Bacterial Metataxonomic Profile and Putative Functional Behavior
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Download Download
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. -
A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp
International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1 -
Fmicb-09-02926 November 29, 2018 Time: 17:35 # 1
fmicb-09-02926 November 29, 2018 Time: 17:35 # 1 ORIGINAL RESEARCH published: 30 November 2018 doi: 10.3389/fmicb.2018.02926 Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios Juanjo Rodríguez1*, Christine M. J. Gallampois2, Sari Timonen1, Agneta Andersson3,4, Hanna Sinkko5, Peter Haglund2, Åsa M. M. Berglund3, Matyas Ripszam6, Daniela Figueroa3, Mats Tysklind2 and Owen Rowe1,7 1 Department of Microbiology, University of Helsinki, Helsinki, Finland, 2 Department of Chemistry, Umeå University, Umeå, Sweden, 3 Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden, 4 Umeå Marine Research Centre (UMF), Umeå University, Hörnefors, Sweden, 5 Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland, 6 MSCi ApS Laboratory, Skovlunde, Denmark, 7 Helsinki Commission (HELCOM), Baltic Marine Environment Protection Commission, Helsinki, Finland Coastal ecosystems are highly dynamic and can be strongly influenced by climate Edited by: change, anthropogenic activities (e.g., pollution), and a combination of the two Alison Buchan, The University of Tennessee, pressures. As a result of climate change, the northern hemisphere is predicted to Knoxville, United States undergo an increased precipitation regime, leading in turn to higher terrestrial runoff Reviewed by: and increased river inflow. This increased runoff will transfer terrestrial dissolved organic Veljo Kisand, University of Tartu, Estonia matter (tDOM) and anthropogenic contaminants to coastal waters. Such changes can Andrew C. Singer, directly influence the resident biology, particularly at the base of the food web, and can Natural Environment Research influence the partitioning of contaminants and thus their potential impact on the food Council (NERC), United Kingdom web. -
Genomic Analysis of a Freshwater Actinobacterium, “Candidatus
J. Microbiol. Biotechnol. (2017), 27(4), 825–833 https://doi.org/10.4014/jmb.1701.01047 Research Article Review jmb Genomic Analysis of a Freshwater Actinobacterium, “Candidatus Limnosphaera aquatica” Strain IMCC26207, Isolated from Lake Soyang Suhyun Kim, Ilnam Kang, and Jang-Cheon Cho* Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea Received: January 16, 2017 Revised: February 3, 2017 Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilution- Accepted: February 6, 2017 to-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene First published online sequences indicated that strain IMCC26207 formed a distinct lineage in the order February 7, 2017 Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously *Corresponding author identified bacterial taxa was “Candidatus Microthrix parvicella” with 16S rRNA gene sequence Phone: +82-32-860-7711; similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater Fax: +82-32-232-0541; actinobacterium, is reported with the description of the genome properties and annotation E-mail: [email protected] summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. -
Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches
Microorganisms 2015, 3, 667-694; doi:10.3390/microorganisms3040667 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches Antonio García-Moyano 1,*, Andreas Erling Austnes 1, Anders Lanzén 1,2, Elena González-Toril 3, Ángeles Aguilera 3 and Lise Øvreås 1 1 Department of Biology, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway; E-Mails: [email protected] (A.E.A.); [email protected] (A.L.); [email protected] (L.Ø.) 2 Neiker-Tecnalia, Basque Institute for Agricultural Research and Development, c/Berreaga 1, E48160 Derio, Spain 3 Instituto de Técnica Aeroespacial, Centro de Astrobiología (CAB-CSIC), Ctra. Torrejón-Ajalvir km 4, E-28850 Madrid, Spain; E-Mails: [email protected] (E.G.-T); [email protected] (A.A.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +47-5558-8187; Fax: +47-5558-4450. Academic Editor: Ricardo Amils Received: 27 July 2015 / Accepted: 29 September 2015 / Published: 13 October 2015 Abstract: Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. -
The Case of the Red Pigment Miltos
Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome: The case of the red pigment miltos E. Photos-Jones a,b, C.W.Knapp c, D. Venieri d, G.E.Christidis f, C.Elgy e, E. Valsami-Jones e, I. Gounaki c and N.C.Andriopoulou f. a Analytical Services for Art and Archaeology (Ltd), Glasgow G12 8JD, UK b Archaeology, School of Humanities, University of Glasgow, Glasgow G12 8QQ, UK c Civil and Environmental Engineering, University of Strathclyde, Glasgow G1 1XQ, UK d School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece e School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK f School of Mineral Resources Engineering, Technical University of Crete, 73100 Chania, Greece Journal of Archaeological Science: Reports. Volume 22, December 2018, Pages 179-192 https://doi.org/10.1016/j.jasrep.2018.07.017 corresponding author address: [email protected] Abstract This paper introduces a holistic approach to the study of Greco-Roman (G-R) lithotherapeutics. These are the minerals or mineral combinations that appear in the medical and scientific literature of the G-R world. It argues that they can best be described not simply in terms of their bulk chemistry/mineralogy but also their ecological microbiology and nanofraction component. It suggests that each individual attribute may have underpinned the bioactivity of the lithotherapeutic as an antibacterial, antifungal or other. We focus on miltos, the highly prized, naturally fine, red iron oxide-based mineral used as a pigment, in boat maintenance, agriculture and medicine. -
Thermophilic and Alkaliphilic Actinobacteria: Biology and Potential Applications
REVIEW published: 25 September 2015 doi: 10.3389/fmicb.2015.01014 Thermophilic and alkaliphilic Actinobacteria: biology and potential applications L. Shivlata and Tulasi Satyanarayana * Department of Microbiology, University of Delhi, New Delhi, India Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive Edited by: compounds, which find multifarious applications. Wen-Jun Li, Sun Yat-Sen University, China Keywords: Actinobacteria, thermophiles, alkaliphiles, polyextremophiles, bioactive compounds, enzymes Reviewed by: Erika Kothe, Friedrich Schiller University Jena, Introduction Germany Hongchen Jiang, The phylum Actinobacteria is one of the most dominant phyla in the bacteria domain (Ventura Miami University, USA et al., 2007), that comprises a heterogeneous Gram-positive and Gram-variable genera. The Qiuyuan Huang, phylum also includes a few Gram-negative species such as Thermoleophilum sp. (Zarilla and Miami University, USA Perry, 1986), Gardenerella vaginalis (Gardner and Dukes, 1955), Saccharomonospora -
Actinobacteria Isolated from Mineral Ores in Peru
ACTINOBACTERIA ISOLATED FROM MINERAL ORES IN PERU Jasmin Hurtado*1, Sara Liz Pacheco1, Patricia Sheen2 and Daniel Ugarte1 Address(es): Jasmin Hurtado, 1Universidad Peruana Cayetano Heredia, Facultad de Ciencias y Filosofía, Laboratorio de Biotecnología Ambiental, Av. Honorio Delgado 430, Lima 31, Lima, Perú, (511) 319-0000. 2 Universidad Peruana Cayetano Heredia, Facultad de Ciencias y Filosofía, Laboratorio de Biología Molecular y Bioinformática, Av. Honorio Delgado 430, Lima 31, Lima, Perú, (511) 319-0000. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2018.7.4.366-370 ARTICLE INFO ABSTRACT Received 13. 10. 2017 A total of twenty-four isolates of actinobacteria from arsenopyrite, pyrite, polymetallic sulfides and magnetite from Peruvian mining Revised 6. 11. 2017 zones have been used with the purpose of characterizing them by morphological, physiological and molecular studies for future Accepted 20. 12. 2017 biotechnological applications. 23 strains were identified as Streptomyces and1 as Actinomadura sp.95% and 70% of the strains were Published 1. 2. 2018 able to grow at pH 3.5 and pH 2, respectively. Only 19% of them were able to oxidize iron at pH 2. Also, they have been tested by growth on arsenopyrite tailings and Streptomyces sp. E1 and Streptomycesvariabilis AB5 leached 19.1 % and 15.5 % of arsenic, respectively, while the control without inoculum only showed 2.5% of leaching. Results indicate that these strains show important Regular article characteristics for leaching processes. Keywords: Streptomyces, Actinomadura, minerals, bacterial leaching, arsenopyrite INTRODUCTION MATERIAL AND METHODS There is a wide diversity of microorganisms developing on mineral ores, Strains and growth medium concentrates and tailings. -
Effects of Organic Pollutants on Bacterial Communities Under
