DOCSLIB.ORG

Supplementary Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Information 1 Supplementary Information 2 3 Homogeneous selection promotes microdiversity in the glacier-fed stream 4 microbiome 5 6 Stilianos Fodelianakis1, Alex D. Washburne2,3, Massimo Bourquin1, Paraskevi Pramateftaki1, 7 Tyler J. Kohler1, Michail Styllas1, Matteo Tolosano1, Vincent De Staercke1, Martina Schön1, 8 Susheel Bhanu Busi4, Jade Brandani1, Paul Wilmes4, Hannes Peter1 & Tom J. Battin1 9 10 1Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Federale de 11 Lausanne 12 2Department of Microbiology and Immunology, Montana State University, USA 13 3Selva Analytics, LLC, Bozeman, Montana, USA 14 4Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of 15 Luxembourg, Esch-sur-Alzette, Luxembourg 16 17 Supplementary Results 18 19 Detailed taxonomic diversity 20 The communities in the different glacier-fed streams were both rich in terms of the 21 number of detected SVs and in terms of the number of taxonomic groups. We detected 8186 SVs 22 in total and 640 ± 60 SVs per glacier-fed stream on average. In terms of taxonomy, there were 36 23 assigned bacterial Phyla, 112 Classes, 162 Orders, 156 Families and 159 Genera present in the 24 sampled communities. The most diverse and abundant Phyla were Proteobacteria (3267 SVs, 25 34.4-90.2% of total cells per sample), Bacteroidetes (1324 SVs, 1.8-31.9% of total cells per 26 sample) and Planctomycetes (728 SVs, 0.5-9.9% of total cells per sample) and the most diverse 27 and abundant Classes within these three phyla were Betaproteobacteria (1429 SVs, 15.2-78.8% 28 of total cells per sample), Saprospirae (481 SVs, 0.09-13.4% of total cells per sample) and 29 Planctomycetia (539 SVs, 0.4-8.5% of total cells per sample), respectively (Fig. S6). 30 31 Core microbiome 32 The core microbiome, which we defined as the taxonomic units present in at least one 33 sample at every reach, included 11 Phyla, 20 Classes, 29 Orders, 18 Families and 11 Genera 34 (Fig. 1, Table S2). The 11 Genera within the core microbiome included a total of 1133 SVs 35 (13.9% of the total SVs) that comprised on average 34.8% (13.6 – 62%) of the total cells per 36 gram of dry sediment per community. Six core Genera were taxonomically affiliated to 37 Betaproteobacteria; Methylotenera, Polaromonas, Rhodoferax, Leptothrix, Methylibium and 38 Rubrivivax, containing 541 SVs and comprising on average 25.1% of the total cells per gram of 39 dry sediment per community. Two core Genera were affiliated to Planctomycetes; Gemmata and 40 Planctomyces, containing 258 SVs and comprising on average 1.3% of the total cells per gram of 41 dry sediment per community. Two core Genera were affiliated to Alphaproteobacteria; 42 Hyphomicrobium and Novosphingobium, containing 113 SVs and comprising on average 3.5% 43 of the total cells per gram of dry sediment per community. One core Genus was affiliated to 44 Bacteroidetes; Flavobacterium, containing 205 SVs and comprising on average 3% of the total 45 cells per gram of dry sediment per community, and one Genus was affiliated to Nitrospirae; 46 Nitrospira, containing 20 SVs and comprising on average 1.9% of the total cells per gram of dry 47 sediment per community. 48 49 Environmental drivers of bacterial β-diversity 50 Using distance-based redundancy analysis and a forward stepwise model building, we 51 found that seven of the recorded environmental parameters, namely conductivity, dissolved 52 oxygen, latitude, chl-α content, pH, water temperature and turbidity, could collectively explain 53 43.5% of the variance in the Bray-Curtis (BC) dissimilarity among the samples (Fig. S4, Table 54 S6). Conductivity had the highest proportion of variance explained (14.1%), followed by 55 dissolved oxygen (8.1%), latitude (5.7%), chl-α content (5.6%) and pH (4.3%) while the rest of 56 the variables explained low proportions of variance (1.4-2.3%). 