DOCSLIB.ORG

Investigating Bacterial Community Structure Over Temporal and Spatial Scales in the Northwest Atlantic Ocean

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Investigating Bacterial Community Structure Over Temporal and Spatial Scales in the Northwest Atlantic Ocean INVESTIGATING BACTERIAL COMMUNITY STRUCTURE OVER TEMPORAL AND SPATIAL SCALES IN THE NORTHWEST ATLANTIC OCEAN by Jackie Zorz Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia February 2016 © Copyright by Jackie Zorz, 2016 Table of Contents List of Tables ...................................................................................................................... v List of Figures ................................................................................................................... vii Abstract ............................................................................................................................... x List of Abbreviations and Symbols Used .......................................................................... xi Acknowledgements ........................................................................................................... xii Chapter 1: Introduction ....................................................................................................... 1 Chapter 2: Bacterial Community Structure of the Scotian Shelf ........................................ 5 2.0 Abstract ......................................................................................................................... 5 2.1 Introduction ................................................................................................................... 5 2.2 Materials and Methods ................................................................................................ 10 2.2.1 Sample Collection ................................................................................................ 10 2.2.2 Flow Cytometry.................................................................................................... 11 2.2.3 DNA Extraction.................................................................................................... 11 2.2.4 Amplification and Library Preparation ................................................................ 12 2.2.5 Illumina MiSeq Sequencing ................................................................................. 12 2.2.6 QIIME 16S rRNA Data Analysis ......................................................................... 13 2.2.7 Statistical Analysis and Data Visualization ......................................................... 15 2.3 Results ......................................................................................................................... 18 2.3.1 Environmental Parameters ................................................................................... 18 2.3.2 Community Composition and Alpha Diversity .................................................... 22 2.3.3 Beta Diversity, Biogeography and Patterns in Spatial Distribution ..................... 32 2.3.4 Multivariate Analysis of Abundance Data and Correlation Analyses ................. 39 2.3.5 Thebaud Platform Station – Comprehensive analysis of the bacterial community surrounding an offshore oil and gas platform ............................................ 45 2.4 Discussion ................................................................................................................... 48 2.4.1 Assumptions and Cautions when interpreting 16S rRNA sequencing data ......... 48 2.4.2 Bacterial Composition of Scotian Shelf ............................................................... 49 2.4.3 Beta Diversity, Biogeography and Patterns in Spatial Distribution ..................... 54 2.4.4 Multivariate Analysis of Abundance and Correlation Analyses .......................... 59 2.4.4.1. Group Effects: Season, MLD and Location ................................................. 64 2.4.4.2 Responses to Environmental Gradients ......................................................... 68 ii 2.4.4.3 Co-occurrence and Exclusion Patterns of Bacteria in the Scotian Shelf ....... 69 2.4.5 Thebaud Platform Station – Comprehensive analysis of the bacterial community surrounding an offshore oil and gas platform ............................................ 71 2.4.6 Conclusions .......................................................................................................... 73 Chapter 3: Investigating Bacterial Communities through Frequent Sampling of Deep Waters in the Bedford Basin, Canada ............................................................................... 75 3.0 Abstract ....................................................................................................................... 75 3.1 Introduction ................................................................................................................. 76 3.2 Materials and Methods ................................................................................................ 78 3.2.1 Sample Collection ................................................................................................ 78 3.2.2 DNA Extraction.................................................................................................... 79 3.2.3 Amplification and Library Preparation ................................................................ 79 3.2.4 Illumina MiSeq Sequencing ................................................................................. 80 3.2.5 QIIME 16S rRNA Data Analysis ......................................................................... 80 3.2.6 Statistical Analysis and Data Visualization ......................................................... 81 3.3 Results ......................................................................................................................... 