DOCSLIB.ORG

Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots fmicb-08-02667 January 9, 2018 Time: 17:50 # 1 ORIGINAL RESEARCH published: 11 January 2018 doi: 10.3389/fmicb.2017.02667 Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots Belinda C. Martin1,2*, Deirdre Gleeson3, John Statton1,2,4, Andre R. Siebers1†, Pauline Grierson1,5, Megan H. Ryan3 and Gary A. Kendrick1,2,4 1 School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia, 2 UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia, 3 School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia, 4 Western Australian Marine Science Institution, Perth, WA, Australia, 5 West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia Edited by: Seagrass roots host a diverse microbiome that is critical for plant growth and health. Essaid Ait Barka, Composition of microbial communities can be regulated in part by root exudates, but University of Reims Champagne-Ardenne, France the specifics of these interactions in seagrass rhizospheres are still largely unknown. As Reviewed by: light availability controls primary productivity, reduced light may impact root exudation Julien Tremblay, and consequently the composition of the root microbiome. Hence, we analyzed the National Research Council influence of light availability on root exudation and community structure of the root Canada (NRC–CNRC), Canada Nicola Tomasi, microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis University of Udine, Italy and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms Hannes Schmidt, University of Vienna, Austria for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and *Correspondence: fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing Belinda C. Martin revealed that microbial diversity, composition and predicted function were strongly [email protected] influenced by the presence of seagrass roots, such that root microbiomes were unique † Present address: to each seagrass species. Reduced light availability altered seagrass root exudation, Andre R. Siebers, Department of Aquatic Ecology, as characterized using fluorescence spectroscopy, and altered the composition of EAWAG, Dübendorf, Switzerland seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light Specialty section: This article was submitted to reduction to invoke a cascade of changes from alterations in root exudation to a Plant Microbe Interactions, reduction in putative beneficial microorganisms and, ultimately, confirms the importance a section of the journal Frontiers in Microbiology of the seagrass root environment – a critical, but often overlooked space. Received: 06 September 2017 Keywords: root microbiome, seagrass, exudation, light, dredging, Sulfurimonas, 16S rDNA, PARAFAC-EEM Accepted: 21 December 2017 Published: 11 January 2018 Citation: INTRODUCTION Martin BC, Gleeson D, Statton J, Siebers AR, Grierson P, Ryan MH It has long been established that roots of terrestrial plants are colonized by a diverse assemblage and Kendrick GA (2018) Low Light of microbes that collectively function as a ‘microbiome.’ These microbiomes are critical for Availability Alters Root Exudation plant growth and health via their influence on biogeochemical cycling and nutrient acquisition, and Reduces Putative Beneficial Microorganisms in Seagrass Roots. induction of host defense to pathogens and disease and production of plant growth regulators Front. Microbiol. 8:2667. (see reviews by Reinhold-Hurek et al. (2015) and Alegria Terrazas et al. (2016). Seagrasses, having doi: 10.3389/fmicb.2017.02667 evolved from land plants, are also colonized by a diverse microbial community that are believed Frontiers in Microbiology | www.frontiersin.org 1 January 2018 | Volume 8 | Article 2667 fmicb-08-02667 January 9, 2018 Time: 17:50 # 2 Martin et al. Seagrass Root Microbiomes and Light to carry out metabolic functions important for their hosts Currently, our knowledge of seagrass root exudation rates including nitrogen fixation (Bagwell et al., 2002; Garcias- and composition is limited to a few studies, most from several Bonet et al., 2016), sulfate reduction and oxidation (Küsel decades ago (Brylinsky, 1977; Penhale and Smith, 1977; Wetzel et al., 2006), phosphate solubilisation (Ghosh et al., 2012) and Penhale, 1979; Wood and Hayasaka, 1981; Moriarty et al., and nutrient turnover (Duarte et al., 2005; Trevathan-Tackett 1986; Holmer et al., 2001). These studies highlight the diversity et al., 2017). However, we are still in the early stages in root exudation patterns (composition and concentration) of understanding seagrass–microbe interactions; consequently, among different seagrass species. It has also been shown that whole-organism (seagrass C microbiome) adaptability, metabolic seagrass metabolism shifts under anoxia (Hasler-Sheetal et al., diversity and, therefore, resilience of the seagrass and microbiome 2015), which can lead to increased exudation of carbon from to environmental change remains largely unexplored. roots as fermentation products (Smith et al., 1988). The species- Seagrass meadows provide a multitude of beneficial ecosystem specific nature of root exudation and the change in exudation in services including, habitat structure, carbon sequestration, reduced light could in turn influence the composition of the root primary food sources and protection from coastal erosion microbiome. However, this top-down