57 The samples had a distinct clustering pattern along the first constrained axis that 58 explained 18.8% of the total BC variance (Fig. S4). The left axis side was characterized by a 59 low-dispersion cluster of samples from turbulent streams with high conductivity, pH and 60 dissolved oxygen, and the right axis side was characterized by a high-dispersion cluster of 61 samples from warmer streams with higher chl-α content. The second constrained axis explained 62 8.7% of total BC variance and was mostly associated with latitude, suggesting that a part of 63 community variability can be explained by geographic legacies. Samples from the same stream 64 but at different reaches (UP and DN) clustered mostly together and the variance explained by the 65 factor “reach” was non-significant. 66 Supplementary Figures 67 68 Figure S1. The location of the sampled glacier-fed streams (GFS) at the Southern Alps of 69 New Zealand. GFS are assigned numbers from 1 to 21 (excluding 4) for operational purposes. 70 Map colors correspond to the altitude as per the legend on the right. Mantel correlation Mantel -0.002 0.000 0.002 0.004 0.000 0.002 0.004 0.006 0.008 0.010 71 Distance class index 72 Figure S2. Mantel correlogram between phylogenetic distances and niche distances among 73 all the Sequence Variants. Filled squares correspond to significant correlations and empty 74 squares correspond to non-significant correlations. The phylogenetic distances were Hellinger- 75 transformed before the correlations. The niche distances were calculated as the Euclidean 76 distances of standardized niche optima regarding the environmental parameters that explained a 77 significant proportion of β-diversity as per the db-RDA analysis, namely conductivity, dissolved 78 oxygen, latitude, chl-α, pH, water temperature and turbidity. 0.7 0.8 0.5 0.6 0.3 0.4 0.4 0.5 0.6 Relative abundance of clades under selection under clades of abundance Relative Relative species richness of clades under selection clades of richness species Relative 1e+05 5e+05 5e+06 5e+07 1e+05 5e+05 5e+06 5e+07 A −1 B −1 Cells gram of dry sediment Cells gram of dry sediment 79 80 Figure S3. The inverse relationship between the relative species richness (A) and the 81 relative abundance (B) of phylogenetic clades under environmental selection and total 82 bacterial cell density A. The relative species richness of the clades under environmental 83 selection (y-axis) as a function of total bacterial cell density (x-axis, in log-scale). B. The 84 relative abundance of the clades under environmental selection (y-axis) as a function of 85 total bacterial cell density (x-axis, in log-scale). Adjusted R2= 0.252, and 0.282, for panels A 86 and B, respectively. For both panels p<<0.001 and n=119. 88 88 77 99 8 21 9 77 21 9 9 77 1 9 21 21 21 Reach 2020 lat 222 2 DN 2 202020 20 6 UP 3 10 DO 17 66 3 101818 17 11311101918 1810 turb 1717 13 13 1 1010191818 17 13 6 0 1 1919 pH 17 6 1111 19 Conductivity (μS cm-1) 3 3 Cond 131313 12 1111 125 3 1212 1212 water_temp 11 15 100 15 15 Chla 15 75 15 50 1616 -1 1616 16 25 55 55 CAP2 (19.2% of fitted, 8.7% of total variance) oftotal 8.7% fitted, (19.2% of CAP2 1414 -1.0 -0.5 0.0 0.5 1.0 CAP1 (41% of fitted, 18.8% of total variance) 87 88 Figure S4. The constrained ordination plot of the distance-based redundancy analysis on 89 the BC dissimilarity of bacterial communities from all the sampled streams. Factors 90 included in the model are plotted as vectors. Samples are colored based on conductivity that was 91 the factor explaining most of the BC variance, as per the legend on the middle right. Sample 92 symbols are given according to the reach as per the legend on the upper right. Numbers above 93 samples indicate the location of the stream as per Figure S1. Axes are scaled based on the 94 variance they explain. Cond: conductivity, DO: dissolved oxygen, lat: latitude, Chla: chl-α 95 content, water_temp: water temperature, turb: turbidity. 96 97 Figure S5. Flow cytometry scatterplot of green (FITC-H – x-axis) versus red (PerCP-H – y- 98 axis) fluorescence of a typical sediment fixed extract. The polygon delineates the gate used for 99 counting cells, which is based on events with disproportionately more green fluorescence 100 compared to red fluorescence because of SybrGreen staining. On the contrary, debris is shown 101 on the middle left as a dense cluster of events with higher red:green fluorescence ratio. 