Kings Without Crowns: Analysis of Abundant Bacilli in Different Soil Ecosystems

Total Page:16

File Type:pdf, Size:1020Kb

Kings Without Crowns: Analysis of Abundant Bacilli in Different Soil Ecosystems Kings without crowns: Analysis of abundant bacilli in different soil ecosystems Vesela A. Tzeneva Promotor: Prof. dr. W. M. de Vos Hoogleraar Microbiologie Wageningen Universiteit Co-promotoren: Dr. H. Smidt Universitair Docent, Laboratorium voor Microbiologie Wageningen Universiteit Dr. A. D. L. Akkermans Universitair Hoofddocent, Laboratorium voor Microbiologie Wageningen Universiteit Promotiecommissie: Prof. Dr. P. de Vos Universiteit Gent, Belgiё Prof. Dr. J. D. van Elsas Rijksuniversiteit Groningen Prof. Dr. A. H. C. van Bruggen Wageningen Universiteit Dr. Ir. J. Dolfing Globalviewmanagement, Deventer Dit onderzoek is uitgevoerd binnen de onderzoekschool SENSE 2 Kings without Crowns: Analysis of abundant bacilli in different soil ecosystems Vesela A. Tzeneva Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. Dr. M.J. Kropff, in het openbaar te verdedigen op maandag 9 oktober 2006 des namiddags te 16.00 uur in de Aula. 3 Vesela A. Tzeneva – Kings without crowns: Analysis of abundant bacilli in different soil ecosystems – 2006 Thesis Wageningen University, Wageningen, The Netherlands – With summary in Dutch ISBN – 90-9020989-1 4 Посвещавам на Татко Dedicated to my Father 5 6 Content Abstract 9 Chapter 1 Introduction 11 Chapter 2 Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini 35 Chapter 3 Development and application of a selective PCR DGGE approach to detect a recently cultivated Bacillus-group predominant in the soil 55 Chapter 4 Riding the ecological time machine: succession of abundant soil bacteria in reclaimed land 79 Chapter 5 Eukaryotic diversity in historical soil samples 99 Chapter 6 Effect of soil drying and storage on the bacterial and eukaryotic diversity monitored by DGGE 117 Chapter 7 Comparative genomics of Bacillus benzoevorans related strains using a Bacillus subtilis microarray 141 Chapter 8 Discussion 155 Summary 171 Samenvatting 175 Acknowledgement 179 List of Publications 183 About the Author 185 7 8 Abstract This study describes culture-dependent as well as culture-independent strategies to monitor diversity and abundance of Bacillus benzoevorans-related soil bacteria. These bacteria are wide spread around the world, inhabiting a variety of terrestrial environments. A distinguishing feature of the family Bacillaceae is their ability to form endospores. This capacity makes the genus Bacillus amenable to retrospective and biogeographical studies, as their endospores provide the means for survival under environmental conditions of stress, allowing their detection later on. For the rapid detection of B. benzoevorans-related populations in soil samples selective cultivation media and group-specific primers and probes were developed. Using these techniques the global distribution of this group was demonstrated and indicated their adaptive capacity to diverse soil ecosystems. A unique soil sample archive provided insight in the microbiological impact of land reclamation and flooding. Using multivariate statistical approaches were used to assess the microbial community dynamics over time and in response to the changing environmental conditions. Found in a variety of soil ecosystems, microorganisms related to B. benzoevorans seem to be able to populate a broad range of niches, which indicates a high degree of metabolic versatility and strong adaptive capability. Moreover, they account for a significant part of the total bacterial community (up to 30 %). Based on our exploratory study the importance of their role is just indicated, but not acknowledged yet. Therefore, it is proposed to regard B. benzoevorans relatives as ‘kings without crowns’; as this group of bacteria deserves more scientific attention in future studies aiming to unravel their eco-physiology and functionality as major players of the soil microbiota. 9 10 CHAPTER 1 INTRODUCTION Chapter 1 General introduction A single shovel full of rich garden soil contains more species of organisms than can be found seen aboveground in the entire Amazon rain forest. The soil ecosystem is known to provide ecological niches for an extremely high number of microorganisms (94). The relationship between the diversity of living organisms and the ecosystem functions has become an important issue of modern microbial ecology. Microbial communities in the soil are involved in major processes, essential for the existence and sustainability of any terrestrial ecosystem, i.e. decomposition of organic matter (27) and mineralization of nutrients in soil (8). Alongside with this important ecosystem-defining function, soil microorganisms, mainly bacteria and fungi, provide an essential contribution to a wealth of other processes, including nitrogen fixation, solubilization of parent rock minerals, synthesis of plant-growth-promoting and other physiologically active substances, etc. Moreover, microorganisms take part in the decomposition of toxic inorganic and organic pollutants in the soil (13, 25, 82, 83, 85). When excluding plants, soil organisms can be largely divided into bacteria, archaea and eukarya (fungi, protozoa, nematodes, arthropods and earthworms). Among these, bacteria, archaea and fungi comprise the majority of the soil microbiota and are functionally important communities for soil fertility. In agricultural and grassland soils bacteria often are the predominant group (42). Soil microbiota The genus Bacillus The genus Bacillus, belonging to the family Bacillaceae within the Firmicutes, was first discovered by Ferdinand Cohn in 1872 with Bacillus subtilis as the first member. A distinguishing feature of the family is their ability to form endospores. Endospores are structures formed within bacterial cells that enable the cell to resist environmental conditions of stress. The members of the genus Bacillus are furthermore characterized as Gram-positive, rod-shaped, and aerobic or facultatively anaerobic (70). In Bergey's Manual of Systematic Bacteriology (1st ed. 1986), the G+C content of known species of Bacillus is listed to range from 32 to 69% (46), illustrating the genomic heterogeneity of the genus. Variations are observed from species to species, and sometimes 12 Introduction profound differences in G+C content are even found among strains within a species. For example, the G+C content of the B. megaterium group ranges from 36 to 45%. According to the “Bacterial Nomenclature up-to-date” (DSMZ -Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany, http://www.dsmz.de/bactnom/bactname.htm), there are currently 188 species and 6 subspecies recognized in the genus Bacillus (available data in May 2006). A large number of valid species have been designated and novel species are discovered regularly, as evidenced by the fact that only since 2005, 29 novel species have been described. The genus Bacillus is both taxonomically and metabolically diverse. The primary habitat is the soil and associated plants or rivers, although some species are pathogenic for mammals (e.g. B. anthracis) and insects (e.g. B. sphaericus, B. thuringensis) (103). Bacilli form an important part of the microbiota in many soils, and many species are of considerable practical importance. Some Bacillus spp., including those that are thermophilic, are crucial for biotechnological applications Figure 1. Electron micrograph of B. cereus ATCC 10987 (T. Lindbäck, as they are sources of enzymes and other products of http://mlstoslo.uio.no/bacillus.html, industrial interest (7). Other Bacillus spp., such as B. accession date: 13 June 2006). thuringensis, B. subtilis, B. cereus and B. sphaericus, play important roles as biological control agents of different phytopathogenic organisms (24, 75, 86). Some members of the genus Bacillus are able to produce antibiotics. The majority of these antibiotics are low-molecular-weight peptides with different biological activities, including antimicrobial, antiviral, and antitumor activities (41), and several Bacillus isolates obtained from soil and plants have recently been reported to be capable of enzymatic inactivation of N-acyl homoserine lactone quorum sensing signals (19). The ability of Bacillus to form highly resistant endospores imparts an enormous competitive advantage in environments such as soil, where long periods of drought and nutrient deprivation are common (103). At least 4% of the 4.2 Mbp large B. subtilis genome, comprising 4100 protein-encoding genes (51), is dedicated to the processes of sporulation, germination and out-growth. Bacteria in temperate soils must be able to adapt rapidly to changes in ambient temperatures. For this purpose the B. subtilis genome encodes numerous stress proteins, including the chaperones (44). The ability of Bacillus spp. to secrete a wide variety of extracellular depolymerases is a major factor contributing to their colonisation in soil. Genes encoding secreted amylases, arabinases, chitonases, mannanases, cellulases and xylanases are 13 Chapter 1 evident in the genome sequence. Proteases are also frequently encountered, both intracellular and extracellular, the latter allowing for the use of protein as sources of both carbon and nitrogen (103). To date, the complete genomes of 12 strains of Bacillus have been elucidated, which all showed to be relatively large, ranging from 4.2 Mbp (B. halodurans C-125) to 5.6 Mbp (B anthracis AMES 0581) (http://genomesonline.org, accession date: 18 March 2006). This might reflect the ability of bacilli to survive and adapt to frequent
Recommended publications
  • Investigation of Bacteria Associated with Australian Wine Grapes Using Cultural and Molecular Methods
    Investigation of bacteria associated with Australian wine grapes using cultural and molecular methods Sung Sook Bae A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy University of New South Wales Food Science and Technology School of Chemical Engineering and Industrial Chemistry Sydney, Australia 2005 i DECLARATION I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of materials which have been accepted for the award of any other degree or diploma at UNSW or any other education institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project’s design and conception or in style, presentation and linguistic expression is acknowledged. Sung Sook Bae ii ACKNOWLEDGEMENTS I owe a tremendous debt of gratitude to numerous individuals who have contributed to the completion of this work, and I wish to thank them for their contribution. Firstly and foremost, my sincere appreciation goes to my supervisor, Professor Graham Fleet. He has given me his time, expertise, constant guidance and inspiration throughout my study. I also would like to thank my co-supervisor, Dr. Gillian Heard for her moral support and words of encouragement. I am very grateful to the Australian Grape and Wine Research Development and Corporation (GWRDC) for providing funds for this research.
