DOCSLIB.ORG

Hydrogen and Carbon Monoxide-Utilizing Kyrpidia Spormannii Species from Pantelleria Island, Italy

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hydrogen and Carbon Monoxide-Utilizing Kyrpidia Spormannii Species from Pantelleria Island, Italy fmicb-11-00951 May 15, 2020 Time: 16:54 # 1 ORIGINAL RESEARCH published: 19 May 2020 doi: 10.3389/fmicb.2020.00951 Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy Carmen Hogendoorn1, Arjan Pol1, Nunzia Picone1, Geert Cremers1, Theo A. van Alen1, Antonina L. Gagliano2, Mike S. M. Jetten1, Walter D’Alessandro2, Paola Quatrini3 and Huub J. M. Op den Camp1* 1 Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands, 2 Istituto Nazionale di Geofisica e Vulcanologia, Palermo, Italy, 3 Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy Volcanic and geothermal areas are hot and often acidic environments that emit geothermal gasses, including H2, CO and CO2. Geothermal gasses mix with air, creating Edited by: conditions where thermoacidophilic aerobic H2- and CO-oxidizing microorganisms Axel Schippers, could thrive. Here, we describe the isolation of two Kyrpidia spormannii strains, which Federal Institute for Geosciences can grow autotrophically by oxidizing H2 and CO with oxygen. These strains, FAVT5 and and Natural Resources, Germany COOX1, were isolated from the geothermal soils of the Favara Grande on Pantelleria Reviewed by: Philippe Constant, Island, Italy. Extended physiology studies were performed with K. spormannii FAVT5, Institut National de la Recherche and showed that this strain grows optimally at 55◦C and pH 5.0. The highest growth Scientifique (INRS), Canada ± −1 Marianne Quéméneur, rate is obtained using H2 as energy source (mmax 0.19 0.02 h , doubling time UMR7294 Institut Méditerranéen 3.6 h). K. spormannii FAVT5 can additionally grow on a variety of organic substrates, d’Océanographie (MIO), France including some alcohols, volatile fatty acids and amino acids. The genome of each strain *Correspondence: encodes for two O2-tolerant hydrogenases belonging to [NiFe] group 2a hydrogenases Huub J. M. Op den Camp [email protected] and transcriptome studies using K. spormannii FAVT5 showed that both hydrogenases are expressed under H2 limiting conditions. So far no Firmicutes except K. spormannii Specialty section: FAVT5 have been reported to exhibit a high affinity for H2, with a Ks of 327 ± 24 nM. The This article was submitted to Extreme Microbiology, genomes of each strain encode for one putative CO dehydrogenase, belonging to Form a section of the journal II aerobic CO dehydrogenases. The genomic potential and physiological properties of Frontiers in Microbiology these Kyrpidia strains seem to be quite well adapted to thrive in the harsh environmental Received: 21 January 2020 Accepted: 21 April 2020 volcanic conditions. Published: 19 May 2020 Keywords: Kyrpidia spormannii,H2, [NiFe]-hydrogenases, CO, thermoacidophilic, phylogeny Citation: Hogendoorn C, Pol A, Picone N, Cremers G, van Alen TA, Gagliano AL, INTRODUCTION Jetten MSM, D’Alessandro W, Quatrini P and Op den Camp HJM Volcanic and geothermal areas represent the result of the dynamics involving the deeper layers of (2020) Hydrogen and Carbon Monoxide-Utilizing Kyrpidia the earth and resulting in the emission of several gases from volcanic soils. In general, geothermal spormannii Species From Pantelleria gases are mainly composed of H2O and CO2 as the most dominant species, and other minor Island, Italy. Front. Microbiol. 11:951. species as the more reduced gases H2S, CH4,H2, CO, and NH3 (Oppenheimer et al., 2014). The doi: 10.3389/fmicb.2020.00951 abundance of the latter gases, and consequently their impact to the atmosphere, is strictly related to Frontiers in Microbiology| www.frontiersin.org 1 May 2020| Volume 11| Article 951 fmicb-11-00951 May 15, 2020 Time: 16:54 # 2 Hogendoorn et al. H2 and CO-Oxidizing Kyrpidia spormannii the energy of the system, the water-rock interactions, gas- very important because any variation in its amount may indicate gas interactions and also to the gas-biota interactions. In some variations of the hydrothermal system. CO can be oxidized fact, the minor gas species represent the driving forces for under aerobic and anaerobic conditions (Robb and Techtmann, the establishment of an active microbial community (Shock 2018). Anaerobic CO-oxidizing bacteria have been detected in et al., 2010; Lindsay et al., 2019). Commonly, geothermal soils geothermal springs of neutral pH (Brady et al., 2015). In