The Metal Oxides of Abandoned Tin Mining Pit Waters As an Indicator for Bacterial Diversity Andri Kurniawan
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Taxonomic and Chemical Assessment of Exceptionally Abundant Rock Mine Biofilm
Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm Karolina Tomczyk-Żak1, Paweª Szczesny2,3, Robert Gromadka4 and Urszula Zielenkiewicz1 1 Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland 2 Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland 3 Department of Bioinformatics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland 4 Laboratory of DNA Sequencing and Oligonucleotides Synthesis, Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland ABSTRACT Background. An exceptionally thick biofilm covers walls of ancient gold and arsenic Zªoty Stok mine (Poland) in the apparent absence of organic sources of energy. Methods and Results. We have characterized this microbial community using culture- dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock. Submitted 13 April 2017 Conclusions. -
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http://wjst.wu.ac.th Natural Sciences Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria Megga Ratnasari PIKOLI1,*, Irawan SUGORO2 and Suharti3 1Department of Biology, Faculty of Science and Technology, Universitas Islam Negeri Syarif Hidayatullah Jakarta, Ciputat, Tangerang Selatan, Indonesia 2Center for Application of Technology of Isotope and Radiation, Badan Tenaga Nuklir Nasional, Jakarta Selatan, Indonesia 3Department of Chemistry, Faculty of Science and Computation, Universitas Pertamina, Simprug, Jakarta Selatan, Indonesia (*Corresponding author’s e-mail: [email protected], [email protected]) Received: 7 September 2017, Revised: 11 September 2018, Accepted: 29 October 2018 Abstract Studies that explore the diversity of microorganisms in unusual (extreme) environments have become more common. Our research aims to predict the diversity of bacteria that inhabit an extreme environment, a coal mine’s soil with pH of 2.93. Soil samples were collected from the soil at a depth of 12 meters from the surface, which is a clay layer adjacent to a coal seam in Tanjung Enim, South Sumatera, Indonesia. A culture-independent method, the polymerase chain reaction based denaturing gradient gel electrophoresis, was used to amplify the 16S rRNA gene to detect the viable-but-unculturable bacteria. Results showed that some OTUs that have never been found in the coal environment and which have phylogenetic relationships to the rare actinobacteria Actinomadura, Actinoallomurus, Actinospica, Streptacidiphilus, Aciditerrimonas, and Ferrimicrobium. Accordingly, the highly acidic soil in the coal mine is a source of rare actinobacteria that can be explored further to obtain bioactive compounds for the benefit of biotechnology. -
Bacterial Diversity in the Surface Sediments of the Hypoxic Zone Near
ORIGINAL RESEARCH Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea Qi Ye, Ying Wu, Zhuoyi Zhu, Xiaona Wang, Zhongqiao Li & Jing Zhang State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China Keywords Abstract Bacteria, Changjiang Estuary, hypoxia, Miseq Illumina sequencing, sediment Changjiang (Yangtze River) Estuary has experienced severe hypoxia since the 1950s. In order to investigate potential ecological functions of key microorgan- Correspondence isms in relation to hypoxia, we performed 16S rRNA-based Illumina Miseq Qi Ye, East China Normal University, State Key sequencing to explore the bacterial diversity in the surface sediments of the Laboratory of Estuarine and Coastal Research, hypoxic zone near the Changjiang Estuary and in the East China Sea (ECS). 3663 North Zhongshan Road, SKLEC Building, Room 419, Shanghai 200062, China. The results showed that numerous Proteobacteria-affiliated sequences in the sedi- Tel: 86-021-52124974; ments of the inner continental shelf were related to both sulfate-reducing and Fax: 86-021- 62546441; sulfur-oxidizing bacteria, suggesting an active sulfur cycle in this area. Many E-mail: [email protected] sequences retrieved from the hypoxic zone were also related to Planctomycetes from two marine upwelling systems, which may be involved in the initial break- Funding Information down of sulfated heteropolysaccharides. Bacteroidetes, which is expected to degrade This study was funded by the Shanghai Pujiang high-molecular-weight organic matter, was abundant in all the studied stations Talent Program (12PJ1403100), the National except for station A8, which was the deepest and possessed the largest grain Natural Science Foundation of China (41276081), the Key Project of Chinese size. -
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. -
The Bacterial Communities of Sand-Like Surface Soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang
The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang To cite this version: Yang Wang. The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA). Agricultural sciences. Université Paris-Saclay, 2015. English. NNT : 2015SACLS120. tel-01261518 HAL Id: tel-01261518 https://tel.archives-ouvertes.fr/tel-01261518 Submitted on 25 Jan 2016 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. NNT : 2015SACLS120 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N°577 Structure et Dynamique des Systèmes Vivants Spécialité de doctorat : Sciences de la Vie et de la Santé Par Mme Yang WANG The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Thèse présentée et soutenue à Orsay, le 23 Novembre 2015 Composition du Jury : Mme. Marie-Claire Lett , Professeure, Université Strasbourg, Rapporteur Mme. Corinne Cassier-Chauvat , Directeur de Recherche, CEA, Rapporteur M. Armel Guyonvarch, Professeur, Université Paris-Sud, Président du Jury M. -
Lifestyle Preferences Drive the Structure and Diversity of Bacterial and Archaeal Communities in a Small Riverine Reservoir
