Curriculum Vitae
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Physiological Characteristics of Magnetospirillum Gryphiswaldense
www.nature.com/scientificreports OPEN Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth Received: 18 October 2016 Accepted: 21 April 2017 under high-iron and low-oxygen Published: xx xx xxxx conditions Qing Wang1,5, Xu Wang1,5, Weijia Zhang2,5, Xianyu Li3, Yuan Zhou1, Dan Li1, Yinjia Wang4, Jiesheng Tian1,5, Wei Jiang1,5, Ziding Zhang 1, Youliang Peng1, Lei Wang4, Ying Li1,5 & Jilun Li1,5 Magnetosome formation by Magnetospirillum gryphiswaldense MSR-1 is dependent on iron and oxygen levels. We used transcriptome to evaluate transcriptional profiles of magnetic and non-magnetic MSR-1 cells cultured under high-iron and low-iron conditions. A total of 80 differentially expressed genes (DEGs) were identified, including 53 upregulated and 27 downregulated under high-iron condition. These DEGs belonged to the functional categories of biological regulation, oxidation-reduction process, and ion binding and transport, and were involved in sulfur metabolism and cysteine/methionine metabolism. Comparison with our previous results from transcriptome data under oxygen-controlled conditions indicated that transcription of mam or mms was not regulated by oxygen or iron signals. 17 common DEGs in iron- and oxygen-transcriptomes were involved in energy production, iron transport, and iron metabolism. Some unknown-function DEGs participate in iron transport and metabolism, and some are potential biomarkers for identification ofMagnetospirillum strains. IrrA and IrrB regulate iron transport in response to low-oxygen and high-iron signals, respectively. Six transcription factors were predicted to regulate DEGs. Fur and Crp particularly co-regulate DEGs in response to changes in iron or oxygen levels, in a proposed joint regulatory network of DEGs. -
Accretion of Water in Carbonaceous Chondrites: Current Evidence and Implications for the Delivery of Water to Early Earth
ACCRETION OF WATER IN CARBONACEOUS CHONDRITES: CURRENT EVIDENCE AND IMPLICATIONS FOR THE DELIVERY OF WATER TO EARLY EARTH Josep M. Trigo-Rodríguez1,2, Albert Rimola3, Safoura Tanbakouei1,3, Victoria Cabedo Soto1,3, and Martin Lee4 1 Institute of Space Sciences (CSIC), Campus UAB, Facultat de Ciències, Torre C5-parell-2ª, 08193 Bellaterra, Barcelona, Catalonia, Spain. E-mail: [email protected] 2 Institut d’Estudis Espacials de Catalunya (IEEC), Edif.. Nexus, c/Gran Capità, 2-4, 08034 Barcelona, Catalonia, Spain 3 Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain. E-mail: [email protected] 4 School of Geographical and Earth Sciences, University of Glasgow, Gregory Building, Lilybank Gardens, Glasgow G12 8QQ, UK. Manuscript Pages: 37 Tables: 2 Figures: 10 Keywords: comet; asteroid; meteoroid; meteorite; minor bodies; primitive; tensile strength Accepted in Space Science Reviews (SPAC-D-18-00036R3, Vol. Ices in the Solar System) DOI: 10.1007/s11214-019-0583-0 Abstract: Protoplanetary disks are dust-rich structures around young stars. The crystalline and amorphous materials contained within these disks are variably thermally processed and accreted to make bodies of a wide range of sizes and compositions, depending on the heliocentric distance of formation. The chondritic meteorites are fragments of relatively small and undifferentiated bodies, and the minerals that they contain carry chemical signatures providing information about the early environment available for planetesimal formation. A current hot topic of debate is the delivery of volatiles to terrestrial planets, understanding that they were built from planetesimals formed under far more reducing conditions than the primordial carbonaceous chondritic bodies. -
Magnetotactic Bacteria and Their Application in Medicine