effect on the microbiome (Orth et al., 2006). Because seagrasses have a relatively high has not yet been investigated. requirement for light (minimal 11% surface irradiance versus The aim of this research was to assess the impact of light 1% for phytoplankton), they are restricted to growing in shallow reduction on root exudation and the root microbiome of three coastal environments, which also makes them vulnerable to tropical seagrasses Halophila ovalis, Halodule uninervis and human and natural activities that can reduce light penetration Cymodocea serrulata. These three species commonly grow in (e.g., eutrophication, dredging and cyclones) (Orth et al., 2006; mixed meadows in the northwest of Western Australia. In a Ralph et al., 2007; Waycott et al., 2009). A reduction in light previous study we found that root exudation in these three species availability reduces photosynthetic performance and therefore was increased when light availability was reduced in a fluctuating impacts negatively on growth, productivity and overall survival pattern (Martin et al., 2017). In the present work, we test if the of the plant (Biber et al., 2009; Yaakub et al., 2014). Seagrasses impact of light reduction also affects the root microbiome of these avoid negative impacts from short-term light reductions by seagrass species through alterations in root exudation and if any modifications to their physiology and metabolism; thus, light variation in the root microbiome among the seagrass species is reduction of more than 1 month may be required to affect growth related to variation in exudation profiles. We selected these three (Longstaff and Dennison, 1999; Ralph et al., 2007; McMahon seagrass species as they all have relatively fast growth rates and et al., 2013). In contrast, microbial communities can respond are quick to respond to environmental disturbance compared to rapidly to disturbance (Allison and Martiny, 2008) and therefore larger seagrass species (Kilminster et al., 2015). We addressed monitoring their composition could prove an effective early three hypotheses: (i) the composition and predicted function of indicator of environmental fluctuations and ecosystem change. the root microbiome will differ among seagrass species and also Composition of root-associated microbial communities is be distinct from the surrounding sediment, (ii) root exudation controlled by factors at several scales, including those arising will be increased by low and/or fluctuating light availability, from interactions with other microbes (e.g., competition, cross- and (iii) microbial composition and predicted function will be feeding) as well as regulated at an environmental (e.g., pH, influenced by light availability, but in a seagrass species-specific temperature) or host level (plant) (Wagner et al., 2016; Widder manner. et al., 2016; Wemheuer et al., 2017). One of the most important ways in which microbial composition can be regulated from the host level in terrestrial plants is via the exudation of MATERIALS AND METHODS compounds from plant roots. Exudates can shape communities that are specific to the plant species or even plant genotype Site Description and Seagrass Collection by selectively stimulating or inhibiting particular microbial Seagrass species were collected from Useless Loop in Shark ◦ 0 ◦ 0 populations (Haichar et al., 2012; Chaparro et al., 2014; Alegria Bay, Western Australia, in May 2015 (26 07 S 113 24 E). Shark Terrazas et al., 2016; Kawasaki et al., 2016; Martin et al., 2016). Bay is a subtropical marine embayment that is characterized This root exudate–microbe interaction has been demonstrated to by phosphorus-limited carbonate sediments and a hyper-salinity some extent for seagrass species. For example, bacteria isolated gradient extending from north (∼36 psu) to south
Load more

Recommended publications
  • Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots
    Research Collection Journal Article Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots Author(s): Martin, Belinda C.; Gleeson, Deirdre; Statton, John; Siebers, Andre R.; Grierson, Pauline; Ryan, Megan H.; Kendrick, Gary A. Publication Date: 2018-01 Permanent Link: https://doi.org/10.3929/ethz-b-000316064 Originally published in: Frontiers in Microbiology 8, http://doi.org/10.3389/fmicb.2017.02667 Rights / License: Creative Commons Attribution 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library fmicb-08-02667 January 9, 2018 Time: 17:50 # 1 ORIGINAL RESEARCH published: 11 January 2018 doi: 10.3389/fmicb.2017.02667 Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots Belinda C. Martin1,2*, Deirdre Gleeson3, John Statton1,2,4, Andre R. Siebers1†, Pauline Grierson1,5, Megan H. Ryan3 and Gary A. Kendrick1,2,4 1 School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia, 2 UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia, 3 School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia, 4 Western Australian Marine Science Institution, Perth, WA, Australia, 5 West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia Edited by: Seagrass roots host a diverse microbiome that is critical for plant growth and health. Essaid Ait Barka, Composition of microbial communities can be regulated in part by root exudates, but University of Reims Champagne-Ardenne, France the specifics of these interactions in seagrass rhizospheres are still largely unknown.
