DOCSLIB.ORG

Diversity of the Photosynthetic Bacterial Communities in Highly Eutrophicated Yamagawa Bay Sediments

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Diversity of the Photosynthetic Bacterial Communities in Highly Eutrophicated Yamagawa Bay Sediments Biocontrol Science, 2020, Vol. 25, No. 1, 25—33 Original Diversity of the Photosynthetic Bacterial Communities in Highly Eutrophicated Yamagawa Bay Sediments ISLAM TEIBA1,3, TAKESHI YOSHIKAWA2＊, SUGURU OKUNISHI2, MAKOTO IKENAGA4, MOHAMMED EL BASUINI2,3, HIROTO MAEDA2 1 The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan 2 Research Field in Fisheries; Agriculture, Fisheries and Veterinary Medicine Area; Research and Education Assembly; Kagoshima University; 4-50-20 Shimoarata, Kagoshima 890-0056, Japan 3 Faculty of Agriculture, Tanta University, Sebrbay, Tanta, El-Gharbia Governorate, Arab Republic of Egypt 4 Research Field in Agriculture; Agriculture, Fisheries and Veterinary Medicine Area; Research and Education Assembly; Kagoshima University; 1-21-24 Korimoto, Kagoshima 890-8580, Japan Received 24 September, 2019/Accepted 5 November, 2019 Yamagawa Bay, located in Ibusuki, Kagoshima Prefecture, Japan, is a geographically enclosed coastal marine inlet, and its deteriorating seabed sediments are under an anoxic, reductive, sulfide-rich condition. In order to gain insight into diversity of anoxygenic photosynthetic bacteria（ AnPBs） and their ecophysiological roles in the sediments, three approaches were adopted: isolation of AnPBs, PCR-DGGE of 16S rDNA, and PCR-DGGE of pufM. Among the bacterial isolates, relatives of Rhodobacter sphaeroides were most dominant, possibly contributing to transforming organic pollutants in the sediments. Abundance of Chlorobium phaeobacteroides BS1 was suggested by 16S rDNA PCR-DGGE. It could reflect intensive stratification and resultant formation of the anoxic, sulfide-rich layer in addition to extreme low-light adaptation of this strain. Diverse purple non-sulfur or sulfur bacteria as well as aerobic anoxygenic photoheterotrophs were also detected by pufM PCR-DGGE, which could be associated with organic or inorganic sulfur cycling. The outcome of the present study highlights ecophysiologically important roles of AnPBs in the organically polluted marine sediments. Key words : 16S rDNA / Anoxygenic photosynthetic bacteria / Eutrophicated marine sediment / PCR- DGGE / pufM. INTRODUCTION bottom-water hypoxia and sulfide accumulation in the sediment（ Ide, 2012）. Coastal aquatic systems are highly susceptible and Aquatic microbiota vary spatio-temporarily due to can be directly or indirectly affected by adjacent terres- changes of their surrounding environment, and compo- trial ecosystems, anthropogenic activities and climate sition and dominancy of the bacterial assemblages are change. Yamagawa Bay is a coastal basin located in highly correlated to the environmental conditions; thus, Ibusuki, Kagoshima Prefecture, Japan with a central elucidation of the community structure enable us to depth of up to 50 m with a shallow entrance of 8 m. The understand physicochemical status of the environments, geographical feature gives rise to reduction of the water especially of the sediments. exchange and makes the water stagnant for a long time, Anoxygenic photosynthetic bacteria（ AnPBs） are allowing deposition of organic matters and resulting in Gram-negative prokaryotes, performing anoxygenic photosynthesis with pigments such as bacteriochloro- ＊Corresponding author. Tel: +81-99-286-4191, Fax: +81-99- phylls（ Bchl） and carotenoids. They convert light energy 286-4015, E-mail : yoshi（a）fish.kagoshima-u.ac.jp into chemical energy and grow autotrophically by using 26 T. YOSHIKAWA ET AL. carbon dioxide as a sole source of carbon. Major groups 0.1; Na2MoO4·2H2O, 0.02; shown