1,300 1,200 1,100 1,000 900 800 700 600 NumberSequence Variants of 500 400 300 200 100 0 -1000 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 102 Sequencing Depth 103 Figure S6. The rarefaction curves of the generated 16S rRNA gene amplicons from all the 104 samples. The number of sequences is shown on the x-axis and the number of observed sequence 105 variants (SVs) are shown on the y-axis. Rarefaction was performed at intervals of 100 sequences 106 with 10 permutations per sequence interval at a sequencing depth of up to 10,000 reads. The 107 range of the obtained values is represented with boxplots. Different colors represent different 108 samples. GL1 GL2 GL3 GL5 GL6 GL7 GL8 GL9 GL10 GL11 GL12 GL13 GL14 GL15 GL16 GL17 GL18 GL19 GL20 GL21 0.00 −0.25 Class [Chloracidobacteria] [Pedosphaerae] [Saprospirae] Alphaproteobacteria −0.50 Betaproteobacteria Epsilonproteobacteria Flavobacteriia Relative abundance Relative Gammaproteobacteria Others −0.75 Planctomycetia −1.00 DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP DN UP 109 110 Figure S7.
Load more

Recommended publications
  • Novel Copper-Containing Membrane Monooxygenases (Cummos) Encoded by Alkane- Utilizing Betaproteobacteria
    Lawrence Berkeley National Laboratory Recent Work Title Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane- utilizing Betaproteobacteria. Permalink https://escholarship.org/uc/item/8z48x96q Journal The ISME journal, 14(3) ISSN 1751-7362 Authors Rochman, Fauziah F Kwon, Miye Khadka, Roshan et al. Publication Date 2020-03-01 DOI 10.1038/s41396-019-0561-2 Peer reviewed eScholarship.org Powered by the California Digital Library University of California 1 1 2 1Novel copper-containing membrane monooxygenases 2(CuMMOs) encoded by alkane-utilizing Betaproteobacteria 3 4Running title: Novel CuMMOs in Betaproteobacteria 5 6Fauziah F. Rochman1, Miye Kwon2, Roshan Khadka1, Ivica Tamas1,3, Azriel 7Abraham Lopez-Jauregui1,4, Andriy Sheremet1, Angela Smirnova1, Rex R. 8Malmstrom5, Sukhwan Yoon2, Tanja Woyke5, Peter F. Dunfield1*, Tobin J. 9Verbeke1 10 111 Department of Biological Sciences, University of Calgary, 2500 University 12Dr. NW Calgary AB Canada T2N 1N4 132 Department of Civil and Environmental Engineering, Korea Advanced 14Institute of Science and Technology, Daejeon, Korea 153Department of Biology and Ecology, University of Novi Sad Novi Sad, Serbia 164 Instituto Tecnologico y de Estudios Superiores de Monterrey, Chihuahua, 17Mexico 185 Department of Energy Joint Genome Institute, Walnut Creek, California, 19USA. 20 21*Corresponding author: [email protected]; 403-220-2469 22 3 2 4 23Competing interests: The authors declare that they have no competing 24interests. 5 3 6 25Abstract 26Copper-containing membrane monooxygenases (CuMMOs) are encoded by 27xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, 28or some short chain alkanes and alkenes. In a metagenome constructed from 29an oilsands tailings pond we detected an xmoCABD gene cluster with <59% 30derived amino acid identity to genes from known bacteria.
    [Show full text]
  • Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
    The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified;
    [Show full text]
  • Virulence Determinants, Drug Resistance and Mobile Genetic
    Lau et al. Cell & Bioscience 2011, 1:17 http://www.cellandbioscience.com/content/1/1/17 Cell & Bioscience RESEARCH Open Access Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis Susanna KP Lau1,2,3,4*†, Gilman KM Wong4†, Alan KL Tsang4†, Jade LL Teng4, Rachel YY Fan4, Herman Tse1,2,3,4, Kwok-Yung Yuen1,2,3,4 and Patrick CY Woo1,2,3,4* Abstract Background: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler’s diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements. Results: For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to b-lactam (n = 10) and multidrug efflux (n = 54).