83 3.3.1 Environmental Parameters ................................................................................... 83 3.3.2 Bacterial Community Analysis at 60 m – Alpha Diversity .................................. 86 3.3.3 Bacterial Community Analysis at 60 m – Beta Diversity .................................... 91 3.3.4 Dynamics of Individual OTUs – Rare and Indicator Species at 60 m ................. 95 3.3.5 Intrusion Events.................................................................................................. 107 3.3.5.1 First Intrusion – March 5th to March 12th 2014 (weeks 10-11) ................... 107 3.3.5.2 Second Intrusion – July 8th to July 15th (weeks 28-29) ............................... 108 3.4 Discussion ................................................................................................................. 111 3.4.1 Establishing a Microbial Time Series in the Bedford Basin through use of High Throughput Sequencing ..................................................................................... 111 3.4.2 Environmental Variation in the Bedford Basin in 2014 ..................................... 112 3.4.3 Bacterial Community Analysis at 60 m – Alpha and Beta Diversity................. 113 3.4.4 Dynamics of Individual OTUs – Rare and Indicator Species at 60 m ............... 116 3.4.5 Intrusion Events.................................................................................................. 121 3.4.6 Conclusion .......................................................................................................... 124 Chapter 4: Conclusion..................................................................................................... 125 4.1 Comparing Scotian Shelf and Bedford Basin ........................................................... 125 iii 4.2 Future Directions ...................................................................................................... 128 4.2.1 Future Directions Scotian Shelf ......................................................................... 128 4.2.2 Future Directions Bedford Basin........................................................................ 129 References ....................................................................................................................... 131 Appendix 1: Supplementary Information ....................................................................... 149 iv List of Tables Table 2.1. Summary of taxonomic information from the OTUs that represented at least 5% of the community composition…………………………………………………15 Table 2.2. Parameters from the linear regressions of environmental variables and the Shannon Diversity Index for stations grouped by season………………………………..29 Table 2.3. Results from Partial Mantel tests of Spearman’s correlation between all environmental variables, geographic distance, and individual environmental variable gradients and abundance matrices performed on all sites………………………………..36 Table 2.4. Results from Partial Mantel Tests of Spearman’s correlation between all environmental variables, geographic distance, and individual environmental variable gradients, with abundance matrices split into season and depth groups…………………37 Table 2.5. Description of significant correlations associated with at least 2/3 of the taxa in each cluster from Figure 2.15. …………………………………………………..59 Table 2.6. Descriptions of select taxa that are significantly affected by group and environmental explanatory variables. …………………………………………………...60 Table 3.1. Results of temporal Mantel and Partial Mantel Tests of community similarity and environmental variables at 60 m depth…………………………………...94 Table 3.2. OTUs that fit the “Abundant Specialist” classification where they occur in less than 50% of samples at 60 m but become conditionally abundant as they reach over 1% of community abundance
Load more

Recommended publications
  • Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
    microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%).
    [Show full text]
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
    [Show full text]
  • Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
    Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally.
    [Show full text]
  • Downloaded from the NCBI Genome Portal (Table S1)
    J. Microbiol. Biotechnol. 2021. 31(4): 601–609 https://doi.org/10.4014/jmb.2012.12054 Review Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M Sang-Hyeok Cho1, Yujin Jeong1, Eunju Lee1, So-Ra Ko3, Chi-Yong Ahn3, Hee-Mock Oh3, Byung-Kwan Cho1,2*, and Suhyung Cho1,2* 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 2KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 3Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan- genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species.
    [Show full text]
  • Diversity of Cultivated and Metabolically Active Aerobic Anoxygenic Phototrophic Bacteria Along an Oligotrophic Gradientthe in Mediterranean Sea C
    Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 8, 4421–4457, 2011 Biogeosciences www.biogeosciences-discuss.net/8/4421/2011/ Discussions doi:10.5194/bgd-8-4421-2011 © Author(s) 2011. CC Attribution 3.0 License. This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1INSU-CNRS, UMR 7144, Observatoire Oceanologique´ de Roscoff, Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR 7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR 6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Accepted: 29 April 2011 – Published: 5 May 2011 Correspondence to: C. Jeanthon (jeanthon@sb-roscoff.fr) Published by Copernicus Publications on behalf of the European Geosciences Union. 4421 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterio- plankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of 5 AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria.