as grams per 100 are purple non-sulfur bacteria, purple sulfur bacteria, mL）, 1mL/L. green sulfur bacteria and green non-sulfur bacteria For AnPB isolation, a double layer agar technique （Koblížek et al., 2006）. Aerobic anoxygenic phototro- was used by spreading the enriched cultures on Basic phic bacteria, accounting for up to 10% of bacterial I plates with 1.5% of agar and then covering the plates communities in the marine euphotic zones（ Yutin et with 1.2% agar. The agar plates were incubated anaer- al., 2007）, also produce Bchl a and complement their obically with Anaeropack Kenki system（ Mitsubishi Gas energy requirements by harvesting light under an aerobic Chemical, Tokyo, Japan） under the same condition condition. Habitats of AnPBs are restricted by availabil- as above. Pure isolates were obtained by sequential ity of light and electron donors including reduced sulfur isolation from colonies with different morphology and or organic compounds for their phototrophic growth maintained in Basic I liquid or agar plate media for further as well as redox potential（ van Gemerden and Mas, application. 1995; Guyoneaud et al., 1996）. Therefore, community structure of the phototrophs will be a good bioindica- Determination of the 16S rDNA nucleotide sequences tor reflecting their ambient pollution levels, especially Liquid cultures of the isolates were centrifuged to in the organically polluted marine sediments, resulting obtain cell pellets, from which the bacterial DNA were in eutrophication, oxygen depletion and high sulfide extracted with DNeasy Plant Mini Kit（ Qiagen, Hilden, concentration. Germany）. Genes of 16S rRNA were amplified by PCR The aim of this study is to gain insight into diver- using a universal primer set 27F and 1525R（ TABLE sity of AnPBs in the Yamagawa Bay sediments. Three 1）. A reaction mixture of PCR consisted of 1 x ExTaq approaches were adopted: isolation and identification Buffer（ Takara Bio, Otsu, Japan）, 100 µM dNTP Mixture of pigmented anaerobic microorganisms; polymerase （Takara Bio, Otsu, Japan）, 0.5 µM primers and 0.025 chain reaction-denaturing gradient gel electrophore- units·µL-1 ExTaq DNA Polymerase（ Hot Start Version, sis（ PCR-DGGE） of 16S ribosomal RNA（ 16S rRNA） Takara Bio, Otsu, Japan）, and 5 µL of the bacterial DNA genes（ 16S rDNA）; and PCR-DGGE of pufM encoding solutions were added to 100 µL of the mixture. Thermal the M subunit of the reaction center complex. cycling was conducted at 94˚C for 1 min, followed by 25 cycles of denaturation at 94˚C for 30 s, annealing at MATERIALS AND METHODS 58˚C for 30 s and extension at 72˚C for 90 s, and final extension at 72˚C was performed for 7 min. Specific Sample collection amplification of the target gene was confirmed by Sediment samples were collected from Yamagawa subjecting the PCR products to 1.5% agarose gel elec- Bay, Kagoshima, Japan from May to November 2016 trophoresis in TAE buffer（ 40 mM Tris-acetate, pH 8.3, 1 and May 2017 with a G.S. type core sampler（ Ashura）. mM ethylenediaminetetraacetic acid）. Surface sediments within a depth of 10 mm were The amplified 16S rDNA fragments were cleaned up used for bacterial isolation and environmental DNA with ExoSAP-IT（ Affymetrix, Santa Clara, CA, USA）, and preparation. their nucleotide sequences were determined using a set of universal primers, 27F, PrSSU.2F, 1525R and 531R Enrichment and isolation of photosynthetic bacteria （TABLE 1）, with ABI PRISM BigDye Terminator v3.1 Portions of the collected sediments were transferred Cycle Sequencing Kit（ Applied Biosystems, Waltham, into tightly-sealed test tubes filled with 30 mL of Basic MA, USA）. The obtained sequences were assembled I medium（ Hoshino and Kitamura, 1984） and culti- with the program GENETYX-MAC Ver. 19（ Genetyx, vated at 20˚C under 12:12 light:dark cycling condition Tokyo, Japan）. Their most homologous sequences were in order to enrich photosynthetic bacteria. Composition retrieved from the GenBank DNA database with the of the medium is as follows（ concentrations are given program of Basic Local Alignment Search Tool（ BLAST; as grams per liter except as otherwise noted）: KH2PO4, Altschul et al., 1990）. 