addition, are characterized by high temperatures and often a low pH, anaerobic microbial CO consumption has been observed in acidic which may be caused by the presence of H2S and CS2 in hot spring mud of pH 2.9 (Ikeda et al., 2015). In both cases, the emitted gases and their conversion to sulfuric acid by the microbial population was dominated by Firmicutes. Two sulfide-oxidizing microbes (Chiodini et al., 2001; D’Alessandro distinct classes of CO dehydrogenases (CODH) catalyze CO et al., 2009; Smeulders et al., 2011, 2013; Quatrini and transformation. The active site of the CODH from anaerobes Johnson, 2018). Despite the harsh conditions, these hot and contains a sulfur-coordinated Ni in a [Ni-4Fe-5S] cluster (Robb acidic terrestrial areas harbor distinctive microbial communities and Techtmann, 2018) and can be monofunctional producing (Colman et al., 2019a,b; Lindsay et al., 2019). Analyses of CO2 or bifunctional producing acetyl-CoA and H2. Aerobic soil microbial communities show that at low pH and high CO-oxidizers, or carboxydotrophs, possess heterotrimeric CO temperature, the dominant phyla differ from areas with moderate dehydrogenases with an active site containing a [Mo-Cu] temperature and neutral pH (Strazzulli et al., 2017). Beside cluster in the CoxL subunit. The other components are a temperature and acidity, the available nutrients determine the flavoprotein (CoxM) and an iron-sulfur protein (CoxS). These microbial composition. enzyme complexes catalyze the unidirectional conversion of Gagliano et al.(2016) showed that 99% of the sequences CO to CO2. The aerobic [Mo-Cu]-CO dehydrogenases can be obtained at the FAV1 site at the geothermal soils of the Favara categorized in two groups, Form I and Form II (King and Grande (Pantelleria Island) could be assigned to four main phyla: Weber, 2007). Biochemical analysis showed that Form I has Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi. At highest CO oxidation rates and is responsible for aerobic growth the FAV2 site 98% of the sequences were distributed in on CO. Form II is phylogenetically closer related to Form I only three phyla Proteobacteria, Firmicutes and Actinobacteria. CO dehydrogenase than to other enzymes of the molybdenum Especially Chloroflexi were much less represented than in FAV1. hydroxylases family. So far, no firm evidence is reported for C Apparently sites with low NH4 concentration are dominated by CO oxidation by Form II enzymes, suggesting that Form II CO C a diverse methanotrophic community, whereas high NH4 soils dehydrogenases may also catalyze the oxidation of a different harbor thermo-acidophilic chemolithotrophs, despite CH4 being substrate (Cunliffe, 2011). present. Alphaproteobacterial methanotrophs were isolated from In the upper layer of geothermal soils air is mixed with the C the low NH4 site (Gagliano et al., 2014). Previously, key players geothermal gasses (Gagliano et al., 2016). Since soil porosity in the conversion of H2S, CS2, and CH4 from the Solfatara is higher than in the deeper soil horizon and the uprising geothermal area near Naples, Italy, have been isolated and hydrothermal flux lost part of its energy, this results in conditions characterized (Pol et al., 2007; Smeulders et al., 2011, 2013; where (micro)aerobic H2 and CO-oxidizing bacteria could thrive. van Teeseling et al., 2014). Besides H2S, CS2 and CH4,H2 Here, we used samples of the Favare grande soil to enrich H2- and CO are available and suitable electron donors for novel oxidizing microorganisms. After serial dilution to extinction of chemolithoautotrophs in geothermal soils. In this study, we active enrichments we isolated and characterized two Kyrpidia focused on H2 and CO-utilizing bacteria from the Favara Grande spormannii species capable of using H2 and CO as sole energy geothermal site on Pantelleria Island, Italy. These hot and acidic source. We show that the genomic potential and physiological soils are characterized by H2 (5-168,000 ppm) and CO (1.6- properties of the two Kyrpidia strains seem very suited to thrive 26 ppm) emissions (D’Alessandro et al., 2009) and in situ in harsh volcanic conditions. H2 consumption was already observed (Gagliano et al., 2016). Both H2 and CO have a high potential as electron donor for microbial growth. MATERIALS AND METHODS H2 is an important electron donor in acidic and neutral hot springs (Spear et al., 2005) and can be used in a Geological Setting lithotrophic lifestyle under aerobic or anaerobic conditions. Pantelleria Island is a quiescent volcano located in the Oxidation of H2 is catalyzed by the enzyme hydrogenase, Sicily Channel, and characterized by several hydrothermal which can be classified as [NiFe]-, [FeFe]-, or [Fe]-hydrogenase manifestations as mofettes, fumaroles and passive degassing from depending on the metal ion in the active site (Lubitz et al., geothermal soils. The main exhalative area is Favara Grande, 2014). Hydrogenases are found among many different phyla, where soil temperatures can reach 115◦C at 5 cm of depth such as Proteobacteria, Firmicutes, Cyanobacteria, Chloroflexi, and soil pH may be down to 3. The