    [Show full text]
  • Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales
    GBE Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales Vandana Viswanathan1,2, Anushree Narjala1, Aravind Ravichandran1, Suvratha Jayaprasad1,and Shivakumara Siddaramappa1,* 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru, Karnataka, India 2Manipal University, Manipal, Karnataka, India *Corresponding author: E-mail: [email protected]. Accepted: February 10, 2017 Data deposition: Genome sequences were downloaded from GenBank, and their accession numbers are provided in table 1. Abstract The order Sphingomonadales, containing the families Erythrobacteraceae and Sphingomonadaceae, is a relatively less well-studied phylogenetic branch within the class Alphaproteobacteria. Prophage elements are present in most bacterial genomes and are important determinants of adaptive evolution. An “intact” prophage was predicted within the genome of Sphingomonas hengshuiensis strain WHSC-8 and was designated Prophage IWHSC-8. Loci homologous to the region containing the first 22 open reading frames (ORFs) of Prophage IWHSC-8 were discovered among the genomes of numerous Sphingomonadales.In17genomes, the homologous loci were co-located with an ORF encoding a putative superoxide dismutase. Several other lines of molecular evidence implied that these homologous loci represent an ancient temperate bacteriophage integration, and this horizontal transfer event pre-dated niche-based speciation within the order Sphingomonadales. The “stabilization” of prophages in the genomes of their hosts is an indicator of “fitness” conferred by these elements and natural selection. Among the various ORFs predicted within the conserved prophages, an ORF encoding a putative proline-rich outer membrane protein A was consistently present among the genomes of many Sphingomonadales. Furthermore, the conserved prophages in six Sphingomonas sp. contained an ORF encoding a putative spermidine synthase.
    [Show full text]
  • A Novel Bacterial Thiosulfate Oxidation Pathway Provides a New Clue About the Formation of Zero-Valent Sulfur in Deep Sea
    The ISME Journal (2020) 14:2261–2274 https://doi.org/10.1038/s41396-020-0684-5 ARTICLE A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea 1,2,3,4 1,2,4 3,4,5 1,2,3,4 4,5 1,2,4 Jing Zhang ● Rui Liu ● Shichuan Xi ● Ruining Cai ● Xin Zhang ● Chaomin Sun Received: 18 December 2019 / Revised: 6 May 2020 / Accepted: 12 May 2020 / Published online: 26 May 2020 © The Author(s) 2020. This article is published with open access Abstract Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA − – – – − 1234567890();,: 1234567890();,: in converting thiosulfate to tetrathionate ( O3S S S SO3 ), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions.
    [Show full text]
  • Extreme Environments and High-Level Bacterial Tellurite Resistance
    microorganisms Review Extreme Environments and High-Level Bacterial Tellurite Resistance Chris Maltman 1,* and Vladimir Yurkov 2 1 Department of Biology, Slippery Rock University, Slippery Rock, PA 16001, USA 2 Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; [email protected] * Correspondence: [email protected]; Tel.: +724-738-4963 Received: 28 October 2019; Accepted: 20 November 2019; Published: 22 November 2019 Abstract: Bacteria have long been known to possess resistance to the highly toxic oxyanion tellurite, most commonly though reduction to elemental tellurium. However, the majority of research has focused on the impact of this compound on microbes, namely E. coli, which have a very low level of resistance. Very little has been done regarding bacteria on the other end of the spectrum, with three to four orders of magnitude greater resistance than E. coli. With more focus on ecologically-friendly methods of pollutant removal, the use of bacteria for tellurite remediation, and possibly recovery, further highlights the importance of better understanding the effect on microbes, and approaches for resistance/reduction. The goal of this review is to compile current research on bacterial tellurite resistance, with a focus on high-level resistance by bacteria inhabiting extreme environments. Keywords: tellurite; tellurite resistance; extreme environments; metalloids; bioremediation; biometallurgy 1. Introduction Microorganisms possess a wide range of extraordinary abilities, from the production of bioactive molecules [1] to resistance to and transformation of highly toxic compounds [2–5]. Of great interest are bacteria which can convert the deleterious oxyanion tellurite to elemental tellurium (Te) through reduction. Currently, research into bacterial interactions with tellurite has been lagging behind investigation of the oxyanions of other metals such as nickel (Ni), molybdenum (Mo), tungsten (W), iron (Fe), and cobalt (Co).