    [Show full text]
  • Isolation, Characterization, and Applications of Rhizobiophages
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2014-10-02 Isolation, characterization, and applications of rhizobiophages Halmillawewa, Anupama Halmillawewa, A. (2014). Isolation, characterization, and applications of rhizobiophages (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/26680 http://hdl.handle.net/11023/1912 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Isolation, characterization, and applications of rhizobiophages by Anupama P. Halmillawewa A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES CALGARY, ALBERTA AUGUST, 2014 © Anupama Halmillawewa 2014 Abstract Rhizobiophages are the group of bacteriophages that infect rhizobia. The rhizobia constitute a bacterial group that includes members of several different genera and are capable of nodulating legume plant roots, and providing a source of fixed nitrogen for the plant. Rhizobiophages can play a vital role in the Rhizobium-legume symbiosis by altering the population dynamics of the rhizobia present in the rhizosphere, which can be used in agriculture to improve the efficacy of commercial Rhizobium inoculants and mitigate the Rhizobium competition problem. As a prerequisite for the application of such technology, a thorough understanding of rhizobiophage biology is required.
    [Show full text]
  • Sites in the Virginia-Washington, D.C.-Maryland Metro Area to Observe Or Collect Bacteria That Precipitate Iron and Manganese Oxides1
    SITES IN THE VIRGINIA-WASHINGTON, D.C.-MARYLAND METRO AREA TO OBSERVE OR COLLECT BACTERIA THAT PRECIPITATE IRON AND MANGANESE OXIDES1 by Eleanora I. Robbins U.S. Geological Survey Open-File Report 98-202 April 24, 1998 1 This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards. This publication is intended to be used along with U.S. Geological Survey EarthFax (1-800- USA-MAPS) What's the Red in the Water? What's the Black on the Rocks? What's the Oil on the Surface? and < http: //pubs.usgs. gov/publications/text/Norriemicrobes. html > SITES IN THE VIRGINIA-WASHINGTON, D.C.-MARYLAND METRO AREA TO OBSERVE OR COLLECT BACTERIA THAT PRECIPITATE IRON AND MANGANESE OXIDES VIRGINIA VA Site 1A. Fairfax County, Huntley Meadows Park: From the Beltway (495), go south on US 1. Turn right onto Lockheed Blvd.; travel to end of Lockheed Blvd., and then turn CAREFULLY into the Park at the sign. Park in parking lot, walk along the wetland path to the beginning of the boardwalk. Look to the right (north) and see red patches in the water where ground water is discharging. This ground water is anoxic and carries reduced iron. The iron bacteria here (predominantly Leptothrix ochracea^ oxidize the iron and turn it into a red flocculate. If you move the flocculate aside, you can see the underlying black color formed where the reducing bacteria reduce the iron to its black state in the zone of reduction in the mud. As you walk along the boardwalk, you will see much evidence of the iron bacterium, Leptothrix discophora] that forms glassy-looking patches that appear, at first glance, to be an nil-film VA Site IB.
    [Show full text]
  • Microbial Ecology of Full-Scale Wastewater Treatment Systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi
    www.nature.com/scientificreports OPEN Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Received: 28 November 2017 Accepted: 21 January 2018 Bacteria and Fungi Published: xx xx xxxx Alejandro Gonzalez-Martinez1, Maija Sihvonen1, Barbara Muñoz-Palazon2, Alejandro Rodriguez-Sanchez2, Anna Mikola1 & Riku Vahala1 Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in infuent and bioreactors were classifed as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassifed Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All infuents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors. Undoubtedly, microbial ecology of bioprocesses is a factor of major importance for the functioning of biopro- cesses, especially wastewater treatment (WWT) systems1.