www.nature.com/scientificreports OPEN Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir Carles Borrego1,2, Sergi Sabater1,3* & Lorenzo Proia1,4 Spatial heterogeneity along river networks is interrupted by dams, afecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil diferences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Diferences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir. Spatial heterogeneity of river networks results from the sequence of lotic segments—which promote the transport and quick transformation of materials—and lentic segments such as large pools and wetlands—which mostly contribute to the process and storage of organic matter 1,2. -
Microbial Diversity in Rhizosphere Soil of Soybean Grass Under Different Cultivation Methods in an Alpine Region
Microbial diversity in rhizosphere soil of soybean grass under different cultivation methods in an alpine region Ying Zhang ( [email protected] ) Qinghai University Wenhui Liu Qinghai University Xilai Li Qinghai University Zhiying Zhang Qinghai University Beibei Su Qinghai University Ri-na Dao Qinghai University Yan Wang Qinghai University Research article Keywords: Avena sativa L., Vicia sativa L., high-throughput sequencing, clean culture, mixed seeding Posted Date: June 3rd, 2020 DOI: https://doi.org/10.21203/rs.3.rs-31329/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background A large number of studies have shown that soybean grass with mixed seeding cultivation can signicantly improve the yield and quality of forage grass compared with clean culture cultivation.This study explores the differences in the characteristics of the composition and diversity of the microbial community in the rhizosphere of soybean grasses between clean culture and mixed seeding methods in an alpine region. We used high-throughput sequencing technology to determine the microbial diversity and analytical methods to determine the physicochemical characteristics of plant rhizosphere soil of Avena sativa L. and Vicia sativa L. Results There were no signicant differences in pH, total nitrogen, total phosphorus, and total potassium in the rhizosphere soil samples of soybean grasses under the clean culture and mixed seeding methods, while there were signicant differences in the available nitrogen, available phosphorus, available potassium, and organic matter content (P < 0.05). The bacterial diversity of the rhizosphere soil of Avena sativa L. was the highest under the clean culture method, and the fungal diversity of the rhizosphere soil of Vicia sativa L. -
Microbial Community Composition in Acid Mine Drainage Lake of Xiang
This article was downloaded by: [Zhejiang University] On: 11 April 2013, At: 17:31 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Geomicrobiology Journal Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/ugmb20 Microbial Community Composition in Acid Mine Drainage Lake of Xiang Mountain Sulfide Mine in Anhui Province, China Chunbo Hao a b , Lina Zhang a b , Lihua Wang a b , Siyuan Li a b & Hailiang Dong a c a Geomicrobiology Laboratory, State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Beijing, China b School of Water Resources and Environment, China University of Geosciences, Beijing, China c Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA Accepted author version posted online: 18 Apr 2012.Version of record first published: 14 Sep 2012. To cite this article: Chunbo Hao , Lina Zhang , Lihua Wang , Siyuan Li & Hailiang Dong (2012): Microbial Community Composition in Acid Mine Drainage Lake of Xiang Mountain Sulfide Mine in Anhui Province, China, Geomicrobiology Journal, 29:10, 886-895 To link to this article: http://dx.doi.org/10.1080/01490451.2011.635762 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. -
Chemolithotrophic Nitrate-Dependent Fe(II)-Oxidizing Nature of Actinobacterial Subdivision Lineage TM3
The ISME Journal (2013) 7, 1582–1594 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3 Dheeraj Kanaparthi1, Bianca Pommerenke1, Peter Casper2 and Marc G Dumont1 1Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany and 2Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Limnology of Stratified Lakes, Stechlin, Germany Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitrate- dependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitrate- dependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 Â 104 autotrophic and 1 Â 107 heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to B0.6% of bacterial 13 16S rRNA gene sequences. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Bacterial and Archaeal Communities in Lake Nyos Stratification and Microbial Communities of Ace Lake, Antarctica: a Review of the (Cameroon, Central Africa)
OPEN Bacterial and archaeal communities in SUBJECT AREAS: Lake Nyos (Cameroon, Central Africa) ENVIRONMENTAL Rosine E. Tiodjio1, Akihiro Sakatoku1, Akihiro Nakamura1, Daisuke Tanaka1, Wilson Y. Fantong3, SCIENCES Kamtchueng B. Tchakam1, Gregory Tanyileke3, Takeshi Ohba2, Victor J. Hell3, Minoru Kusakabe1, MOLECULAR ECOLOGY Shogo Nakamura1 & Akira Ueda1 Received 1Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 17 April 2014 930-8555, Japan, 2Department of Chemistry, School of Science, University of Tokai, Kanagawa 259-1292, Japan, 3Institute of Accepted Mining and Geological Research, P.O. Box 4110, Yaounde´, Cameroon. 4 August 2014 Published The aim of this study was to assess the microbial diversity associated with Lake Nyos, a lake with an unusual 21 August 2014 chemistry in Cameroon. Water samples were collected during the dry season on March 2013. Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. The results indicate a stratification of both communities along the water column. Altogether, the physico-chemical data and microbial sequences Correspondence and suggest a close correspondence of the potential microbial functions to the physico-chemical pattern of the requests for materials lake. We also obtained evidence of a rich microbial diversity likely to include several novel microorganisms should be addressed to of environmental importance in the large unexplored microbial reservoir of Lake Nyos. R.E.T. (d1278301@ ems.u-toyama.ac.jp; icroorganisms constitute a substantial proportion of the biosphere. Their number is at least two to three edwigetiodjio@gmail. orders of magnitude larger than that of all the plant and animal cells combined, constituting about 60% com) M of the earth’s biomass1; besides, they are very diverse.