    [Show full text]
  • Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
    Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen.
    [Show full text]
  • Universidade Federal Do Pampa Campus São Gabriel Programa De Pós-Graduação Stricto Sensu Em Ciências Biológicas
    UNIVERSIDADE FEDERAL DO PAMPA CAMPUS SÃO GABRIEL PROGRAMA DE PÓS-GRADUAÇÃO STRICTO SENSU EM CIÊNCIAS BIOLÓGICAS PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA SÃO GABRIEL, RS, BRASIL. 2014 PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA Dissertação apresentada ao programa de Pós- Graduação Stricto Sensu em Ciências Biológicas da Universidade Federal do Pampa, como requisito parcial para obtenção do Título de Mestre em Ciências Biológicas. Orientador: Prof. Dr. Luiz Fernando Wurdig Roesch São Gabriel 2014 AGRADECIMENTOS À Universidade Federal do Pampa e ao Programa de Pós-Graduação em Ciências Biológicas, por minha formação profissional. Ao Prof. Luiz Fernando Wurdig Roesch, pela orientação durante estes dois anos de mestrado. Ao Prof. Antônio Batista Pereira pela coleta do material durante a XXX Operação Antártica Brasileira (OPERANTAR). À FAPERGS/CAPES, pela concessão da bolsa. RESUMO Neste estudo, foram analisadas e comparadas comunidades bacterianas do solo de uma pinguineira da Ilha Seymour (Península Antártica) em termos de abundância, estrutura, diversidade e rede de interações, a fim de se identificar padrões de interação entre os vários grupos de bactérias presentes em solos ornitogênicos em diferentes profundidades (camadas). A análise das sequências revelou a presença de oito filos distribuídos em diferentes proporções entre as Camadas 1 (0-8 cm), 2 (20-25 cm) e 3 (35-40 cm). De acordo com os índices de diversidade, a Camada 3 apresentou os maiores valores de riqueza, diversidade e uniformidade quando comparado com as Camadas 1 e 2.
    [Show full text]
  • Bacterial Avidins Are a Widely Distributed Protein Family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H
    Laitinen et al. BMC Ecol Evo (2021) 21:53 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01784-y RESEARCH ARTICLE Open Access Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H. Laitinen1†, Tanja P. Kuusela1†, Sampo Kukkurainen1†, Anssi Nurminen1, Aki Sinkkonen2 and Vesa P. Hytönen1,3* Abstract Background: Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classifed potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Results: Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal patho- gens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fx nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fxing bacteria. Conclusions: Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological signifcance of biotin-binding capacity.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland).
