A Rhizosphere-Scale Investigation of Root Effects on Wetland Methane Dynamics
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The Lichens' Microbiota, Still a Mystery?
fmicb-12-623839 March 24, 2021 Time: 15:25 # 1 REVIEW published: 30 March 2021 doi: 10.3389/fmicb.2021.623839 The Lichens’ Microbiota, Still a Mystery? Maria Grimm1*, Martin Grube2, Ulf Schiefelbein3, Daniela Zühlke1, Jörg Bernhardt1 and Katharina Riedel1 1 Institute of Microbiology, University Greifswald, Greifswald, Germany, 2 Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria, 3 Botanical Garden, University of Rostock, Rostock, Germany Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name- giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses Edited by: confirm the partition of functions in lichen partnerships. The ample functional diversity Nathalie Connil, Université de Rouen, France of the mycobiont contrasts the predominant function of the photobiont in production Reviewed by: (and secretion) of energy-rich carbohydrates, and the cyanobiont’s contribution by Dirk Benndorf, nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and Otto von Guericke University community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify Magdeburg, Germany Guilherme Lanzi Sassaki, the bacterial community present on L. -
Draft Genome Sequence of Acidobacteria Group 1 Acidipila Sp
GENOME SEQUENCES crossm Draft Genome Sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, Isolated from Forest Soil Luiz A. Domeignoz-Horta,a Kristen M. DeAngelis,a Grace Poldb aDepartment of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA bGraduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, USA ABSTRACT Here, we present the genome sequence of a member of the group I Acidobacteria, Acidipila sp. strain EB88, which was isolated from temperate forest soil. Like many other members of its class, its genome contains evidence of the potential to utilize a broad range of sugars. roup I Acidobacteria are abundant members of acidic-soil microbial communities G(1), typically characterized by slow growth, heterotrophy, and the production of copious extracellular polysaccharides (2). Within this group, members of the genus Acidipila are characterized as acidophilic heterotrophs that use sugars as favored growth substrates (3, 4). Acidipila sp. strain EB88 was isolated from the Ͻ0.8-m size fraction of a deciduous forest mineral soil slurry plated onto VL45 plus glucose-yeast extract (GYE) medium (5). It was selected for sequencing based on the paucity of cultivated group I Acidobacteria, its peculiar bright-red waxy colonies on solid medium, and its undetectable growth in liquid medium unless a solid substrate, such as sand, is added. DNA was prepared for sequencing by repeatedly freeze-thawing 9-day-old biomass scraped from pH 5 R2A medium and extracted using the Qiagen genomic DNA protocol. Sequencing at UMass Worcester using the PacBio RS II sequencer resulted in 476,266 filtered reads, with a mean length of 3,208 bp. -
Edaphobacter Dinghuensis Sp. Nov., an Acidobacterium Isolated from Lower Subtropical Forest Soil Jia Wang,3 Mei-Hong Chen,3 Ying-Ying Lv, Ya-Wen Jiang and Li-Hong Qiu
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 276–282 DOI 10.1099/ijsem.0.000710 Edaphobacter dinghuensis sp. nov., an acidobacterium isolated from lower subtropical forest soil Jia Wang,3 Mei-hong Chen,3 Ying-ying Lv, Ya-wen Jiang and Li-hong Qiu Correspondence State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Li-hong Qiu Guangzhou 510275, PR China [email protected] An aerobic bacterium, designated DHF9T, was isolated from a soil sample collected from the lower subtropical forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Cells were Gram-stain-negative, non-motile, short rods that multiplied by binary division. Strain DHF9T was an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.5–5.5 (optimum pH 4.0) and at 10–33 8C (optimum 28–33 8C). Growth was inhibited at NaCl concentrations above 2.0 % (w/v). The major fatty acids were iso-C15 : 0,C16 : 0 and C16 : 1v7c. The polar lipids consist of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids, two unidentified polar lipids and an unidentified glycolipid. The DNA G+C content was 57.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the genus Edaphobacter in subdivision 1 of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.0 % to Edaphobacter modestus Jbg-1T. Based on phylogenetic, chemotaxonomic and physiological analyses, it is proposed that strain DHF9T represents a novel species of the genus Edaphobacter, named Edaphobacter dinghuensis sp. nov. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergol
applied sciences Article Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland Magdalena Dyda 1,2,* , Agnieszka Laudy 3, Przemyslaw Decewicz 4 , Krzysztof Romaniuk 4, Martyna Ciezkowska 4, Anna Szajewska 5 , Danuta Solecka 6, Lukasz Dziewit 4 , Lukasz Drewniak 4 and Aleksandra Skłodowska 1 1 Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] 2 Research and Development for Life Sciences Ltd. (RDLS Ltd.), Miecznikowa 1/5a, 02-096 Warsaw, Poland 3 Laboratory of Environmental Analysis, Museum of King John III’s Palace at Wilanow, Stanislawa Kostki Potockiego 10/16, 02-958 Warsaw, Poland; [email protected] 4 Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] (P.D.); [email protected] (K.R.); [email protected] (M.C.); [email protected] (L.D.); [email protected] (L.D.) 5 The Main School of Fire Service, Slowackiego 52/54, 01-629 Warsaw, Poland; [email protected] 6 Department of Plant Molecular Ecophysiology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +48-786-28-44-96 Citation: Dyda, M.; Laudy, A.; Abstract: The aim of the presented investigation was to describe seasonal changes of microbial com- Decewicz, P.; Romaniuk, K.; munity composition in situ in different biocenoses on historical sandstone of the Northern Pergola in Ciezkowska, M.; Szajewska, A.; the Museum of King John III’s Palace at Wilanow (Poland). -
Pró-Reitoria De Pós-Graduação E Pesquisa Stricto Sensu Em Ciências Genômicas E Biotecnologia
Pró-Reitoria de Pós-Graduação e Pesquisa Stricto Sensu em Ciências Genômicas e Biotecnologia IDENTIFICAÇÃO, ISOLAMENTO E CARACTERIZAÇÃO DE BACTÉRIAS DE SOLO DE CERRADO PERTENCENTES AO FILO ACIDOBACTERIA Autor: Virgilio Hipólito Lemos de Castro Orientadora: Drª Cristine Chaves Barreto Brasília - DF 2011 VIRGILIO HIPÓLITO LEMOS DE CASTRO IDENTIFICAÇÃO, ISOLAMENTO E CARACTERIZAÇÃO DE BACTÉRIAS DE SOLO DE CERRADO PERTENCENTES AO FILO ACIDOBACTERIA Dissertação apresentada ao Programa de Pós- Graduação Stricto Sensu em Ciências Genômicas e Biotecnologia da Universidade Católica de Brasília, como requisito para obtenção do Título de Mestre em Ciências Genômicas e Biotecnologia. Orientadora: Drª. Cristine Chaves Barreto Brasília 2011 C355i Castro, Virgilio Hipólito Lemos de. Identificação, isolamento e caracterização de bactérias de solo de cerrado pertencentes ao filo acidobactéria – 2011. 76f. : il.; 30 cm Dissertação (mestrado – Universidade Católica de Brasília, 2011). Orientação: Cristine Chaves Barreto Ficha1. elaborada Bactéria. 2.pela Composição Biblioteca doPós solo.-Graduação 3. Biotecnologia. da UCB I. Barreto , Cristine Chaves, orient. II. Título. CDU 579 Dissertação de autoria de Virgilio Hipólito Lemos de Castro, intitulada “IDENTIFICAÇÃO, ISOLAMENTO E CARACTERIZAÇÃO DE BACTÉRIAS DE SOLO DE CERRADO PERTENCENTES AO FILO ACIDOBACTERIA”, apresentada como requisito para obtenção do grau de Mestre em Ciências Genômicas e Biotecnologia da Universidade Católica de Brasília em 27 de junho, defendida e aprovada pela banca examinadora abaixo -
Microbial Community Analysis in Soil (Rhizosphere) and the Marine (Plastisphere) Environment in Function of Plant Health and Biofilm Formation
