Process Performance and Microbial Community Structure in Thermophilic Trickling Biofilter Reactors for Biogas Upgrading
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Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella Thermoacetica and Moorella Thermoautotrophica
Downloaded from orbit.dtu.dk on: Oct 09, 2021 Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica Redl, Stephanie Maria Anna; Poehlein, Anja; Esser, Carola; Bengelsdorf, Frank R.; Jensen, Torbjørn Ølshøj; Jendresen, Christian Bille; Tindall, Brian J.; Daniel, Rolf; Dürre, Peter; Nielsen, Alex Toftgaard Published in: Frontiers in Microbiology Link to article, DOI: 10.3389/fmicb.2019.03070 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Redl, S. M. A., Poehlein, A., Esser, C., Bengelsdorf, F. R., Jensen, T. Ø., Jendresen, C. B., Tindall, B. J., Daniel, R., Dürre, P., & Nielsen, A. T. (2020). Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica. Frontiers in Microbiology, 10, [3070]. https://doi.org/10.3389/fmicb.2019.03070 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
Volume 2 Issue 1, January 2013
Journal of Petroleum Science Research (JPSR) Volume 2 Issue 1, January 2013 www.jpsr.org Interaction of Oppositely Charged Polymer– Surfactant System Based on Surface Tension Measurements Anis A. Ansari1, M. Kamil*,2 and Kabir‐ud‐Din3 1University Polytechnic *,2 Department of Petroleum Studies 3Department of Chemistry Aligarh Muslim University, Aligarh‐202002, U.P., India [email protected]; [email protected]; [email protected] Corresponding Author:*E‐mail: [email protected] (M. Kamil) Abstract mixture are driven by hydrophobic, dipolar, and The interaction between oppositely charged polymer‐ electrostatic forces. When surfactants are introduced surfactant systems has been studied using surface tension into a solution containing oppositely charged polymer, measurements wherein the dependence of interaction strong electrostatic interactions are referred as phenomenon over the presence of anionic polyelectrolyte ‘strongly interacting system’, as the attractive sodium carboxymethylcellulose (NaCMC) with variation of electrostatic forces are extremely important in the tail length of cationic surfactants, cetyltrimethylammonium oppositely charged polymer and surfactant [3‐5]. There bromide (CTAB), tetradecyltrimethylammonium bromide has been significant research work focusing on the (TTAB), and dodecyltrimethylammonium bromide (DTAB) interaction of oppositely charged polyelectrolytes and was investigated. It is observed that the cationic surfactants surfactants in recent years [6‐24]. induced cooperative binding with the anionic polyelectrolyte at critical aggregation concentration (cac) and the cac values Surfactants in the presence of an oppositely charged are considerably lower than the corresponding critical polyelectrolyte start forming aggregates with the micelle concentration (cmc) for each of the surfactant polyelectrolyte when surfactant concentration exceeds irrespective of their hydrophobic tail size. The cmc of its critical aggregation concentration (cac). -
Conversion of Hemicelluloses and D-Xylose Into Ethanol by the Use Of
'DKC’tSO Conversion of hemicellulose and D-xylose into ethanol by the use of thermophilic anaerobic bacteria Mikrobiologiske unders0gelser af termofile anaerobe bakterier som omssetter hemicellulose til ethanol DTU MAY 0 5 1998 EFP-94-0009 Department of Environmental Science and Engineering Technical University of Denmark L DISCLAIMER Portions of this document may be illegible electronic image products. Images are produced from the best available original document. Head of project: Associate professor Birgitte K. Ahring, Department of Environmental Science and Engineering, Technical University of Denmark Employees at Department of Environmental Science and Engineering, Technical University of Denmark: Peter Sommer (Ph.D. student) formerly Peter Nielsen Anette Hprdum L0th (technician) Dette projekt er associeret med Nordisk Ministerrad, Energiforskningen 1995-1997 List of Papers 1. Larsen