    [Show full text]
  • Complete Genome Sequence of Lytic Bacteriophage RG-2014 That Infects
    Bhattacharjee et al. Standards in Genomic Sciences (2017) 12:82 DOI 10.1186/s40793-017-0290-y SHORTGENOMEREPORT Open Access Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1 Ananda Shankar Bhattacharjee1,4, Amir Mohaghegh Motlagh1,5, Eddie B. Gilcrease2, Md Imdadul Islam1, Sherwood R. Casjens2,3 and Ramesh Goel1* Abstract A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively. The phage was found to be a dsDNA virus belonging to the Podoviridae family. It has an isometric icosahedrally shaped capsid with a diameter of 85 nm. The complete genome of the isolated phage was sequenced and determined to be 73.8 kbp in length with a G + C content of 59.9%. Significant similarities in gene homology and order were observed between Delftia phage RG-2014 and the E. coli phage N4 indicating that it is a member of the N4-like phage group. Keywords: Bacteriophage, Delftia tsuruhatensis, Multidrug resistant, Biofouling, Biofilm, Genome, Podoviridae Introduction significant biodegradation capability [3, 4]. A recently The occurrence and spread of antibiotic resistant bac- described species, closely related to Delftia acidovorans, teria in the environment are regarded as environmental Delftia tsuruhatensis, has been reported to cause bio- challenges of highest concern in the twenty-first century.
    [Show full text]
  • Bioelectrochemical Oxidation of Organics by Alkali-Halotolerant Anodophilic Biofilm Under Nitrogen-Deficient, Alkaline and Saline Conditions
    RESEARCH REPOSITORY This is the author’s final version of the work, as accepted for publication following peer review but without the publisher’s layout or pagination. The definitive version is available at: https://doi.org/10.1016/j.biortech.2017.08.157 Mohottige, T.N.W., Ginige, M.P., Kaksonen, A.H., Sarukkalige, R. and Cheng, K.Y. (2017) Bioelectrochemical oxidation of organics by alkali-halotolerant anodophilic biofilm under nitrogen-deficient, alkaline and saline conditions. Bioresource Technology, 245 . pp. 890-898. http://researchrepository.murdoch.edu.au/id/eprint/38599/ Copyright: © 2017 Elsevier Ltd It is posted here for your personal use. No further distribution is permitted. Accepted Manuscript Bioelectrochemical oxidation of organics by alkali-halotolerant anodophilic bi- ofilm under nitrogen-deficient, alkaline and saline conditions Tharanga N. Weerasinghe Mohottige, Maneesha P. Ginige, Anna H. Kaksonen, Ranjan Sarukkalige, Ka Yu Cheng PII: S0960-8524(17)31471-2 DOI: http://dx.doi.org/10.1016/j.biortech.2017.08.157 Reference: BITE 18766 To appear in: Bioresource Technology Received Date: 13 July 2017 Revised Date: 23 August 2017 Accepted Date: 25 August 2017 Please cite this article as: Mohottige, N.W., Ginige, M.P., Kaksonen, A.H., Sarukkalige, R., Cheng, K.Y., Bioelectrochemical oxidation of organics by alkali-halotolerant anodophilic biofilm under nitrogen-deficient, alkaline and saline conditions, Bioresource Technology (2017), doi: http://dx.doi.org/10.1016/j.biortech. 2017.08.157 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript.
    [Show full text]
  • Acclimatisation of Microbial Consortia to Alkaline Conditions and Enhanced Electricity Generation
    Zhang E, Zhaia W, Luoa Y, Scott K, Wang X, Diaoa G. Acclimatisation of microbial consortia to alkaline conditions and enhanced electricity generation. Bioresource Technology 2016, 211, 736-742. Copyright: © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license DOI link to article: http://dx.doi.org/10.1016/j.biortech.2016.03.115 Date deposited: 06/06/2016 Embargo release date: 04 April 2017 This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence Newcastle University ePrints - eprint.ncl.ac.uk Acclimatization Acclimatisation of microbial consortia to alkaline conditions itandy enhanced es electricity generation in microbial fuel cells under strong alkaline conditions Enren Zhang*a, Wenjing Zhaia, Yue Luoa, Keith Scottb, Xu Wangc, and Guowang Diaoa a Department of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou city, 225002, China b School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle NE1 7RU, United Kingdom c School of Resource and Environmental Sciences, Wuhan University, Wuhan, 430079, China ; Air-cathode microbial fuel cells (MFCs), obtained by inoculatinged with the an aerobic activated sludge, sampled from a brewery waste treatment, were activated over about a one month period, at pH 10.0, to obtain the alkaline MFCs. The alkaline MFCs produced stable power of 118 -2 -3 -2 mW m (or 23.6 W m ) and the a maximum power density of 213 mW m at pH 10.0. The Commented [KS1]: Mention the substrate used performance of the MFCs was further enhanced to produce a stable power of 140 mW m-2 and the a maximum power density of 235 mW m-2 by increasing pH to 11.0.