Chem cal ist si ry y & h P B f i o o Dasdag and Bektas. J Phys Chem Biophys 2014, 4:2 p l h a Journal of Physical Chemistry & y n s r DOI: 10.4172/2161-0398.1000141 i u c o s J ISSN: 2161-0398 Biophysics ResearchReview Article Article OpenOpen Access Access Magnetotactic Bacteria and their Application in Medicine Suleyman Dasdag1* and Hava Bektas2 1Department of Biophysics, Medical School of Dicle University, Diyarbakir, Turkey 2Department of Biophysics, Medical School of Yuzuncu Yil University, Van / Turkey Abstract It is a known fact how the magnetic field of the Earth is very important for life. Relation between living systems and the earth magnetic field has been investigated for many years. Birds and their migration routes are the first one of the things that comes to mind when we state living things. The Earth’s magnetic field is still accepted to be the main factor for birds and other flying living beings to complete their travels correctly. The changes in migration routes, which are observed from time to time, are sometimes said to be due to the changes in the magnetic field. However, no light has been shed to this matter yet. The Earth’s magnetic field has not been sufficiently studied, and its role on small living models such as bacteria has not been adequately discussed. One of the best examples in this field is relation between the Earth’s magnetic field and “magnetotactic bacteria (MTB)”, which were discovered by Salvatore Bellini in 1963. Currently, it is claimed that magnetotactic bacteria have a widespread use in microbiology, mineralogy, limnology, physics, biophysics, chemistry, biochemistry, geology, crystallography, and astrobiology. -
A New Occurrence of Terrestrial Native Iron in the Earth's Surface
geosciences Article A New Occurrence of Terrestrial Native Iron in the Earth’s Surface: The Ilia Thermogenic Travertine Case, Northwestern Euboea, Greece Christos Kanellopoulos 1,2,* ID , Eugenia Valsami-Jones 3,4, Panagiotis Voudouris 1, Christina Stouraiti 1 ID , Robert Moritz 2, Constantinos Mavrogonatos 1 ID and Panagiotis Mitropoulos 1,† 1 Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15784 Athens, Greece; [email protected] (P.V.); [email protected] (C.S.); [email protected] (C.M.); [email protected] (P.M.) 2 Section of Earth and Environmental Sciences, University of Geneva, Rue des Maraichers 13, 1205 Geneva, Switzerland; [email protected] 3 School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; [email protected] 4 Department of Earth Sciences, Natural History Museum London, Cromwell Road, London SW7 5BD, UK * Correspondence: [email protected] † Professor Panagiotis Mitropoulos has passed away in 2017. Received: 6 April 2018; Accepted: 23 July 2018; Published: 31 July 2018 Abstract: Native iron has been identified in an active thermogenic travertine deposit, located at Ilia area (Euboea Island, Greece). The deposit is forming around a hot spring, which is part of a large active metallogenetic hydrothermal system depositing ore-bearing travertines. The native iron occurs in two shapes: nodules with diameter 0.4 and 0.45 cm, and angular grains with length up to tens of µm. The travertine laminae around the spherical/ovoid nodules grow smoothly, and the angular grains are trapped inside the pores of the travertine. -
Detection of a Bacterial Group Within the Phylum Chloroflexi And
Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases. -
MACKINAWITE from SOUTH AFRICA W. C J. Van RDNSBU*.O, Geological Surtey Oj Soulh Africa, Preloria, Soulh A.[Ri Co, L. Lrbnunsbyc
TI.IE AMERICAN MINERALOGIST, VOL 52, JULY AUGUST, 1967 MACKINAWITE FROM SOUTH AFRICA W. C J. vAN RDNSBU*.o,Geological Surtey oJ Soulh Africa, Preloria,Soulh A.[rico, AND L. LrBnuNsByc, Deparlment of Geology,Llnit:ersity of Pretoria, Pre!oria,Soul h Africa. ABSTRAcT Mackinawite has been identified in mafic and ultramafic rocks of the Bushveld igneous complex and Insizwa and also in the carbonatite and pegmatoid of Loolekop, Phalaborrva complex in South Africa. The mineral occurs predominantly as somewhat irregular to oriented intergrowths in pentlandite in all these occurrences and less commonly as regular oriented lamellae in chalcopyrite and rarely in cubanite. The textural evidence suggests that mackinawite may represent an exsolution product of pentlandite, chalcopyrite and cubanite. INrnonucrroN The iron sulphide, mackinawite was recently named in a paper by Evans, et al, (1964). Natural occurrencesof this mineral f rom Finland were describedby- Kouvo et al (1963)and from the Muskox intrusion in Canada by Chamberlain and Delabio (1965). During the presentinvestigation mackinawite was distinguishedfrom valleriite in the carbonatite and pegmatoid of Loolekop, Phalaborwa complex, in the Bushveld igneous complex, and from Insizwa, Cape Province.The mode of occurrenceof the mackinawite in the carbonatite difiers somewhatfrom that in the mafic rocks of Insizwa and the Bush- veld complex. MrNnn.q.rocv The physicaland optical propertiesof mackinawitefrom the Bushveid complex,Insizwa and Loolekop are very similar and are in closeagree- ment with the propertiesgiven for the same mineral from the Muskox intrusion by Chamberlain and Delabio (1965). The mineral takes a fairly good polish,particularly after buffing with a chromic oxide slurry. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