http://www.diva-portal.org This is the published version of a paper published in Frontiers in Microbiology. Citation for the original published paper (version of record): Rodríguez, J., Gallampois, C., Timonen, S., Andersson, A., Sinkko, H. et al. (2018) Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios Frontiers in Microbiology, 9: 2926 https://doi.org/10.3389/fmicb.2018.02926 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-153774 fmicb-09-02926 November 29, 2018 Time: 17:35 # 1 ORIGINAL RESEARCH published: 30 November 2018 doi: 10.3389/fmicb.2018.02926 Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios Juanjo Rodríguez1*, Christine M. J. Gallampois2, Sari Timonen1, Agneta Andersson3,4, Hanna Sinkko5, Peter Haglund2, Åsa M. M. Berglund3, Matyas Ripszam6, Daniela Figueroa3, Mats Tysklind2 and Owen Rowe1,7 1 Department of Microbiology, University of Helsinki, Helsinki, Finland, 2 Department of Chemistry, Umeå University, Umeå, Sweden, 3 Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden, 4 Umeå Marine Research Centre (UMF), Umeå University, Hörnefors, Sweden, 5 Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland, 6 MSCi ApS Laboratory, Skovlunde, Denmark, 7 Helsinki Commission (HELCOM), Baltic Marine Environment Protection Commission, Helsinki, Finland Coastal ecosystems are highly dynamic and can be strongly influenced by climate Edited by: change, anthropogenic activities (e.g., pollution), and a combination of the two Alison Buchan, The University of Tennessee, pressures. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Characterization of Bacterial Communities in Lithobionts and Soil Niches from Victoria Valley, Antarctica Marc W
FEMS Microbiology Ecology, 92, 2016, fiw051 doi: 10.1093/femsec/fiw051 Advance Access Publication Date: 4 March 2016 Research Article RESEARCH ARTICLE Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica Marc W. Van Goethem1, Thulani P. Makhalanyane1,†, Angel Valverde1, Stephen C. Cary2 and Don A. Cowan1,∗ 1Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynwood Road, Pretoria 0028, South Africa and 2Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton 3120, New Zealand ∗Corresponding author: Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0028, South Africa. Tel: +27-12-420-5873; E-mail: [email protected] One sentence summary: Characterization of general bacterial and cyanobacterial populations from soil and lithibiontic microbial communities (hypoliths and endoliths) of Victoria Valley, Antarctica. Editor: Dirk Wagner †Thulani P. Makhalanyane, http://orcid.org/0000-0002-8173-1678 ABSTRACT Here we provide the first exploration of microbial diversity from three distinct Victoria Valley edaphic habitats, namely lithobionts (hypoliths, endoliths) and surface soils. Using a combination of terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene amplicon pyrosequencing we assess community structure and diversity patterns, respectively. Our analysis revealed that habitat type (endolithic versus hypolithic versus surface soils) significantly influenced bacterial community composition, even though dominant phyla such as Actinobacteria (41%of total reads) were common to all samples. Consistent with previous surveys in other Dry Valley ecosystems, we found that lithobionts were colonized by a few highly dominant phylotypes (such as Gemmatimonas and Leptolyngbya). Our analyses also show that soil bacteria were more diverse and evenly distributed than initially expected based on previous evidence. -
Changes in the Microbial Community of Lubomirskia Baicalensis Affected by Red Sponge Disease
Stephen F. Austin State University SFA ScholarWorks Electronic Theses and Dissertations 5-2018 Changes in the microbial community of Lubomirskia baicalensis affected by Red Sponge Disease Colin Rorex Stephen F Austin State University, [email protected] Follow this and additional works at: https://scholarworks.sfasu.edu/etds Part of the Bioinformatics Commons, Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Marine Biology Commons, Other Genetics and Genomics Commons, and the Other Immunology and Infectious Disease Commons Tell us how this article helped you. Repository Citation Rorex, Colin, "Changes in the microbial community of Lubomirskia baicalensis affected by Red Sponge Disease" (2018). Electronic Theses and Dissertations. 189. https://scholarworks.sfasu.edu/etds/189 This Thesis is brought to you for free and open access by SFA ScholarWorks. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of SFA ScholarWorks. For more information, please contact [email protected]. Changes in the microbial community of Lubomirskia baicalensis affected by Red Sponge Disease Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License. This thesis is available at SFA ScholarWorks: https://scholarworks.sfasu.edu/etds/189 Changes in the microbial community of Lubomirskia baicalensis affected by Red Sponge Disease By Colin Boyd Rorex, Bachelor of Arts Presented to the Faculty of the Graduate School of Stephen F. Austin State University In Partial Fulfillment Of the Requirements For the Degree of Masters of Science STEPHEN F. AUSTIN STATE UNIVERSITY May, 2018 Changes in the microbial community of Lubomirskia baicalensis affected by Red Sponge Disease By Colin Boyd Rorex, Bachelor of Arts APPROVED: Alexandra Martynova-Van Kley, Thesis Director James Van Kley, Committee Member Kenneth Farrish, Committee Member Matthew Kwiatkowski, Committee Member Pauline Sampson, Ph.D.