Load more

Recommended publications
  • Microbial Diversity of Molasses Containing Tobacco (Maassel) Unveils Contamination with Many Human Pathogens
    European Review for Medical and Pharmacological Sciences 2021; 25: 4919-4929 Microbial diversity of molasses containing tobacco (Maassel) unveils contamination with many human pathogens M.A.A. ALQUMBER Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia Abstract. – OBJECTIVE: Tobacco smoking drugs in today’s modern world. Different meth- remains a worldwide health issue, and the use of ods are currently used to consume tobacco, in- flavored varieties (maassel) embedded in glyc- cluding cigarettes, cigars and waterpipes1. Water- erine, molasses, and fruit essence via shisha pipe (shisha) smoking continues to rise globally2. paraphernalia (waterpipe) is growing globally. Smoking flavored tobacco (maassel), through the 16S rRNA gene pyrosequencing was conduct- shisha, is becoming a global preventable cause of ed on 18 different varieties representing 16 fla- 3,4 vors and three brands in order to study the mi- morbidity and mortality . crobiota of maassel and find whether it contains Scientists studied the chemical composition of pathogenic bacteria. tobacco for many years and illustrated the total MATERIALS AND METHODS: The samples number of chemicals identified in tobacco during were selected randomly from the most utilized the years from 1954 to 20055. In addition, a com- brands within Albaha, Saudi Arabia as deter- prehensive review of these chemicals’ classifica- mined through a questionnaire of 253 smok- ers. In addition, ten-fold serially diluted sam- tion, concentration and changes with time due ples were inoculated on blood agar, MacConkey to changes in the shape, design and composition agar, half-strength trypticase soy agar and malt of cigarettes was reported almost a decade ago6.
    [Show full text]
  • Aerosol Microbiome Over the Mediterranean Sea Diversity and Abundance
    atmosphere Article Aerosol Microbiome over the Mediterranean Sea Diversity and Abundance Esra Mescioglu 1,* , Eyal Rahav 2, Natalia Belkin 2, Peng Xian 3, Jordan M. Eigenza 4 , Ania Vichik 2, Barak Herut 2 and Adina Paytan 5 1 Earth and Planetary Science, University of California, Santa Cruz, CA 95060, USA 2 Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 3108000, Israel 3 Marine Meteorology Division, Naval Research Laboratory, 7 Grace Hopper Avenue, Monterey, CA 93940, USA 4 Biomolecular Engineering, University of California, Santa Cruz, CA 95060, USA 5 Institute of Marine Science, University of California, Santa Cruz, CA 95060, USA * Correspondence: [email protected] Received: 18 June 2019; Accepted: 24 July 2019; Published: 1 August 2019 Abstract: Prokaryotic microbes can become aerosolized and deposited into new environments located thousands of kilometers away from their place of origin. The Mediterranean Sea is an oligotrophic to ultra-oligotrophic marginal sea, which neighbors northern Africa (a major source of natural aerosols) and Europe (a source of mostly anthropogenic aerosols). Previous studies demonstrated that airborne bacteria deposited during dust events over the Mediterranean Sea may significantly alter the ecology and function of the surface seawater layer, yet little is known about their abundance and diversity during ‘background’ non-storm conditions. Here, we describe the abundance and genetic diversity of airborne bacteria in 16 air samples collected over an East-West transect of the entire Mediterranean Sea during non-storm conditions in April 2011. The results show that airborne bacteria represent diverse groups with the most abundant bacteria from the Firmicutes (Bacilli and Clostridia) and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) phyla.
    [Show full text]
  • Food Waste Composting and Microbial Community Structure Profiling
    processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health.