    [Show full text]
  • Crenn Et Al. 2018.Pdf
    Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux, Christian Jeanthon To cite this version: Klervi Crenn, Delphine Duffieux, Christian Jeanthon. Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.2879. 10.3389/fmicb.2018.02879. hal-02130560 HAL Id: hal-02130560 https://hal.archives-ouvertes.fr/hal-02130560 Submitted on 15 May 2019 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. fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations.
    [Show full text]
  • Discovery of Siderophore and Metallophore Production in the Aerobic Anoxygenic Phototrophs
    microorganisms Article Discovery of Siderophore and Metallophore Production in the Aerobic Anoxygenic Phototrophs Steven B. Kuzyk, Elizabeth Hughes and Vladimir Yurkov * Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; [email protected] (S.B.K.); [email protected] (E.H.) * Correspondence: [email protected] Abstract: Aerobic anoxygenic phototrophs have been isolated from a rich variety of environments including marine ecosystems, freshwater and meromictic lakes, hypersaline springs, and biological soil crusts, all in the hopes of understanding their ecological niche. Over 100 isolates were chosen for this study, representing 44 species from 27 genera. Interactions with Fe3+ and other metal(loid) cations such as Mg2+,V3+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Se4+ and Te2+ were tested using a chromeazurol S assay to detect siderophore or metallophore production, respectively. Representatives from 20 species in 14 genera of α-Proteobacteria, or 30% of strains, produced highly diffusible siderophores that could bind one or more metal(loid)s, with activity strength as follows: Fe > Zn > V > Te > Cu > Mn > Mg > Se > Ni > Co. In addition, γ-proteobacterial Chromocurvus halotolerans, strain EG19 excreted a brown compound into growth medium, which was purified and confirmed to act as a siderophore. It had an approximate size of ~341 Da and drew similarities to the siderophore rhodotorulic acid, a member of the hydroxamate group, previously found only among yeasts. This study is the first to discover siderophore production to be widespread among the aerobic anoxygenic phototrophs, which may be another key method of metal(loid) chelation and potential detoxification within their environments. Citation: Kuzyk, S.B.; Hughes, E.; Yurkov, V.
    [Show full text]
  • Multi-Marker Molecular Characterization of Ciliates and Their Endosymbionts
    Facoltà di Scienze Matematiche, Fisiche e Naturali Corso di Laurea Magistrale in Conservazione ed Evoluzione Tesi di Laurea Magistrale Multi-marker molecular characterization of ciliates and their endosymbionts Candidato Vittorio Boscaro Relatore Dott. Giulio Petroni Correlatori Prof. Alberto Castelli Prof. Sergei Fokin Anno Accademico 2010/2011 "!#$%&'()*+&$(%#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!, "!"!#+$-$.&/0#.%)#&1/$'#/%)(0234$(%&0#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!5 !"!"!"#$%&'#(%)*$#%+#$,&-.%$.$#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""/ !"!"0"#1'+')23#4'256)'$#2+*#$,$5'&25.7$#%4#7.3.25'$#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""8 !"!"9"#'7%3%1,#%4#7.3.25'$#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""": !"!"/"#-275').23#'+*%$,&-.%+5$#%4#7.3.25'$#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""; "!6!#3(-/+*-.'#3.'7/'0#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"6 !"0"!"#5<'#&635.=&2)>')#7<2)275').?25.%+#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!0 !"0"0"#+673'2)#))+2#1'+'#$'@6'+7'$#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!8 !"0"9"#7%A!#1'+'#$'@6'+7'#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!B
    [Show full text]
  • Phylogenomics and Signature Proteins for the Alpha Proteobacteria and Its Main Groups Radhey S Gupta* and Amy Mok
    BMC Microbiology BioMed Central Research article Open Access Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups Radhey S Gupta* and Amy Mok Address: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada Email: Radhey S Gupta* - [email protected]; Amy Mok - [email protected] * Corresponding author Published: 28 November 2007 Received: 20 July 2007 Accepted: 28 November 2007 BMC Microbiology 2007, 7:106 doi:10.1186/1471-2180-7-106 This article is available from: http://www.biomedcentral.com/1471-2180/7/106 © 2007 Gupta and Mok; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. Results: We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI- Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz.
    [Show full text]