    [Show full text]
  • Microbial Ecology of Halo-Alkaliphilic Sulfur Bacteria
    Microbial Ecology of Halo-Alkaliphilic Sulfur Bacteria Microbial Ecology of Halo-Alkaliphilic Sulfur Bacteria Proefschrift ter verkrijging van de graad van doctor aan de Technische Universiteit Delft, op gezag van de Rector Magnificus prof. dr. ir. J.T. Fokkema, voorzitter van het College van Promoties in het openbaar te verdedigen op dinsdag 16 oktober 2007 te 10:00 uur door Mirjam Josephine FOTI Master degree in Biology, Universita` degli Studi di Milano, Italy Geboren te Milaan (Italië) Dit proefschrift is goedgekeurd door de promotor: Prof. dr. J.G. Kuenen Toegevoegd promotor: Dr. G. Muyzer Samenstelling commissie: Rector Magnificus Technische Universiteit Delft, voorzitter Prof. dr. J. G. Kuenen Technische Universiteit Delft, promotor Dr. G. Muyzer Technische Universiteit Delft, toegevoegd promotor Prof. dr. S. de Vries Technische Universiteit Delft Prof. dr. ir. A. J. M. Stams Wageningen U R Prof. dr. ir. A. J. H. Janssen Wageningen U R Prof. dr. B. E. Jones University of Leicester, UK Dr. D. Yu. Sorokin Institute of Microbiology, RAS, Russia This study was carried out in the Environmental Biotechnology group of the Department of Biotechnology at the Delft University of Technology, The Netherlands. This work was financially supported by the Dutch technology Foundation (STW) by the contract WBC 5939, Paques B.V. and Shell Global Solutions Int. B.V. ISBN: 978-90-9022281-3 Table of contents Chapter 1 7 General introduction Chapter 2 29 Genetic diversity and biogeography of haloalkaliphilic sulfur-oxidizing bacteria belonging to the
    [Show full text]
  • Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment
    RESEARCH ARTICLE Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment Christophe Leboulanger1*, HeÂlène Agogue 2☯, CeÂcile Bernard3☯, Marc Bouvy1☯, Claire Carre 1³, Maria Cellamare3¤³, Charlotte Duval3³, Eric Fouilland4☯, Patrice Got4☯, Laurent Intertaglia5³, CeÂline Lavergne2³, Emilie Le Floc'h4☯, CeÂcile Roques4³, GeÂrard Sarazin6☯ a1111111111 1 UMR MARBEC, Institut de Recherche pour le DeÂveloppement, Sète-Montpellier, France, 2 UMR LIENSs, Centre National de la Recherche Scientifique, La Rochelle, France, 3 UMR MCAM, MuseÂum National a1111111111 d'Histoire Naturelle, Paris, France, 4 UMR MARBEC, Centre National de la Recherche Scientifique, Sète- a1111111111 Montpellier, France, 5 Observatoire OceÂanologique de Banyuls-sur-Mer, Universite Pierre et Marie Curie, a1111111111 Banyuls-sur-Mer, France, 6 UMR7154 Institut de Physique du Globe de Paris, Universite Paris Diderot, a1111111111 Paris, France ☯ These authors contributed equally to this work. ¤ Current address: Phyto-Quality, 15 rue PeÂtrarque, Paris, France ³ These authors also contributed equally to this work. * [email protected] OPEN ACCESS Citation: Leboulanger C, Agogue H, Bernard C, Bouvy M, Carre C, Cellamare M, et al. (2017) Abstract Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical This study describes, for the first time, the water chemistry and microbial diversity in Dziani Thalassohaline Environment. PLoS ONE 12(1): e0168879. doi:10.1371/journal.pone.0168879 Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6± Editor: Jean-FrancËois Humbert, INRA, FRANCE -1 2- 14.5 g L eq.