L, Nielsen P, Ahring BK Thermoanaerobacter mathranii sp. nov., an ethanol producing extremely thermophilic anaerobic bacterium from a hot-spring in Iceland (1997). Archieves of Microbiology 168:114-119 2. Sommer P, Meinander, NQ, Hahn-Hagerdal B Comparison of the cold methanol and perchloric acid methods for extraction of intracellular metabolites from recombinant, xylose fermenting Saccharomyces cerevisiae. prepared for submission to Applied Microbiology & Biotechnology 3. Sommer P, Ahring BK Measurements of intracellular metabolites and enzymes of the pentose phosphate pathway of Thermoanaerobacter mathranii A3M1 at varying D-xylose concentrations. Prepared for submission to Applied & Environmental Microbiology. 4. Sommer P, Ahring BK Measurements of intracellular metabolites and enzymes in the glycolysis of Thermoanaerobacter mathranii A3M1: The influence of the D-xylose concentration. Prepared for submission to Applied & Environmental Microbiology. Sammenfatning Ethanol er et CCVneutralt braendstof, der kan erstatte bragen af flydende fossile braendstoffer i transportsektoren og derved nedbringe udledningen af CO2 til atmosfaeren. -
Joana Isabel Ferreira Alves Sion
Universidade do Minho Escola de Engenharia Joana Isabel Ferreira Alves sion Microbiology of thermophilic anaerobic syngas conversion hermophilic anaerobic syngas conver Microbiology of t es a Alv eir err Joana Isabel F 3 1 UMinho|20 Julho de 2013 Universidade do Minho Escola de Engenharia Joana Isabel Ferreira Alves Microbiology of thermophilic anaerobic syngas conversion Tese de Doutoramento em Engenharia Química e Biológica Trabalho efectuado sob a orientação da Doutora Diana Zita Machado de Sousa da Doutora Maria Madalena dos Santos Alves e da Doutora Caroline M Plugge Julho de 2013 i Autor: Joana Isabel Ferreira Alves E-mail: [email protected] Telf.: +351 253 604 400 Cart~aocidad~ao: 12071827 T´ıtuloda tese: Microbiology of thermophilic anaerobic syngas conversion Microbiologia da convers~aoanaer´obiade g´asde s´ıntese em condi¸c~oestermof´ılicas Orientadores: Doutora Diana Zita Machado de Sousa Doutora Maria Madalena dos Santos Alves Doutora Caroline M Plugge Ano de conclus~ao: 2013 Doutoramento em Engenharia Qu´ımicae Biol´ogica E´ AUTORIZADA A REPRODUC¸ AO~ INTEGRAL DESTA TESE/TRABALHO APENAS PARA EFEITOS DE INVESTIGAC¸ AO,~ MEDIANTE AUTORIZAC¸ AO~ ESCRITA DO INTERES- SADO, QUE A TAL SE COMPROMETE. Universidade do Minho, 19 de Julho de 2013. Joana Isabel Ferreira Alves - July 2013 Acknowledgments E´ o momento de agradecer a todos os que, de uma forma ou de outra, contribu´ırampara o sucesso do meu trabalho e me ajudaram ao longo dos ´ultimos4 anos. Assim, agrade¸coem primeiro lugar `asminhas orientadoras Diana Sousa, Madalena Alves e Caroline Plugge, por todo o seu trabalho de supervis~aoe orienta¸c~aocient´ıficae por tudo o que me ensinaram. -
A Novel Cellulolytic, Anaerobic, and Thermophilic Bacterium, Moorella Sp
Biosci. Biotechnol. Biochem., 67 (1), 183–185, 2003 Note A Novel Cellulolytic, Anaerobic, and Thermophilic Bacterium, Moorella sp. Strain F21 Shuichi KARITA,1,† Kengo NAKAYAMA,1 Masakazu GOTO,1 Kazuo SAKKA,1 Wan-Jae KIM,1 and Satoru OGAWA2 1Department of Sustainable Resource Science, Faculty of Bioresources, and 2Laboratory of Electron Microscope, School of Medicine, Mie University, Tsu 514-8507, Japan Received June 24, 2002; Accepted September 9, 2002 A cellulolytic and thermophilic anaerobe was isolated and fermenting cellulosic materials to organic acids from soil. This bacterium made a halo on a roll-tube was isolated. In this paper, we identiˆed the strain culture containing Avicel. Analysis of the PCR-based using DNA sequencing of the 16S rRNA coding 16S rRNA gene sequence showed that the bacterium was region and studied the enzyme activities and ferment- closely related to Moorella thermoacetica.Scanning ed products from the strain. electron microscopy showed the bacterium is a rod and Cellulolytic anaerobic bacteria were isolated in has no protuberant structure on the surface of cells anaerobic culture by the roll-tube method. The cul- growing on cellulose, suggesting that this strain is a non- ture medium for isolation was GS medium3) contain- cellulosomal cellulolytic bacterium. Carboxymethyl cel- ing Avicel as the sole carbon source. The bacteria lulase and xylanase activities were detected in the culture were grown at 609Cfor1week.Bacteriamaking broth. A major fermentation product from ball-milled haloes around their colonies were isolated as cellulo- cellulose was acetate. This strain has a potential to con- lyticanaerobes.Thesebacteriawerecultivatedwith vert cellulosic biomass to acetate, directly. -
