvaux 1 and Evelyne Forano 1 1 Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; [email protected] (A.S.); [email protected] (M.D.); [email protected] (E.F.) 2 Chr. Hansen Animal Health & Nutrition, 2970 Hørsholm, Denmark * Correspondence: [email protected] Received: 22 May 2020; Accepted: 7 June 2020; Published: 10 June 2020 Abstract: For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle. Keywords: cattle; STEC colonization; microbiota; bacterial interactions 1. Introduction The domestication of cattle, approximately 10,000 years ago [1], brought a stable supply of protein to the human diet, which was instrumental for the building of our societies.