    [Show full text]
  • Diversity of Anoxygenic Phototrophs in Contrasting Extreme Environments
    ÓäÎ ÛiÀÃÌÞÊvÊÝÞ}iVÊ* ÌÌÀ« ÃÊÊ ÌÀ>ÃÌ}Ê ÝÌÀiiÊ ÛÀiÌà -ICHAEL4-ADIGAN \$EBORAH/*UNG\%LIZABETH!+ARR 7-ATTHEW3ATTLEY\,AURIE!!CHENBACH\-ARCEL4*VANDER-EER $EPARTMENTOF-ICROBIOLOGY 3OUTHERN)LLINOIS5NIVERSITY #ARBONDALE $EPARTMENTOF-ICROBIOLOGY /HIO3TATE5NIVERSITY #OLUMBUS $EPARTMENTOF-ARINE"IOGEOCHEMISTRYAND4OXICOLOGY .ETHERLANDS)NSTITUTEFOR3EA2ESEARCH.)/: $EN"URG 4EXEL 4HE.ETHERLANDS #ORRESPONDING!UTHOR $EPARTMENTOF-ICROBIOLOGY 3OUTHERN)LLINOIS5NIVERSITY #ARBONDALE ), 0HONE&AX% MAILMADIGAN MICROSIUEDU Óä{ "/ ,Ê ""9Ê Ê " -/,9Ê Ê9 "7-/" Ê /" Ê*, -/, /ÊÊ 4HISCHAPTERDESCRIBESTHEGENERALPROPERTIESOFSEVERALANOXYGENICPHOTOTROPHICBACTERIAISOLATEDFROMEXTREMEENVIRONMENTS 4HESEINCLUDEPURPLEANDGREENSULFURBACTERIAFROM9ELLOWSTONEAND.EW:EALANDHOTSPRINGS ASWELLASPURPLENONSULFUR BACTERIAFROMAPERMANENTLYFROZEN!NTARCTICLAKE4HECOLLECTIVEPROPERTIESOFTHESEEXTREMOPHILICBACTERIAHAVEYIELDEDNEW INSIGHTSINTOTHEADAPTATIONSNECESSARYTOCARRYOUTPHOTOSYNTHESISINCONSTANTLYHOTORCOLDENVIRONMENTS iÞÊ7À`à Ì>ÀVÌVÊ ÀÞÊ6>iÞà ÀL>VÕÕÊ­ ÀLÕ®Ê Ìi«`Õ «ÕÀ«iÊL>VÌiÀ> , `viÀ>ÝÊ>Ì>ÀVÌVÕà ,ÃiyiÝÕÃÊë° / iÀV À>ÌÕÊÌi«`Õ Diversity of Anoxygenic Phototrophs 205 1.0 INTRODUCTION Antarctic purple bacteria were enriched using standard Anoxygenic phototrophic bacteria inhabit a variety liquid enrichment methods (Madigan 1988) from the of extreme environments, including thermal, polar, water column of Lake Fryxell, a permanently frozen lake hypersaline, acidic, and alkaline aquatic and terrestrial in the Taylor Valley, McMurdo Dry Valleys, Antarctica habitats (Madigan 2003). Typically, one finds
    [Show full text]
  • Assessing Diversity and Biogeography of Aerobic
    Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes Natalya Yutin, Marcelino Suzuki, Hanno Teeling, Marc Weber, J Venter, Douglas Rusch, Oded Béjà To cite this version: Natalya Yutin, Marcelino Suzuki, Hanno Teeling, Marc Weber, J Venter, et al.. Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2007, 9, pp.1464 - 1475. 10.1111/j.1462- 2920.2007.01265.x. hal-03012626 HAL Id: hal-03012626 https://hal.archives-ouvertes.fr/hal-03012626 Submitted on 18 Nov 2020 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. emi_1265 Environmental Microbiology (2007) doi:10.1111/j.1462-2920.2007.01265.x Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes Natalya Yutin,1 Marcelino T. Suzuki,2* phs were detected using various techniques ranging Hanno Teeling,3 Marc Weber,3 J.
    [Show full text]
  • Ecogenomics and Genome Landscapes of Marine Pseudoalteromonas Phage H105/1
    The ISME Journal (2010), 1–15 & 2010 International Society for Microbial Ecology All rights reserved 1751-7362/10 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1 Melissa Beth Duhaime1,2, Antje Wichels3, Jost Waldmann1, Hanno Teeling1 and Frank Oliver Glo¨ckner1,2 1Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany; 2School of Engineering and Sciences, Jacobs University, Bremen, Germany and 3Biosciences Division, Alfred Wegener Institute for Polar and Marine Research, BAH, Helgoland, Germany Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed ‘ecogenomic’ patterns of Pseudoalteromo- nas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra- genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most ‘host’-adapted proteins also have the strongest bacterial tetra signature, whereas the least ‘host’-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules.
