Heme A-Containing Oxidases Evolved in the Ancestors of Iron Oxidizing
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Microbiology of Barrier Component Analogues of a Deep Geological Repository
Microbiology of Barrier Component Analogues of a Deep Geological Repository by Rachel Beaver A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Biology Waterloo, Ontario, Canada, 2020 ©Rachel Beaver 2020 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions Chapter 2 The Tsukinuno bentonite sampling was coordinated by Erik Kremmer (NWMO). The Opalinus core was received from Niels Burzan and Rizlan Bernier-Latmani (École Polytechnique Fédérale de Lausanne, Switzerland). The Northern Ontario crystalline rock core sampling was coordinated by Jeff Binns (Nuclear Waste Management Organization). Sian Ford (McMaster University) swabbed the outer layer of the Northern Ontario crystalline rocK core and crushed the inner layer. Melody Vachon (University of Waterloo) assisted with the cultivation of anaerobic heterotrophs and SRB. iii Abstract Many countries are in the process of designing and implementing long-term storage solutions for used nuclear fuel. Like many of these countries, Canada is considering a deep geological repository (DGR) wherein used fuel bundles will be placed in copper-coated carbon steel used fuel containers encased in bentonite buffer boxes. Previously published research has simulated aspects of a DGR experimentally to identify DGR conditions that would prevent microbial activity. Although such microcosm-type experiments can observe microbial growth and activity over relatively limited time frames, a DGR will remain functional for at least a million years, and will be exposed to fluctuating environmental conditions. -
Chemical Structures of Some Examples of Earlier Characterized Antibiotic and Anticancer Specialized
Supplementary figure S1: Chemical structures of some examples of earlier characterized antibiotic and anticancer specialized metabolites: (A) salinilactam, (B) lactocillin, (C) streptochlorin, (D) abyssomicin C and (E) salinosporamide K. Figure S2. Heat map representing hierarchical classification of the SMGCs detected in all the metagenomes in the dataset. Table S1: The sampling locations of each of the sites in the dataset. Sample Sample Bio-project Site depth accession accession Samples Latitude Longitude Site description (m) number in SRA number in SRA AT0050m01B1-4C1 SRS598124 PRJNA193416 Atlantis II water column 50, 200, Water column AT0200m01C1-4D1 SRS598125 21°36'19.0" 38°12'09.0 700 and above the brine N "E (ATII 50, ATII 200, 1500 pool water layers AT0700m01C1-3D1 SRS598128 ATII 700, ATII 1500) AT1500m01B1-3C1 SRS598129 ATBRUCL SRS1029632 PRJNA193416 Atlantis II brine 21°36'19.0" 38°12'09.0 1996– Brine pool water ATBRLCL1-3 SRS1029579 (ATII UCL, ATII INF, N "E 2025 layers ATII LCL) ATBRINP SRS481323 PRJNA219363 ATIID-1a SRS1120041 PRJNA299097 ATIID-1b SRS1120130 ATIID-2 SRS1120133 2168 + Sea sediments Atlantis II - sediments 21°36'19.0" 38°12'09.0 ~3.5 core underlying ATII ATIID-3 SRS1120134 (ATII SDM) N "E length brine pool ATIID-4 SRS1120135 ATIID-5 SRS1120142 ATIID-6 SRS1120143 Discovery Deep brine DDBRINP SRS481325 PRJNA219363 21°17'11.0" 38°17'14.0 2026– Brine pool water N "E 2042 layers (DD INF, DD BR) DDBRINE DD-1 SRS1120158 PRJNA299097 DD-2 SRS1120203 DD-3 SRS1120205 Discovery Deep 2180 + Sea sediments sediments 21°17'11.0" -
New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach
BIOTECHNOLOGY – Vol .III – New Opportunities Revealed by Biotechnological Explorations of Extremophiles - Mircea Podar and Anna-Louise Reysenbach NEW OPPORTUNITIES REVEALED BY BIOTECHNOLOGICAL EXPLORATIONS OF EXTREMOPHILES Mircea Podar and Anna-Louise Reysenbach Department of Biology, Portland State University, Portland, OR 97201, USA. Keywords: extremophiles, genomics, biotechnology, enzymes, metagenomics. Contents 1. Introduction 2. Extremophiles and Biomolecules 3. Extremophile Genomics Exposing the Biotechnological Potential 4. Tapping into the Hidden Biotechnological Potential through Metagenomics 5. Unexplored Frontiers and Future Prospects Acknowledgements Glossary Bibliography Biographical Sketches Summary Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of new potential applications for biotechnology. Furthermore, more recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for biotechnological exploration of extremophiles. 1. Introduction Organisms that live at the extremes of pH (>pH 8.5,< pH 5.0), temperature (>45°C, <15°C), pressure (>500 atm), salinity (>1.0M NaCl) and in high concentrations of recalcitrant substances or heavy metals (extremophiles) represent one of the last frontiers for biotechnological and industrial discovery. As we learn more about the -
Microbial Diversity of Molasses Containing Tobacco (Maassel) Unveils Contamination with Many Human Pathogens
European Review for Medical and Pharmacological Sciences 2021; 25: 4919-4929 Microbial diversity of molasses containing tobacco (Maassel) unveils contamination with many human pathogens M.A.A. ALQUMBER Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia Abstract. – OBJECTIVE: Tobacco smoking drugs in today’s modern world. Different meth- remains a worldwide health issue, and the use of ods are currently used to consume tobacco, in- flavored varieties (maassel) embedded in glyc- cluding cigarettes, cigars and waterpipes1. Water- erine, molasses, and fruit essence via shisha pipe (shisha) smoking continues to rise globally2. paraphernalia (waterpipe) is growing globally. Smoking flavored tobacco (maassel), through the 16S rRNA gene pyrosequencing was conduct- shisha, is becoming a global preventable cause of ed on 18 different varieties representing 16 fla- 3,4 vors and three brands in order to study the mi- morbidity and mortality . crobiota of maassel and find whether it contains Scientists studied the chemical composition of pathogenic bacteria. tobacco for many years and illustrated the total MATERIALS AND METHODS: The samples number of chemicals identified in tobacco during were selected randomly from the most utilized the years from 1954 to 20055. In addition, a com- brands within Albaha, Saudi Arabia as deter- prehensive review of these chemicals’ classifica- mined through a questionnaire of 253 smok- ers. In addition, ten-fold serially diluted sam- tion, concentration and changes with time due ples were inoculated on blood agar, MacConkey to changes in the shape, design and composition agar, half-strength trypticase soy agar and malt of cigarettes was reported almost a decade ago6. -