Microbial community analysis in soil (rhizosphere) and the marine (plastisphere) environment in function of plant health and biofilm formation Caroline De Tender Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Biotechnology Promotors: Prof. Dr. Peter Dawyndt Department of Applied mathematics, Computer Science and Statistics Faculty of Science Ghent University Dr. Martine Maes Crop Protection - Plant Sciences Unit Institute for Agricultural, Fisheries and Food Research (ILVO) Ir. Lisa Devriese Fisheries – Animal Sciences Unit Insitute for Agricultural, Fisheries and Food Research (ILVO) Dank je wel! De allerlaatste woorden die geschreven worden voor deze thesis zijn waarschijnlijk de eerste die gelezen worden door velen. Ongeveer vier jaar geleden startte ik mijn doctoraat bij het ILVO. Met volle moed begon ik aan mijn avontuur. Het ging niet altijd even vlot en ik kan eerlijk bekennen dat meerdere grenzen verlegd zijn. Vooral de combinatie van twee onderwerpen bleek niet altijd evident en kostte me meer dan eens bloed, zweet en tranen. Daarentegen bracht het ook vele opportuniteiten. De enige dag kon ik aan het wroeten zijn in de serre, terwijl ik de dag erop op de Simon Stevin sprong (en dit mag letterlijk worden genomen!) om plastic uit zee te vissen. Ja, het was me wel het avontuur… Natuurlijk zou dit allemaal niet mogelijk geweest zijn zonder de hulp van een aantal geweldige mensen. In de eerste plaats, mijn promotoren: Prof. Peter Dawyndt, dr. Martine Maes en natuurlijk Lisa Devriese. Dank je wel om vier jaar geleden het vertrouwen te hebben om mij dit onderzoek toe te wijzen, me steeds in de juiste richting te duwen als ik het Noorden even kwijt was, maar ook voor de gezellige babbels op de bureau. -
Isolation and Characterization of Bacteria in a Toluene-Producing Enrichment Culture Derived from Contaminated Groundwater at a Louisiana Superfund Site
Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School August 2020 Isolation and Characterization of Bacteria in a Toluene-Producing Enrichment Culture Derived from Contaminated Groundwater at a Louisiana Superfund Site Madison Mikes Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Civil and Environmental Engineering Commons, and the Microbiology Commons Recommended Citation Mikes, Madison, "Isolation and Characterization of Bacteria in a Toluene-Producing Enrichment Culture Derived from Contaminated Groundwater at a Louisiana Superfund Site" (2020). LSU Master's Theses. 5206. https://digitalcommons.lsu.edu/gradschool_theses/5206 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. ISOLATION AND CHARACTERIZATION OF BACTERIA IN A TOLUENE- PRODUCING ENRICHMENT CULTURE DERIVED FROM CONTAMINATED GROUNDWATER AT A LOUISIANA SUPERFUND SITE A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agriculture and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Civil and Environmental Engineering by Madison Colleen Mikes B.S., Louisiana State University, 2018 December 2020 1 ACKNOWLEDGEMENTS I would like to take the time to thank all of those who have supported and assisted me during my graduate program. First and foremost, I would like to thank Dr. Bill Moe for all of the time he has spent teaching me and mentoring me through my thesis work. -
The First Representative of the Globally Widespread Subdivision 6 Acidobacteria, Vicinamibacter Silvestris Gen
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 2971–2979 DOI 10.1099/ijsem.0.001131 The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil Katharina J. Huber,1 Alicia M. Geppert,1 Gerhard Wanner,2 Barbel€ U. Fösel,1 Pia K. Wüst1 and Jörg Overmann1,3 Correspondence 1Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Katharina J. Huber Collection of Microorganisms and Cell Cultures, Braunschweig, Germany [email protected] 2Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Planegg- Martinsried, Germany 3Technical University Braunschweig, Braunschweig, Germany Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6T were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6T was tolerant of a wide range of temperatures (12–40 C) and pH values (4.7–9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. T The major fatty acids of Ac_5_C6 were iso-C17 : 1 !9c,C18 : 1 !7c and iso-C15 : 0. -
Root Exudate Input Stimulates Peatland Recalcitrant DOC Decomposition by R-Strategic Taxa of Gammaproteobacteria and Bacteroidetes