    [Show full text]
  • Dynamics of Bacterial Communities in Two Unpolluted Soils After Spiking with Phenanthrene: Soil Type Specific and Common Responders
    ORIGINAL RESEARCH ARTICLE published: 21 August 2012 doi: 10.3389/fmicb.2012.00290 Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders Guo-Chun Ding, Holger Heuer and Kornelia Smalla* Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany Edited by: Considering their key role for ecosystem processes, it is important to understand the Matthew Fields, Montana State response of microbial communities in unpolluted soils to pollution with polycyclic aro- University, USA matic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Reviewed by: Uwe Strotmann, Fachhochschule Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and con- Gelsenkirchen, Germany trol soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S Yingying Wang, Nankai University, rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of China bacterial communities increasingly deviated with time between spiked and control soils. *Correspondence: In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacte- Kornelia Smalla, Julius Kühn-Institut, Federal Research Centre for ria became only detectable after 63 days, while significant effects on Betaproteobacteria Cultivated Plants, Messeweg 11-12, were detectable in both soils after 21 days. Comparison of the taxonomic distribution of D-38104 Braunschweig, Germany. bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil e-mail: [email protected] type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils.
    [Show full text]
  • Aquatic Microbial Ecology 55:1
    Vol. 55: 1–16, 2009 AQUATIC MICROBIAL ECOLOGY Printed April 2009 doi: 10.3354/ame01277 Aquat Microb Ecol Published online March 18, 2009 OPENPEN ACCESSCCESS FEATURE ARTICLE Vertical diversity of bacteria in an oxygen-stratified humic lake, evaluated using DNA and phospholipid analyses Sami Taipale1, 2, Roger I. Jones2, Marja Tiirola2,* 1University of Washington, Civil and Environmental Engineering, Box 352700, 201 More Hall, Seattle, Washington 98195, USA 2Department of Biological and Environmental Science, PO Box 35, 40014 University of Jyväskylä, Finland ABSTRACT: Microbes play a particularly important role in the food web in lakes with high dissolved organic carbon content. The bacterial community of a polyhumic lake, Mekkojärvi, was studied using DNA techniques and phospholipid fatty acid (PLFA) analysis during the mid-summer period of water column strati- fication. According to the 16S rRNA gene clone libraries and length heterogeneity analysis (LH-PCR), heterotrophic bacteria dominated only in the oxic epilimnion, in which various Actinobacteria (mostly cluster acI-B) and Betaproteobacteria (especially Poly- nucleobacter subcluster PnecC) were common. Se- quences assigned to heterotrophic, methylotrophic, photoautotrophic, and chemoautotrophic genera were all abundant in the oxic-anoxic boundary layer. Methylobacter and Methylophilus were dominant Mekkojärvi, in southern Finland, is one of countless small, genera among methylotrophic bacteria. Sequences humic lakes around the boreal zone; inset: sampling the brown water rich in DOC. assigned to the photoautotrophic green sulfur bac- Photos: Sami Taipale terium Chlorobium sp. dominated in the anoxic water column, in which the microbial PLFA biomass was 6 times higher than in the oxic surface layer. All PLFA- profiles were dominated by 16 monounsaturated fatty INTRODUCTION acids typical of Gram-negative bacteria, whereas iso- and anteiso-branched PLFAs typical of Actinobacteria Microbial foodwebs of humic (dystrophic) lakes were present only in minor proportions.
    [Show full text]
  • Microbial Community of a Gasworks Aquifer and Identification of Nitrate
    Water Research 132 (2018) 146e157 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation * Martin Sperfeld a, Charlotte Rauschenbach b, Gabriele Diekert a, Sandra Studenik a, a Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany ® b JENA-GEOS -Ingenieurbüro GmbH, Saalbahnhofstraße 25c, 07743 Jena, Germany article info abstract Article history: We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the Received 9 August 2017 presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina Received in revised form sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB 18 December 2017 was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated Accepted 18 December 2017 to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) Available online 20 December 2017 and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA Keywords: Environmental pollutions sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, Microbial communities whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Bioremediation Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By Box pathway conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, or- Functional gene marker ganisms related to Azoarcus spp.
    [Show full text]