Methanogenic Activity in Río Tinto, a Terrestrial Mars Analogue R
Methanogenic activity in Río Tinto, a terrestrial Mars analogue R. Amils Centro de Biología Molecular Severo Ochoa (UAM-CSIC) y Centro de Astrobiología (INTA- CSIC) Frascati, noviembre 2009 new insides in the Mars exploration H2O on Mars methane (PFS) it can be concluded that on Mars there are sedimentary rocks that were formed in acidic conditions (acidic lakes or oceans) • possible terrestrial analogs: - submarine hydrothermalism - acidic environments to explore the deep sea requires expensive equipment (Alvin) natural acidic waters natural acidic environments: - areas with volcanic activity 0 SO2 + H2S ——> S + H2O - metal mining activities 3+ 2- + FeS2 + H2O —> Fe + SO4 + H in this case the extreme acidic conditions are promoted by biological activity geomicrobiology of metallic sulfides pyrite, molibdenite, tungstenite (thiosulfate mec.) 3+ 2- 2+ + FeS2+6Fe +3H2O → S2O3 +7Fe +6H 2- 3+ 2- 2+ + S2O3 +8Fe +5H2O → 2SO4 +8Fe +10H Rest of sulfides (polisulfide mec.) 3+ + 2+ 2+ 8MS+8Fe +8H → 8M +4H2Sn+8Fe (n≥2) 3+ o 2+ + 4H2Sn+8Fe → S8 +8Fe +8H o 2- + S8 +4H2O (S oxidizers) → SO4 +8H Bacterias come-meteoritos role of the microbial activity in the leaching of pyrite chemical 3+ reaction Fe Fe2+ microbial activity 2- + SO4 + H Rio Tinto rise at the heart of the Iberian Pyritic Belt Río Tinto is an acidic river, pH 2.3, 100 km long and with a high concentration of soluble metals the iron concentration at the origin is between 15-20 g/l and the sulfate is constant and around 15 g/l geoMICROBIOLOGY combination of conventional microbial ecology techniques and molecular ecology tools A B Phylogeny of acidophilic microorganisms detected in Rio Tinto Actinobacteria Cyanobacteria . -
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. -
Microbial Diversity in Raw Milk and Sayram Ketteki from Southern of Xinjiang, China
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435442; this version posted March 15, 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. Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China DongLa Gao1,2,Weihua Wang1,2*,ZhanJiang Han1,3,Qian Xi1,2, ,RuiCheng Guo1,2,PengCheng Kuang1,2,DongLiang Li1,2 1 College of Life Science, Tarim University, Alaer, Xinjiang , China 2 Xinjiang Production and Construction Corps Key Laboratory of Deep Processing of Agricultural Products in South Xinjiang, Alar, Xinjiang ,China 3 Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang , China *Corresponding author E-mail: [email protected](Weihua Wang) bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435442; this version posted March 15, 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. Abstract Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts -
Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. -
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. -
Single-Cell Genomics Reveals the Lifestyle of Poribacteria, a Candidate Phylum Symbiotically Associated with Marine Sponges
The ISME Journal (2011) 5, 61–70 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges Alexander Siegl1,5, Janine Kamke1, Thomas Hochmuth2,Jo¨rn Piel2, Michael Richter3, Chunguang Liang4, Thomas Dandekar4 and Ute Hentschel1 1Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany; 2Kekule´ Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany; 3Ribocon GmbH, Bremen, Germany and 4Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated ‘whole-genome amplification’. Pyrosequencing of a single amplified genome (SAG) derived from a member of the Poribacteria resulted in nearly 1.6 Mb of genomic information distributed among 554 contigs analyzed in this study. Approximately two-third of the poribacterial genome was sequenced. Our findings shed light on the functional properties and lifestyle of a possibly ancient bacterial symbiont of marine sponges. The Poribacteria are mixotrophic bacteria with autotrophic CO2-fixation capacities through the Wood–Ljungdahl pathway. The cell wall is of Gram-negative origin. The Poribacteria produce at least two polyketide synthases (PKSs), one of which is the sponge-specific Sup-type PKS. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Drylands Soil Bacterial Community Is Affected by Land Use Change and Different Irrigation Practices in the Mezquital Valley
www.nature.com/scientificreports OPEN Drylands soil bacterial community is afected by land use change and diferent irrigation practices in the Received: 23 June 2017 Accepted: 3 January 2018 Mezquital Valley, Mexico Published: xx xx xxxx Kathia Lüneberg1, Dominik Schneider2, Christina Siebe1 & Rolf Daniel 2 Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater afects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specifc adaptations to drought and sodium content in specifc land use systems. Predicted functionality profles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles difered among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identifed potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profles provided extensive understanding of the short- term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands. Drylands are defned as regions with arid, semi-arid, and dry sub humid climate with an annual precipitation/ evapotranspiration potential ratio (P/PET)1 ranging from 0.05 to 0.652.