The Case of the Red Pigment Miltos
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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. -
Table S1. Bacterial Otus from 16S Rrna
Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria -
Microbial Community Dynamics in the Recirculating Nutrient Solution of Tomato Plug Seedlings Cultivated Under Ebb-And-Fow System
Microbial community dynamics in the recirculating nutrient solution of tomato plug seedlings cultivated under ebb-and-ow system Chun-Juan Dong ( [email protected] ) Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers https://orcid.org/0000- 0002-8740-6649 Qian Li Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Ling-Ling Wang Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Qing-Mao Shang Chinese Academy of Agricultural Sciences Institute of Vegetables and Flowers Research article Keywords: Tomato, Bacterial, Fungal, Ebb-and-ow system, Nutrient solution, Illumina sequencing Posted Date: December 2nd, 2019 DOI: https://doi.org/10.21203/rs.2.17978/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/27 Abstract Background: The ebb-and-ow system has ability to recirculate water and nutrients, and offers a good method to control nutrient leaching from greenhouses into the environment. However, the potential for the rapid spread of bacterial and fungal pathogens is the main hindrance for its adoption in vegetable seedlings production. Natural microora has often shown a certain ability to suppress diseases. Results: Here, through 16S rRNA- and ITS1-targeted Illumina sequencing, the dynamic changes in bacterial and fungal communities in the recirculating nutrient solution were characterized for tomato plug seedlings cultivated in an ebb-and-ow system in summer and winter. Both bacterial number and microbial diversity in the nutrient solution increased with recirculating irrigation, and these changes differed between summer and winter. Pseudomonas was among the most predominant bacterial genera in the nutrient solution; its relative abundance gradually increased with recycling in summer but decreased dramatically in winter. -
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. -
Transition from Seed to Root and Effect of Compost Amendment Stefan J
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2006, p. 3975–3983 Vol. 72, No. 6 0099-2240/06/$08.00ϩ0 doi:10.1128/AEM.02771-05 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Succession of Bacterial Communities during Early Plant Development: Transition from Seed to Root and Effect of Compost Amendment Stefan J. Green,1,2† Ehud Inbar,1,2 Frederick C. Michel, Jr.,3 Yitzhak Hadar,1 and Dror Minz2* Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel1; Institute of Water, Soil and Environmental Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, Israel2; and Department of Food, Agricultural, and Biological Engineering, Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio3 Received 23 November 2005/Accepted 27 March 2006 Compost amendments to soils and potting mixes are routinely applied to improve soil fertility and plant growth and health. These amendments, which contain high levels of organic matter and microbial cells, can influence microbial communities associated with plants grown in such soils. The purpose of this study was to follow the bacterial community compositions of seed and subsequent root surfaces in the presence and absence of compost in the potting mix. The bacterial community compositions of potting mixes, seed, and root surfaces sampled at three stages of plant growth were analyzed via general and newly developed Bacteroidetes-specific, PCR-denaturing gradient gel electrophoresis methodologies. These analyses revealed that seed surfaces were colonized primarily by populations detected in the initial potting mixes, many of which were not detected in subsequent root analyses. The most persistent bacterial populations detected in this study belonged to the genus Chryseobacterium (Bacteroidetes) and the family Oxalobacteraceae (Betaproteobacteria). -
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. -
Bacterial Metataxonomic Profile and Putative Functional Behavior
Soil Biology and Biochemistry 119 (2018) 184–193 Contents lists available at ScienceDirect Soil Biology and Biochemistry journal homepage: www.elsevier.com/locate/soilbio Bacterial metataxonomic profile and putative functional behavior associated T with C and N cycle processes remain altered for decades after forest harvest ∗ Ryan M. Mushinskia, ,1, Yong Zhoua, Terry J. Gentryb, Thomas W. Bouttona a Department of Ecosystem Science & Management, Texas A&M University, TAMU 2138, College Station, TX, 77843, United States b Department of Soil & Crop Sciences, Texas A&M University, TAMU 2474, College Station, TX, 77843, United States ARTICLE INFO ABSTRACT Keywords: While the impacts of forest disturbance on soil physicochemical parameters and soil microbial ecology have been Biomass decomposition studied, their effects on microbial biogeochemical function are largely unknown, especially over longer time Nitrogen-cycling scales and at deeper soil depths. This study investigates how differing organic matter removal (OMR) intensities Metagenomic potential associated with timber harvest influence decadal-scale alterations in bacterial community composition and Organic matter removal functional potential in the upper 1-m of the soil profile, 18 years post-harvest in a Pinus taeda L. forest of the Soil bacterial ecology southeastern USA. 16S rRNA amplicon sequencing was used in conjunction with soil chemical analyses to Forest harvest evaluate (i) treatment-induced differences in bacterial community composition, and (ii) potential relationships between those differences and soil biogeochemical properties. Furthermore, functional potential was assessed by using amplicon data to make metagenomic predictions. Results indicate that increasing OMR intensity leads to altered bacterial community composition and the relative abundance of dominant operational taxonomic units (OTUs) annotated to Burkholderia and Aciditerrimonas; however, no significant differences in dominant phyla were observed. -