Root exudate input stimulates peatland recalcitrant DOC decomposition by r-strategic taxa of Gammaproteobacteria and Bacteroidetes Jiří Mastný ( [email protected] ) Jihoceska Univerzita v Ceskych Budejovicich https://orcid.org/0000-0002-5239-5783 Jiří Bárta Jihoceska Univerzita v Ceskych Budejovicich Prirodovedecka Fakulta Eva Kaštovská Jihoceska Univerzita v Ceskych Budejovicich Prirodovedecka Fakulta Tomáš Picek Jihoceska Univerzita v Ceskych Budejovicich Prirodovedecka Fakulta Research Keywords: DOC decomposition, priming effect, peatland, DOC, r-strategic bacteria, microbial community, microbial functions Posted Date: January 17th, 2020 DOI: https://doi.org/10.21203/rs.2.21088/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract Background In peatlands, decomposition of organic matter is limited by harsh environmental conditions and low decomposability of the plant material. Increased microbial decomposition of organic matter in peatland ecosystems may become an important phenomenon in the near future after the expected shift in plant community composition from Sphagnum to vascular plants due to climate change. Such a change in plant community composition will lead to increased root exudates ux to the soil and stimulation of microbial growth and activity. The aim of our study was to evaluate the effect of root exudates on the decomposition of recalcitrant dissolved organic carbon (DOC) and identify the microorganisms responsible for this process. Results Decomposition of recalcitrant DOC was stimulated by a high levels of 13 C labelled root exudates addition whereas it was suppressed by a low levels of root exudates addition. Recalcitrant DOC decomposition was positively related to the exudate C/N ratio as a result of enhanced “microbial nutrient mining” due to a deepening of microbial nutrient limitation. -
Tesis 240515
Geomicrobiology of meromictic, metal-mine pit lakes in the Iberian Pyrite Belt and biotechnological applications María del Carmen Falagán Rodríguez Tesis Doctoral 2015 This PhD project has been funded by the Spanish Ministry of Science and Innovation (BACCHUS research project: “Biotic and Abiotic Controls of Chemical Underwater Stratification of Acidic Pit Lakes of the Iberian Pyrite Belt”; reference number CGL2009-09070) and by the National Programme for the Promotion of Talent and Its Employability, Sub-Programme for Training (BES- 2010-039799) and Sub-Programme for Mobility (Spanish Ministry of Science and Innovation). Other additional funds were received from the Gobierno Vasco (Grupo de Investigación IT-762- 13) and the European Science Foundation under the program “The Functionality of Iron Minerals in Environmental Processes” (FIMIN). Geomicrobiology of meromictic, metal-mine pit lakes in the Iberian Pyrite Belt and biotechnological applications TESIS DOCTORAL 2015 María del Carmen FALAGÁN RODRÍGUEZ Directores Javier Sánchez-España Iñaki Yusta Arnal This thesis was also supervised by D. Barrie Johnson School of Biological Sciences Bangor University ACKNOWLEDGEMENTS During the last four years, I have met quite a few people. No matter how briefly our paths crossed, each one of them has helped me bring this work to completion. I would like to underline that the order of the names mentioned below does not change the fact that, without any of them, I would not be here. I have tried to list them chronologically. A long time ago, when I was still a child, someone told me “estudia si quieres ser alguien en la vida” (“Study hard if you want to achieve great things”). -
Structural Variability and Differentiation of Niches in The
www.nature.com/scientificreports OPEN Structural variability and diferentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis) Zong‑Sheng Yuan1, Fang Liu2, Zhen‑Yu Liu3, Qiu‑Liang Huang4, Guo‑Fang Zhang4 & Hui Pan1* The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and fowering. The fowering of moso bamboo has been a focus of study. The mechanism of fowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its fowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of fowering and nonfowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with diferent fowering stages of moso bamboo. We identifed 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo difered signifcantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed diferent structures of microbial communities between bamboo that is fowering and not fowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may afect the fowering time of moso bamboo. Our results delineate the complex host‑microbe interactions of this plant.