Genomic Insights Into the Uncultured Genus &Lsquo
The ISME Journal (2014) 8, 2463–2477 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae Wei Lin1,2,7, Aihua Deng3,7, Zhang Wang4, Ying Li2,5, Tingyi Wen3, Long-Fei Wu2,6, Martin Wu4 and Yongxin Pan1,2 1Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of the Earth’s Deep Interior, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China; 2France-China Bio-Mineralization and Nano-Structures Laboratory, Chinese Academy of Sciences, Beijing, China; 3CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; 4Department of Biology, University of Virginia, Charlottesville, VA, USA; 5State Key Laboratory of Agro-Biotechnology and Laboratoire International Associe Franco-Chinois de Bio-Mineralisation et Nano-Structures, College of Biological Sciences, China Agricultural University, Beijing, China and 6Laboratoire de Chimie Bacte´rienne, Aix-Marseille Universite´, CNRS, Marseille Cedex 20, France Magnetotactic bacteria (MTB) of the genus ‘Candidatus Magnetobacterium’ in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magneto- somes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named ‘Ca. -
1471-2164-13-670.Pdf
Hobley et al. BMC Genomics 2012, 13:670 http://www.biomedcentral.com/1471-2164/13/670 RESEARCH ARTICLE Open Access Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria Laura Hobley1,3, Thomas R Lerner1,4, Laura E Williams2, Carey Lambert1, Rob Till1, David S Milner1, Sarah M Basford1, Michael J Capeness1, Andrew K Fenton1,5, Robert J Atterbury1,6, Maximilian ATS Harris1 and R Elizabeth Sockett1* Abstract Background: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. Results: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Regulation of Nitrogen Fixation in Rhodospirillum Rubrum Through Proteomics and Beyond
Regulation of nitrogen fixation in Rhodospirillum rubrum Through proteomics and beyond Tiago Toscano Selão ©Tiago Toscano Selão, Stockholm 2010 ISBN 978-91-7447-125-0, pp 1 – 71 Printed in Sweden by US-AB, Stockholm 2010 Distributor: Department of Biochemistry and Biophysics Cover image: Three-dimensional rendering of the Gaussian peaks for a 2D-PAGE gel, generated using PDQuest 7.3.0. Dedicado aos meus pais e à memória dos meus avós. Publication list The work presented on this thesis is based on the following publications, referred to in the text by the corresponding Roman numerals: I – Selão, T. T. , Nordlund, S. and Norén, A. ”Comparative proteomic studies in Rhodospirillum rubrum grown under different nitrogen conditions”, J Prot Res , 2008, 7: p. 3267-75 II – Teixeira, P. F.*, Selão, T. T. *, Henriksson, V., Wang, H., Norén, A. and Nordlund, S. ”Diazotrophic growth of Rhodospirillum rubrum with 2-oxoglutarate as sole carbon source affects the regulation of nitrogen metabolism as well as the soluble proteome”, Res. Microb., 2010, in press III – Selão, T. T. , Branca, R., Lehtiö, J., Chae, P. S., Gellman, S. H., Rasmussen, S., Nordlund, S. and Norén, A. ”Identification of the chromatophore membrane complexes formed under different nitrogen conditions in Rhodospirillum rubrum ”, submitted IV – Selão, T. T. *, Teixeira, P. F.* and Nordlund, S. ”The activity of dinitrogenase reductase ADP-ribosyltransferase of Rhodospirillum rubrum is controlled through reversible complex formation with the PII protein GlnB”, manuscript V – Selão, T. T. , Edgren, T., Wang, H., Norén, A. and Nordlund, S. ”The effect of pyruvate on the metabolic regulation of nitrogenase activity in Rhodospirillum rubrum with darkness as switch-off effector”, submitted * Authors contributed equally Additional publications Vintila, S., Selão, T.