A Meta-Analysis of the Publicly Available Bacterial and Archaeal Sequence Diversity in Saline Soils
World J Microbiol Biotechnol (2013) 29:2325–2334 DOI 10.1007/s11274-013-1399-9 ORIGINAL PAPER A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils Bin Ma • Jun Gong Received: 19 April 2013 / Accepted: 3 June 2013 / Published online: 12 June 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract An integrated view of bacterial and archaeal Halorubrum and Thermofilum were the dominant archaeal diversity in saline soil habitats is essential for understanding genera in saline soils. Rarefaction analysis indicated that less the biological and ecological processes and exploiting than 25 % of bacterial diversity, and approximately 50 % of potential of microbial resources from such environments. archaeal diversity, in saline soil habitats has been sampled. This study examined the collective bacterial and archaeal This analysis of the global bacterial and archaeal diversity in diversity in saline soils using a meta-analysis approach. All saline soil habitats can guide future studies to further available 16S rDNA sequences recovered from saline soils examine the microbial diversity of saline soils. were retrieved from publicly available databases and sub- jected to phylogenetic and statistical analyses. A total of Keywords Archaea Á Bacteria Á Halophilic Á Microbial 9,043 bacterial and 1,039 archaeal sequences, each longer diversity Á Saline soil than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known Introduction bacterial phyla, with Proteobacteria (44.9 %), Actinobacte- ria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Saline soils are increasingly abundant as a consequence of Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being pre- irrigation and desertification processes (Rengasamy 2006). -
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. -
Distribution of Long Linear and Branched Polyamines in the Thermophiles Belonging to the Domain Bacteria
Journal of Japanese Society for Extremophiles (2008) Vol.7 (1) Journal of Japanese Society for Extremophiles (2008), Vol. 7, 10-20 ORIGINAL PAPER Hamana Ka,b,e, Hosoya Ra, Yokota Ac, Niitsu Md, Hayashi He and Itoh Tb Distribution of long linear and branched polyamines in the thermophiles belonging to the domain Bacteria a Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan. bJapan Collection of Microorganisms, RIKEN, BioResource Center, Wako, Saitama 351-0198, Japan. c Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan. d Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0290, Japan. e Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan. Corresponding author : Koei Hamana, [email protected] Phone : +81-27-220-8916, FAX : +81-27-220-8999 Received: April 3, 2008/ Reviced:May 26, 2008/ Acepted:June 3, 2008 Abstract Cellular polyamines of 44 newly validated have been published in eubacteria 15, 16). However, the eubacterial thermophiles growing at 45-80℃, belonging degree of thermophily is roughly estimated and not to eight orders (six phyla) of the domain Bacteria, were defined exactly. The cellular occurrence of long linear analyzed by HPLC and GC. A quaternary branched and/or branched polyamines in extremely thermophilic penta-amine, N4-bis(aminopropyl)norspermidine, was (or hyperthermophilic) eubacteria suggested that the found in Hydrogenivirga and Sulfurihydrogenibium extreme thermophiles (or hyperthermophiles) may have belonging to the order of Aquificales. Another some novel polyamine synthetic abilities possibly quaternary branched penta-amine, N4-bis(aminopropyl) associated with their thermophily 8-11, 13-15, 18, 23, 24). -
List of Bacterial Orders.Pdf
A.Phylum Acidobacteria I. Class Acidobacteria i. Acidobacteriales i Acidobacteriaceae 1 Acidobacterium 2 Edaphobacter 3 Terriglobus II.Class Holophagae i. Acanthopleuribacterales i Acanthopleuribacteraceae 1 Acanthopleuribacter ii. Holophagales i Holophagaceae 1 Geothrix 2 Holophaga B.Phylum Actinobacteria I. Class Actinobacteria i. Sphaerobacteridae i Sphaerobacterales 1 Sphaerobacterineae a Sphaerobacteraceae i Sphaerobacter ii. Rubrobacteridae i Rubrobacterales 1 Rubrobacterineae a Conexibacteraceae i Conexibacter b Patulibacteraceae i Patulibacter c Rubrobacteraceae i Rubrobacter d Solirubrobacteraceae i Solirubrobacter e Thermoleophilaceae i Thermoleophilum iii. Coriobacteridae i Coriobacteriales 1 Coriobacterineae a Coriobacteriaceae i Atopobium ii Collinsella iii Coriobacterium iv Cryptobacterium v Denitrobacterium vi Eggerthella vii Olsenella viii Slackia iv. Actinobacteridae i Bifidobacteriales 1 Bifidobacteriaceae a Aeriscardovia b Alloscardovia c Bifidobacterium d Gardnerella e Metascardovia f Parascardovia g Scardovia 2 Unclassified ii Actinomycetales 1 Streptosporangineae a Thermomonosporaceae i Actinocorallia ii Actinomadura iii Excellospora iv Spirillospora v Thermomonospora b Nocardiopsaceae i Nocardiopsis ii Streptomonospora iii Thermobifida c Streptosporangiaceae i Acrocarpospora ii Herbidospora iii Microbispora iv Microtetraspora v Nonomuraea vi Planobispora vii Planomonospora viii Planotetraspora ix Sphaerisporangium x Streptosporangium xi Thermopolyspora 2 Streptomycineae a Sterptomycetaceae i Actinopycnidium ii Actinosporangium