    [Show full text]
  • Supplement of Biogeosciences, 16, 4229–4241, 2019 © Author(S) 2019
    Supplement of Biogeosciences, 16, 4229–4241, 2019 https://doi.org/10.5194/bg-16-4229-2019-supplement © Author(s) 2019. This work is distributed under the Creative Commons Attribution 4.0 License. Supplement of Identifying the core bacterial microbiome of hydrocarbon degradation and a shift of dominant methanogenesis pathways in the oil and aqueous phases of petroleum reservoirs of different temperatures from China Zhichao Zhou et al. Correspondence to: Ji-Dong Gu ([email protected]) and Bo-Zhong Mu ([email protected]) The copyright of individual parts of the supplement might differ from the CC BY 4.0 License. 1 Supplementary Data 1.1 Characterization of geographic properties of sampling reservoirs Petroleum fluids samples were collected from eight sampling sites across China covering oilfields of different geological properties. The reservoir and crude oil properties together with the aqueous phase chemical concentration characteristics were listed in Table 1. P1 represents the sample collected from Zhan3-26 well located in Shengli Oilfield. Zhan3 block region in Shengli Oilfield is located in the coastal area from the Yellow River Estuary to the Bohai Sea. It is a medium-high temperature reservoir of fluvial face, made of a thin layer of crossed sand-mudstones, pebbled sandstones and fine sandstones. P2 represents the sample collected from Ba-51 well, which is located in Bayindulan reservoir layer of Erlian Basin, east Inner Mongolia Autonomous Region. It is a reservoir with highly heterogeneous layers, high crude oil viscosity and low formation fluid temperature. It was dedicated to water-flooding, however, due to low permeability and high viscosity of crude oil, displacement efficiency of water-flooding driving process was slowed down along the increase of water-cut rate.
    [Show full text]
  • In the Oyster Crassostrea Rivularis Gould
    Central Annals of Clinical Cytology and Pathology Bringing Excellence in Open Access Short Communication *Corresponding author Xinzhong Wu, South China Sea Institute of Oceanography, Chinese Academy of Sciences, China, Identification of Rickettsia-Like Email: Submitted: 19 January 2016 Organism (RLO) in the Oyster Accepted: 17 April 2017 Published: 19 April 2017 ISSN: 2475-9430 Crassostrea rivularis Gould Copyright Yang Zhang1#, Jing Fang2#, Jingfeng Sun3, and Xinzhong Wu1,2* © 2017 Wu et al. 1South China Sea Institute of Oceanography, Chinese Academy of Sciences, China OPEN ACCESS 2Ocean College, Qinzhou University, China 3Aquaculture College, Tianjin Agriculture University, China Keywords #Yang Zhang and Jing Fang contributed equally to this work • Oyster Crassostrea rivularis Gould (also known as Crassostrea ariakensis) Abstract • Rickettsia-like organism (RLO) • 16S rDNA The oyster Crassostrea rivularis Gould (also known as Crassostrea ariakensisis) an • Phylogeny important bivalve species cultured in southeastern China. Since 1992, these oysters • In situ hybridization have suffered high mortality during winter and spring. An intracellular rickettsia-like organism (RLOs) was proposed as the causative agent. In this study, RLOs were purified from the gill and digestive gland of dying oyster (C. rivularis Gould), and their 16S rDNA was amplified from the purified products. To eliminate non-specific bacterial 16S rDNA contamination, the cloned products of bacterial 16S rDNA from gill RLO were screened by the probes of bacterial 16S rDNA amplified from the digestive gland RLO. Finally, the five strongest hybridized dots were picked out and sequenced. The RLO’s 16S rDNA sequence was reconfirmed and the pathogen was found only in epithelia cells by in situ hybridization (ISH) using specific probes.
    [Show full text]