    [Show full text]
  • Rare Phytomyxid Infection on the Alien Seagrass Halophila Stipulacea In
    Research Article Mediterranean Marine Science Indexed in WoS (Web of Science, ISI Thomson) and SCOPUS The journal is available on line at http://www.medit-mar-sc.net DOI: http://dx.doi.org/10.12681/mms.14053 Rare phytomyxid infection on the alien seagrass Halophila stipulacea in the southeast Aegean Sea MARTIN VOHNÍK1,2, ONDŘEJ BOROVEC1,2, ELIF ÖZGÜR ÖZBEK3 and EMINE ŞÜKRAN OKUDAN ASLAN4 1 Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, 25243 Czech Republic 2 Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, 12844 Czech Republic 3 Marine Biology Museum, Antalya Metropolitan Municipality, Antalya, Turkey 4 Department of Marine Biology, Faculty of Fisheries, Akdeniz University, Antalya, Turkey Corresponding author: [email protected] Handling Editor: Athanasios Athanasiadis Received: 31 May 2017; Accepted: 9 October 2017; Published on line: 8 December 2017 Abstract Phytomyxids (Phytomyxea) are obligate endosymbionts of many organisms such as algae, diatoms, oomycetes and higher plants including seagrasses. Despite their supposed significant roles in the marine ecosystem, our knowledge of their marine diversity and distribution as well as their life cycles is rather limited. Here we describe the anatomy and morphology of several developmental stages of a phytomyxid symbiosis recently discovered on the petioles of the alien seagrass Halophila stipulacea at a locality in the southeast Aegean Sea. Its earliest stage appeared as whitish spots already on the youngest leaves at the apex of the newly formed rhizomes. The infected host cells grew in volume being filled with plasmodia which resulted in the formation of characteristic macroscopic galls.
    [Show full text]
  • Protist Phylogeny and the High-Level Classification of Protozoa
    Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane).
    [Show full text]
  • Plasmodiophora Brassicae
    Bi et al. Phytopathology Research (2019) 1:12 https://doi.org/10.1186/s42483-019-0018-6 Phytopathology Research RESEARCH Open Access Comparative genomics reveals the unique evolutionary status of Plasmodiophora brassicae and the essential role of GPCR signaling pathways Kai Bi1,2, Tao Chen2, Zhangchao He1,2, Zhixiao Gao1,2, Ying Zhao1,2, Huiquan Liu3, Yanping Fu2, Jiatao Xie1,2, Jiasen Cheng1,2 and Daohong Jiang1,2* Abstract Plasmodiophora brassicae is an important biotrophic eukaryotic plant pathogen and a member of the rhizarian protists. This biotrophic pathogen causes clubroot in cruciferous plants via novel intracellular mechanisms that are markedly different from those of other biotrophic organisms. To date, genomes from six single spore isolates of P. brassicae have been sequenced. An accurate description of the evolutionary status of this biotrophic protist, however, remains lacking. Here, we determined the draft genome of the P. brassicae ZJ-1 strain. A total of 10,951 protein-coding genes were identified from a 24.1 Mb genome sequence. We applied a comparative genomics approach to prove the Rhizaria supergroup is an independent branch in the eukaryotic evolutionary tree. We also found that the GPCR signaling pathway, the versatile signal transduction to multiple intracellular signaling cascades in response to extracellular signals in eukaryotes, is significantly enriched in P. brassicae-expanded and P. brassicae-specific gene sets. Additionally, treatment with a GPCR inhibitor relieved the symptoms of clubroot and significantly suppressed the development of plasmodia. Our findings suggest that GPCR signal transduction pathways play important roles in the growth, development, and pathogenicity of P. brassicae.