0.5; K2HPO4, 0.6;（ NH4）2SO4, 1.0; MgSO4·7H2O, 0.2; NaCl, 0.2; CaCl2·2H2O, 0.05; Na2S2O3·5H2O, 0.1; yeast Bacterial community analyses by 16S rDNA PCR- extract, 0.1; malate, 0.5. The following supplements DGGE were also added: the growth factor solution（ thiamin-HCl, Microbial DNAs in the sediments were extracted using 0.05; nicotinic acid, 0.05; p-aminobenzoic acid, 0.03; PowerSoil DNA Isolation Kit（ MOBio, Carlsbad, CA, vitamin B12, 0.01; pyridoxine-HCl, 0.01; D-biotin, 0.005; USA）. Amplification of their 16S rDNAs was conducted shown as grams per 100 mL）, 1 mL/L; the trace by PCR with the primers 341F-GC and 907R（ TABLE element solution（ EDTA·2Na, 2.0; FeSO4·7H2O, 2.0; 1）; composition of the reaction mixtures was the same H3BO3, 0.1; CoCl2·6H2O, 0.1; ZnCl2, 0.1; MnCl2·4H2O, as above. After initial denaturation at 95˚C for 1 min, PHOTOTROPHS IN MARINE SEDIMENT （ for theprimersetwithaGCclamp:annealingtempera The samethermalsettingasabovewasadopted,except consortia with the color of green, pink or yellow. Totally Totally pinkoryellow. consortia withthecolorof green, ofmicrobial conditionshowedgrowth or anaerobic ments intheBasicIliquidmedium undersemi-anaerobic Isolation andidentification ofphotosyntheticbacteria performed. were and theirhomologysearches determinedusing theprimerpufM557F were sequences Nucleotide analyses. further for excluded were stillheterogeneous bands whosesequenceswere obtained; untilhomogeneous sequenceswere repeated was ers, andsubjectedtoDGGE.Thisprocedure same prim with the excised, re-amplified were bands 30-60% or40-60%ofthedenaturant.Representative polyacrylamide and 10% of shown above, exceptfor respectively. 58-63˚Cand10-12cycles, andcyclenumberswere ture pufM750R, orpufM557FGCandpufM750R the secondrunwithinnerprimersetspufM557Fand furthersubjectedto
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide
    antioxidants Review Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide Ivan Kushkevych 1,* , Veronika Bosáková 1,2 , Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 3,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (V.B.); [email protected] (M.V.) 2 Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic 3 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: Hydrogen sulfide is a toxic compound that can affect various groups of water microorgan- isms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as Citation: Kushkevych, I.; Bosáková, well as the conditions for isolation and cultivation of these microorganisms will be presented. V.; Vítˇezová,M.; Rittmann, S.K.-M.R.
    [Show full text]
  • Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon.
    [Show full text]
  • Comparative Genomic Analysis of Three Pseudomonas
    microorganisms Article Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column Ashish Pathak 1, Paul Stothard 2 and Ashvini Chauhan 1,* 1 Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA; [email protected] 2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-850-412-5119; Fax: +1-850-561-2248 Abstract: The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because Citation: Pathak, A.; Stothard, P.; of their immense metabolic and ecological potential. To obtain a comprehensive understanding on Chauhan, A. Comparative Genomic this aspect, we previously reported on the isolation and preliminary genomic characterization of Analysis of Three Pseudomonas Species three Pseudomonas species isolated from minced oyster tissue (P.