    [Show full text]
  • Alicyclobacillus Spp.: New Insights on Ecology and Preserving Food Quality Through New Approaches
    Microorganisms 2015, 3, 625-640; doi:10.3390/microorganisms3040625 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Review Alicyclobacillus spp.: New Insights on Ecology and Preserving Food Quality through New Approaches Emanuela Ciuffreda, Antonio Bevilacqua, Milena Sinigaglia and Maria Rosaria Corbo * Department of the Science of Agriculture, Food and Environment, University of Foggia, Via Napoli 15, 71122 Foggia, Italy; E-Mails: [email protected] (E.C.); [email protected] (A.B.); [email protected] (M.S.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-08-8158-9232. Academic Editor: Giuseppe Comi Received: 27 July 2015 / Accepted: 29 September 2015 / Published: 10 October 2015 Abstract: Alicyclobacillus spp. includes spore-forming and thermo-acidophilic microorganisms, usually recovered from soil, acidic drinks, orchards and equipment from juice producers. The description of the genus is generally based on the presence of ω-fatty acids in the membrane, although some newly described species do not possess them. The genus includes different species and sub-species, but A. acidoterrestris is generally regarded as the most important spoiler for acidic drinks and juices. The main goal of this review is a focus on the ecology of the genus, mainly on the species A. acidoterrestris, with a special emphasis on the different phenotypic properties and genetic traits, along with the correlation among them and with the primary source of isolation. Finally, the last section of the review reports on some alternative approaches to heat treatments (natural compounds and other chemical treatments) to control and/or reduce the contamination of food by Alicyclobacillus.
    [Show full text]
  • Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea
    microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy.
    [Show full text]
  • From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
    From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.
    [Show full text]
  • Functional Analysis of Multiple Nifb Genes of Paenibacillus Strains in Synthesis of Mo-, Fe- and V- Nitrogenase
    Functional Analysis of Multiple nifB Genes of Paenibacillus Strains in Synthesis of Mo-, Fe- and V- Nitrogenase Qin Li China Agricultural University Haowei Zhang China Agricultural University Liqun Zhang China Agricultural University San-Feng Chen ( [email protected] ) China Agricultural University https://orcid.org/0000-0003-2956-9025 Research Keywords: Paenibacillus, nifB gene, Mo-nitrogenase, alternative nitrogenases Posted Date: April 22nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-444251/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Microbial Cell Factories on July 19th, 2021. See the published version at https://doi.org/10.1186/s12934-021-01629-9. Page 1/20 Abstract Background: Biological nitrogen xation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known. Results: We have analyzed the genomes of the 116 diazotrophic Paenibacillus strains and found that some Paenibacillus strains have 2-4 nifB genes. Phylogeny analysis shows that all nifB genes in Paenibacillus fall into 4 subclasses: the nifB1 being the rst gene within the compact nif gene cluster, the nifB2 being adjacent to anf or vnf genes, the other nifB3 and nifB4 being scattered on genomes.
    [Show full text]
  • Identification and Classification of Known and Putative Antimicrobial Compounds Produced by a Wide Variety of Bacillales Species Xin Zhao1,2 and Oscar P
    Zhao and Kuipers BMC Genomics (2016) 17:882 DOI 10.1186/s12864-016-3224-y RESEARCH ARTICLE Open Access Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species Xin Zhao1,2 and Oscar P. Kuipers1* Abstract Background: Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. Results: We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. Conclusions: Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified. Keywords: Antimicrobials, Bacillales, Bacillus, Genome-mining, Lanthipeptides, Sactipeptides, Thiopeptides, NRPs, PKs Background (bacteriocins) [4], as well as non-ribosomally synthesized Most of the species of the genus Bacillus and related peptides (NRPs) and polyketides (PKs) [5].