    [Show full text]
  • Phylogenomics Supports the Monophyly of the Cercozoa T ⁎ Nicholas A.T
    Molecular Phylogenetics and Evolution 130 (2019) 416–423 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenomics supports the monophyly of the Cercozoa T ⁎ Nicholas A.T. Irwina, , Denis V. Tikhonenkova,b, Elisabeth Hehenbergera,1, Alexander P. Mylnikovb, Fabien Burkia,2, Patrick J. Keelinga a Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada b Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia ARTICLE INFO ABSTRACT Keywords: The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major Cercozoa component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa Rhizaria remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, Phylogeny including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly Phylogenomics of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from Single-cell transcriptomics newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12′ group, and phyloge- nomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.
    [Show full text]
  • Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus Methanolicus
    International Journal of Molecular Sciences Article Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus methanolicus Marta Irla , Sigrid Hakvåg and Trygve Brautaset * Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology, 7034 Trondheim, Norway; [email protected] (M.I.); [email protected] (S.H.) * Correspondence: [email protected]; Tel.: +47-73593315 Abstract: Genome-wide transcriptomic data obtained in RNA-seq experiments can serve as a re- liable source for identification of novel regulatory elements such as riboswitches and promoters. Riboswitches are parts of the 50 untranslated region of mRNA molecules that can specifically bind various metabolites and control gene expression. For that reason, they have become an attractive tool for engineering biological systems, especially for the regulation of metabolic fluxes in industrial microorganisms. Promoters in the genomes of prokaryotes are located upstream of transcription start sites and their sequences are easily identifiable based on the primary transcriptome data. Bacillus methanolicus MGA3 is a candidate for use as an industrial workhorse in methanol-based biopro- cesses and its metabolism has been studied in systems biology approaches in recent years, including transcriptome characterization through RNA-seq. Here, we identify a putative lysine riboswitch in B. methanolicus, and test and characterize it. We also select and experimentally verify 10 putative B. methanolicus-derived promoters differing in their predicted strength and present their functionality in combination with the lysine riboswitch. We further explore the potential of a B. subtilis-derived purine riboswitch for regulation of gene expression in the thermophilic B. methanolicus, establishing a Citation: Irla, M.; Hakvåg, S.; novel tool for inducible gene expression in this bacterium.
    [Show full text]
  • Abbreviations
    Abbreviations AfDD Acriflavine direct detection AODC Acridine orange direct count ARA Arachidonic acid BPE Bleach plant effluent Bya Billion years ago CFU Colony forming unit DGGE Denaturing gradient gel electrophoresis DHA Docosahexaenoic acid DOC Dissolved organic carbon DOM Dissolved organic matter DSE Dark septate endophyte EN Ectoplasmic net EPA Eicosapentaenoic acid FITC Fluorescein isothiocyanate GPP Gross primary production ITS Internal transcribed spacer LDE Lignin-degrading enzyme LSU Large subunit MAA Mycosporine-like amino acid MBSF Metres below surface Mpa Megapascal MPN Most probable number MSW Molasses spent wash MUFA Monounsaturated fatty acid Mya Million years ago NPP Net primary production OMZ Oxygen minimum zone OUT Operational taxonomic unit PAH Polyaromatic hydrocarbon PCR Polymerase chain reaction © Springer International Publishing AG 2017 345 S. Raghukumar, Fungi in Coastal and Oceanic Marine Ecosystems, DOI 10.1007/978-3-319-54304-8 346 Abbreviations POC Particulate organic carbon POM Particulate organic matter PP Primary production Ppt Parts per thousand PUFA Polyunsaturated fatty acid QPX Quahog parasite unknown SAR Stramenopile Alveolate Rhizaria SFA Saturated fatty acid SSU Small subunit TEPS Transparent Extracellular Polysaccharides References Abdel-Waheb MA, El-Sharouny HM (2002) Ecology of subtropical mangrove fungi with empha- sis on Kandelia candel mycota. In: Kevin D (ed) Fungi in marine environments. Fungal Diversity Press, Hong Kong, pp 247–265 Abe F, Miura T, Nagahama T (2001) Isolation of highly copper-tolerant yeast, Cryptococcus sp., from the Japan Trench and the induction of superoxide dismutase activity by Cu2+. Biotechnol Lett 23:2027–2034 Abe F, Minegishi H, Miura T, Nagahama T, Usami R, Horikoshi K (2006) Characterization of cold- and high-pressure-active polygalacturonases from a deep-sea yeast, Cryptococcus liquefaciens strain N6.