    [Show full text]
  • Downloaded from the JGI’S Genome Portal
    bioRxiv preprint doi: https://doi.org/10.1101/427211; this version posted October 3, 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-ND 4.0 International license. 1 Title: Community structure of phototrophic co-cultures from extreme environments 2 Charles Brooke1, Morgan P. Connolly2, Javier A. Garcia3, Miranda Harmon-Smith4, 3 Nicole Shapiro4, Erik Hawley5, Michael Barton4, Susannah G. Tringe4, Tijana Glavina del 4 Rio4, David E. Culley6, Richard Castenholz7 and *Matthias Hess1, 4 5 6 1Systems Microbiology & Natural Products Laboratory, University of California, Davis, CA 7 2Microbiology Graduate Group, University of California, Davis, CA 8 3Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of 9 California, Davis, CA 10 4DOE Joint Genome Institute, Walnut Creek, CA 11 5Bayer, Pittsburg, PA 12 6LifeMine, Cambridge, MA 13 7University of Oregon, Eugene, OR 14 15 16 *Corresponding author: Matthias Hess 17 University of California, Davis 18 1 Shields Ave 19 Davis, CA 95616, USA 20 P (530) 530-752-8809 21 F (530) 752-0175 22 [email protected] 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/427211; this version posted October 3, 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-ND 4.0 International license. 25 ABSTRACT 26 Cyanobacteria are found in most illuminated environments and are key players in global 27 carbon and nitrogen cycling.
    [Show full text]
  • APP201895 APP201895__Appli
    APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
    microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M.
    [Show full text]
  • Int J Syst Evol Microbiol 67 1
    Author version : International Journal of Systematic and Evolutionary Microbiology, vol.67(6); 2017; 1949-1956 Imhoffiella gen. nov.. a marine phototrophic member of family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov. Nupur1, Mohit Kumar Saini1, Pradeep Kumar Singh1, Suresh Korpole1, Naga Radha Srinivas Tanuku2, Shinichi Takaichi3 and Anil Kumar Pinnaka1* 1Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, INDIA 2CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam-530017, INDIA 3Nippon Medical School, Department of Biology, Kyonan-cho, Musashino 180-0023, Japan Address for correspondence* Dr. P. Anil Kumar Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh – 160 036, INDIA Email: [email protected] Telephone: 00-91-172-6665170 Running title Imhoffiella purpurea sp. nov. Subject category New taxa (Gammaproteobacteria) The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain AK35T is HF562219. A coccoid-shaped phototrophic purple sulfur bacterium was isolated from a coastal surface water sample collected from Visakhapatnam, India. Strain AK35T was Gram-negative, motile, purple colored, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16:0, C18:1 T 7c and C16:1 7c and/or iso-C15:0 2OH (Summed feature 3) were identified.
    [Show full text]
  • Coupled Reductive and Oxidative Sulfur Cycling in the Phototrophic Plate of a Meromictic Lake T
    Geobiology (2014), 12, 451–468 DOI: 10.1111/gbi.12092 Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake T. L. HAMILTON,1 R. J. BOVEE,2 V. THIEL,3 S. R. SATTIN,2 W. MOHR,2 I. SCHAPERDOTH,1 K. VOGL,3 W. P. GILHOOLY III,4 T. W. LYONS,5 L. P. TOMSHO,3 S. C. SCHUSTER,3,6 J. OVERMANN,7 D. A. BRYANT,3,6,8 A. PEARSON2 AND J. L. MACALADY1 1Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 4Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA 6Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Nanyang, Singapore 7Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 8Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA ABSTRACT Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacte- ria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary pro- duction in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate – including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data – as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction.
    [Show full text]
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
    [Show full text]
  • Characterization of Bacterial Communities Associated
    www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5.
    [Show full text]