    [Show full text]
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
    [Show full text]
  • Comparative Genomics and Phylogenomic Analyses of Lysine Riboswitch Distributions in Bacteria
    RESEARCH ARTICLE Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria Sumit Mukherjee1, Danny Barash2, Supratim Sengupta1* 1 Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India, 2 Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 a1111111111 Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative genomics studies of riboswitches focusing on their gross distribution across different bacterial taxa OPEN ACCESS have been carried out recently, systematic functional annotation and analysis of lysine ribos- Citation: Mukherjee S, Barash D, Sengupta S (2017) Comparative genomics and phylogenomic witches and the genes they regulate are still lacking. We analyzed 2785 complete bacterial analyses of lysine riboswitch distributions in genome sequences to systematically identify 468 lysine riboswitches (not counting hits from bacteria. PLoS ONE 12(9): e0184314. https://doi. multiple strains of the same species) and obtain a detailed phylogenomic map of gene-spe- org/10.1371/journal.pone.0184314 cific lysine riboswitch distribution across diverse prokaryotic phyla. We find that lysine ribos- Editor: Young-Hwa Song, Fachhochschule Lubeck, witches are most abundant in Firmicutes and Gammaproteobacteria where they are found GERMANY upstream to both biosynthesis and/or transporter genes. They are relatively rare in all other Received: March 14, 2017 prokaryotic phyla where if present they are primarily found upstream to operons containing Accepted: August 22, 2017 many lysine biosynthesis genes.
    [Show full text]
  • Alicyclobacillaceae Fam. Nov
    Family Firmicutes/“Bacilli”/Bacillales/ Alicyclobacillaceae fam. nov. .......................................................................................................................................................................................... Milton S. da Costa, Universidade de Coimbra, Departamento de Bioquímica, Coimbra 3001-401, Portugal Fred A. Rainey, Louisiana State University, Department of Biological Sciences, 202 Life Sciences Building, Baton Rouge, LA 70001, USA A.li.cy.clo.ba.cil.la’ce.ae. N.L. masc. n. Alicyclobacillus Asahara, Suzuki, Kasai and Yokota 2003, 1542 emend. type genus of the family; -aceae ending to denote a fam- Karavaiko, Bogdanova, Tourova, Kondrat’eva, Tsaplina, ily; N.L. fem. pl. n. Alicyclobacillaceae the Alicyclobacillus Egorova, Krasil’nikova and Zakharchuk 2005, 946. family. .................................................................................. References Cells are straight rods of variable length, generally non- motile. Terminal or subterminal ovoid endospores are Goto, K., K. Mochida, M. Asahara, M. Suzuki, H. Kasai and formed. The majority of the species stain Gram-positive. A. Yokota. 2003. Alicyclobacillus pomorum sp. nov., a novel Strains are non-pigmented. Aerobic with a strictly respiratory thermo-acidophilic, endospore-forming bacterium that type of metabolism, but a few strains reduce nitrate to nitrite does not possess omega-alicyclic fatty acids, and emended 3+ and some reduce Fe . Mesophilic, slightly thermophilic, description of the genus Alicyclobacillus. Int. J. Syst. Evol. and thermophilic, and acidophilic. Menaquinone-7 is the Microbiol. 53: 1537–1544. predominant respiratory quinone. Many species possess ω-cyclohexane or ω-cycloheptane, but some do not. Branched Karavaiko, G.I., T.I. Bogdanova, T.P.Tourova, T.F. Kondrat’eva, chain iso- and anteiso-fatty acids and straight chain fatty acids I.A. Tsaplina, M.A. Egorova, E.N. Krasil’nikova and are present in all species.
    [Show full text]
  • 1 Possible Drivers in Endophyte Diversity and Transmission in The
    Possible Drivers in Endophyte Diversity and Transmission in the Tomato Plant Bacterial Microbiome Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Ana María Vázquez, B.S. Graduate Program in Plant Pathology The Ohio State University 2020 Thesis Committee Dr. María Soledad Benítez-Ponce, Advisor Dr. Christine Sprunger Dr. Jonathan M. Jacobs 1 Copyrighted by Ana María Vázquez 2020 2 Abstract It has been documented that beneficial plant-associated bacteria have contributed to disease suppression, growth promotion, and tolerance to abiotic stresses. Advances in high-throughput sequencing have allowed an increase in research regarding bacterial endophytes, which are microbes that colonize the interior of plants without causing disease. Practices associated with minimizing the use of off-farm resources, such as reduced tillage regimes and crop rotations, can cause shifts in plant-associated bacteria and its surrounding agroecosystem. Integrated crop–livestock systems are an option that can provide environmental benefits by implementing diverse cropping systems, incorporating perennial and legume forages and adding animal manure through grazing livestock. It has been found that crop-livestock systems can increase soil quality and fertility, reduce cost of herbicide use and improve sustainability, especially for farmers in poorer areas of the world. This work explores how crop-livestock systems that integrate chicken rotations can impact tomato plant growth, as well as soil and endophytic bacterial communities. Tomato plants were subjected to greenhouse and field studies where biomass was assessed, and bacterial communities were characterized through culture- dependent and -independent approaches.
    [Show full text]