    [Show full text]
  • Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria
    Lawrence Berkeley National Laboratory Recent Work Title Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria. Permalink https://escholarship.org/uc/item/44j757z8 Journal Microorganisms, 3(1) ISSN 2076-2607 Authors McTaggart, Tami L Beck, David AC Setboonsarng, Usanisa et al. Publication Date 2015-03-20 DOI 10.3390/microorganisms3010094 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Microorganisms 2015, 3, 94-112; doi:10.3390/microorganisms3010094 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria Tami L. McTaggart 1,†, David A. C. Beck 1,3, Usanisa Setboonsarng 1,‡, Nicole Shapiro 4, Tanja Woyke 4, Mary E. Lidstrom 1,2, Marina G. Kalyuzhnaya 2,§ and Ludmila Chistoserdova 1,* 1 Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA; E-Mails: [email protected] (T.L.M.); [email protected] (D.A.C.B.); [email protected] (U.S.); [email protected] (M.E.L.) 2 Department of Microbiology, University of Washington, Seattle, WA 98195, USA; E-Mail: [email protected] 3 eScience Institute, University of Washington, Seattle, WA 98195, USA 4 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA; E-Mails: [email protected] (N.S.); [email protected] (T.W.) † Present address: Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA 92697, USA. ‡ Present address: Denali Advanced Integration, Redmond, WA 98052, USA. § Present address: Biology Department, San Diego State University, San Diego, CA 92182, USA. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-206-616-1913.
    [Show full text]
  • Production of Value-Added Chemicals by Bacillus Methanolicus Strains Cultivated on Mannitol and Extracts of Seaweed Saccharina Latissima at 50◦C
    fmicb-11-00680 April 8, 2020 Time: 19:50 # 1 ORIGINAL RESEARCH published: 09 April 2020 doi: 10.3389/fmicb.2020.00680 Production of Value-Added Chemicals by Bacillus methanolicus Strains Cultivated on Mannitol and Extracts of Seaweed Saccharina latissima at 50◦C Sigrid Hakvåg1, Ingemar Nærdal2, Tonje M. B. Heggeset2, Kåre A. Kristiansen1, Inga M. Aasen2 and Trygve Brautaset1* 1 Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology, Trondheim, Norway, 2 Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway The facultative methylotroph Bacillus methanolicus MGA3 has previously been genetically engineered to overproduce the amino acids L-lysine and L-glutamate and their derivatives cadaverine and g-aminobutyric acid (GABA) from methanol at 50◦C. We here explored the potential of utilizing the sugar alcohol mannitol and seaweed extract (SWE) containing mannitol, as alternative feedstocks for production of chemicals by fermentation using B. methanolicus. Extracts of the brown algae Saccharina latissima Edited by: harvested in the Trondheim Fjord in Norway were prepared and found to contain 12– Nuno Pereira Mira, ∼ University of Lisbon, Portugal 13 g/l of mannitol, with conductivities corresponding to a salt content of 2% NaCl. Reviewed by: Initially, 12 B. methanolicus wild type strains were tested for tolerance to various SWE Stefan Junne, concentrations, and some strains including MGA3 could grow on 50% SWE medium. Technical University of Berlin, Non-methylotrophic and methylotrophic growth of B. methanolicus rely on differences Germany Hao Zhou, in regulation of metabolic pathways, and we compared production titers of GABA Dalian University of Technology, China and cadaverine under such growth conditions.