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment. -
Parshina Et Al., 2010)
fmicb-11-588468 November 10, 2020 Time: 16:0 # 1 ORIGINAL RESEARCH published: 16 November 2020 doi: 10.3389/fmicb.2020.588468 Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species 1 2† 1 3 2 Edited by: Joana I. Alves , Michael Visser , Ana L. Arantes , Bart Nijsse , Caroline M. Plugge , Wei Xiong, M. Madalena Alves1, Alfons J. M. Stams1,2 and Diana Z. Sousa1,2* National Renewable Energy 1 2 Laboratory (DOE), United States Centre of Biological Engineering, University of Minho, Braga, Portugal, Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands, 3 Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Reviewed by: Wageningen, Netherlands Xiuzhu Dong, Institute of Microbiology, Chinese Academy of Sciences, China A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium Tamara N. Nazina, closely related to Desulfofundulus australicus strain AB33T (98% 16S rRNA gene Winogradsky Institute of Microbiology (RAS), Russia sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ *Correspondence: 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as Diana Z. Sousa external electron acceptor. The products formed from CO conversion were H2 and [email protected] acetate. With sulfate, a lower H2/acetate ratio was observed in the product profile, †Present address: Michael Visser, but CO conversion rates were similar to those in the absence of sulfate. The ability National Reference Centre of Plant of D. australicus strain AB33T to use CO was also investigated. D. australicus strain Health, Dutch National Plant AB33T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ Protection Organization, Wageningen, Netherlands 34 kPa) without sulfate. -
Diversity of 16S Rrna Genes Within Individual Prokaryotic Genomes †
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2010, p. 3886–3897 Vol. 76, No. 12 0099-2240/10/$12.00 doi:10.1128/AEM.02953-09 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Diversity of 16S rRNA Genes within Individual Prokaryotic Genomesᰔ† Anna Y. Pei,1‡ William E. Oberdorf,2‡ Carlos W. Nossa,2 Ankush Agarwal,2 Pooja Chokshi,5 Erika A. Gerz,2 Zhida Jin,2 Peng Lee,3 Liying Yang,3 Michael Poles,2 Stuart M. Brown,4 Steven Sotero,4 Todd DeSantis,7 Eoin Brodie,7 Karen Nelson,8 and Zhiheng Pei2,3,6* New York University College of Arts and Science, New York, New York 100121; Departments of Medicine2 and Pathology3 and Center for Health Informatics and Bioinformatics,4 New York University School of Medicine, New York, New York 10016; Tufts University College of Arts and Sciences, Medford, Massachusetts 021555; Department of Veterans Affairs New York Harbor Healthcare System, New York, New York 100106; Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 947207; and J. Craig Venter Institute, Rockville, Maryland 208508 Received 7 December 2009/Accepted 19 April 2010 Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% .(0.81 ؎ 2.22) to 20.38%; 0.55% ؎ 1.46%). -
Insights Into Key Parameters for Bio-Alcohol Production in Syngas Fermentation Using Model Carboxydotrophic Bacteria
INSIGHTS INTO KEY PARAMETERS FOR BIO-ALCOHOL PRODUCTION IN SYNGAS FERMENTATION USING MODEL CARBOXYDOTROPHIC BACTERIA Sara Ramió Pujol Per citar o enllaçar aquest document: Para citar o enlazar este documento: Use this url to cite or link to this publication: http://hdl.handle.net/10803/388041 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art.