    [Show full text]
  • Bacillus Methanolicus Sp
    University of Groningen Bacillus methanolicus sp. nov., a New Species of Thermotolerant, Methanol-Utilizing, Endospore-Forming Bacteria Arfman, Nico; Dijkhuizen, Lubbert; Kirchhof, Gudrun; Ludwig, Wolfgang; Schleifer, Karl-Heinz; Bulygina, Eugenia S.; Chumakov, Konstantin M.; Govorukhina, Natalya I.; Trotsenko, Yuri A.; White, Duncan Published in: International Journal of Systematic Bacteriology DOI: 10.1099/00207713-42-3-439 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 1992 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Arfman, N., Dijkhuizen, L., Kirchhof, G., Ludwig, W., Schleifer, K-H., Bulygina, E. S., Chumakov, K. M., Govorukhina, N. I., Trotsenko, Y. A., White, D., & Sharp, R. J. (1992). Bacillus methanolicus sp. nov., a New Species of Thermotolerant, Methanol-Utilizing, Endospore-Forming Bacteria. International Journal of Systematic Bacteriology, 42(3), 439-445. https://doi.org/10.1099/00207713-42-3-439 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment.
    [Show full text]
  • A Checklist of Egyptian Fungi: I
    Mycosphere 4 (4): 794–807 (2013) ISSN 2077 7019 www.mycosphere.org Article Mycosphere Copyright © 2013 Online Edition Doi 10.5943/mycosphere/4/4/15 A checklist of Egyptian fungi: I. Protozoan fungal analogues Abdel-Azeem AM1* and Salem Fatma M1 1Laboratory of systematic Mycology, Botany and Microbiology Department, Faculty of Science, University of Suez Canal, Ismailia 41522, Egypt. e-mail: [email protected], [email protected] Abdel-Azeem AM, Salem Fatma M 2013 – A checklist of Egyptian fungi: I. Protozoan fungal analogues. Mycosphere 4(4), 794–807, Doi 10.5943/mycosphere/4/4/15 Abstract Records of Egyptian fungi are scattered through a wide array of journals, books, dissertations, and preliminary annotated checklists and compilations. By screening all available sources of information, it was possible to delineate 61 taxa, including 3 varieties, belonging to 29 genera of protozoan fungal analogues that have been reported from Egypt. A provisional key to the identification of reported taxa is given. This is the first species list of protozoan fungus-like analogues from Egypt. Key words – Amoebozoa – biodiversity – Cercozoa – documentation – Liceida – Mycobiota – Physarum Introduction For Egypt, only very few comprehensive assessments of local fungi have been published (e.g. El-Abyad and Abu-Taleb 1993; El-Abyad 1997; Abdel-Azeem, 2010). Documentation of the Egyptian fungi may be dated back to 4500 B.C., when ancient Egyptians produced a number of hieroglyphic reliefs of plants (many of which are psychedelic) on walls and within texts throughout Egypt (Abdel-Azeem 2010). Abdel-Azeem has traced the history of scientific work with fungi in Egypt from its earliest beginnings, almost 200 years ago, through to the present day and published a full review of the history of mycology in Egypt, together with updated assessment of 2281 species of fungi for the country, and an expectation of future perspectives for mycology in Egypt.
    [Show full text]
  • Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria
    Current Biology 22, 1123–1127, June 19, 2012 ª2012 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2012.04.021 Report Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria Matthew W. Brown,1,* Martin Kolisko,1,2 called a sorocarp (Figure 1A). Their life cycles are socially Jeffrey D. Silberman,3 and Andrew J. Roger1,* intricate because each cell retains its individuality yet works 1Centre for Comparative Genomics and Evolutionary with other like-cells to form a variably complex multicellular Bioinformatics, Department of Biochemistry sorocarp. The ‘‘patchy’’ phylogenetic distribution of soro- and Molecular Biology carpic protists across the tree of eukaryotes suggests that 2Centre for Comparative Genomics and Evolutionary they have independently converged upon this analogous Bioinformatics, Department of Biology mode of propagule dispersal, which is also similar to that of Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada the analogous life cycle in myxobacteria [9]. Here we conclu- 3Department of Biological Sciences, University of Arkansas, sively determine the evolutionary position of Guttulinopsis Fayetteville, AR, 72701, USA vulgaris, a ubiquitous but under-studied sorocarpic amoeba, using a phylogenomic approach with one of the largest protein supermatrices assembled to date that encompasses all major Summary groups of eukaryotes. The genus Guttulinopsis, composed of four species, was Multicellular forms of life have evolved many times, indepen- described over a century ago [10] and has been variously dently giving rise to a diversity of organisms such as classified [11, 12]. Guttulinopsis vulgaris is the most common animals, plants, and fungi that together comprise the visible species and can be found globally on the dung of various biosphere.
    [Show full text]