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Purcell AM, Hayer M, Koch BJ, Mau RL, Blazewicz SJ, Dijkstra P, Mack MC, Marks JC, Morrissey EM, Pett‐Ridge J, Rubin RL, Schwartz E, van Gestel NC, Hungate BA. Decreased growth of wild soil microbes after 15 years of transplant-induced warming in a montane meadow. GLOBAL CHANGE BIOLOGY 2022; 28:128-139. [PMID: 34587352 PMCID: PMC9293287 DOI: 10.1111/gcb.15911] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 05/19/2023]
Abstract
The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant-soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response-reduced growth-was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon-specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long-term experimental warming also reduced soil carbon content, likely a consequence of a warming-induced increase in decomposition, as warming-induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long-term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming.
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Affiliation(s)
- Alicia M. Purcell
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michaela Hayer
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Benjamin J. Koch
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Rebecca L. Mau
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Steven J. Blazewicz
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
| | - Paul Dijkstra
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Michelle C. Mack
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Jane C. Marks
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Ember M. Morrissey
- Division of Plant and Soil SciencesWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences DirectorateLawrence Livermore National LabLivermoreCaliforniaUSA
- Life & Environmental Sciences DepartmentUniversity of California MercedMercedCAUSA
| | - Rachel L. Rubin
- Department of Environmental SciencesMount Holyoke CollegeSouth HadleyMassachusettsUSA
| | - Egbert Schwartz
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Natasja C. van Gestel
- Department of Biological Sciences & TTU Climate CenterTexas Tech UniversityLubbockTexasUSA
| | - Bruce A. Hungate
- Department of Biological SciencesCenter for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
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2
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Benavides A, Sanchez F, Alzate JF, Cabarcas F. DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework. PeerJ 2020; 8:e9762. [PMID: 32953263 PMCID: PMC7474881 DOI: 10.7717/peerj.9762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.
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Affiliation(s)
- Andres Benavides
- Grupo GICEI, Facultad de Ingeniería Electrónica, Institución Universitaria Pascual Bravo, Medellín, Antioquia, Colombia
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Friman Sanchez
- Barcelona Supercomputing Center, currently at Smart Variable S.L., Barcelona, Spain
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Medellín, Colombia
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Medellín, Colombia
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3
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Swift SM, Reid KP, Donovan DM, Ramsay TG. Thermophile Lytic Enzyme Fusion Proteins that Target Clostridium perfringens. Antibiotics (Basel) 2019; 8:antibiotics8040214. [PMID: 31717357 PMCID: PMC6963370 DOI: 10.3390/antibiotics8040214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/20/2019] [Accepted: 11/04/2019] [Indexed: 12/04/2022] Open
Abstract
Clostridium perfringens is a bacterial pathogen that causes necrotic enteritis in poultry and livestock, and is a source of food poisoning and gas gangrene in humans. As the agriculture industry eliminates the use of antibiotics in animal feed, alternatives to antibiotics will be needed. Bacteriophage endolysins are enzymes used by the virus to burst their bacterial host, releasing bacteriophage particles. This type of enzyme represents a potential replacement for antibiotics controlling C. perfringens. As animal feed is often heat-treated during production of feed pellets, thermostable enzymes would be preferred for use in feed. To create thermostable endolysins that target C. perfringens, thermophile endolysin catalytic domains were fused to cell wall binding domains from different C. perfringens prophage endolysins. Three thermostable catalytic domains were used, two from prophage endolysins from two Geobacillus strains, and a third endolysin from the deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2). These domains harbor predicted L-alanine-amidase, glucosaminidase, and L-alanine-amidase activities, respectively and degrade the peptidoglycan of the bacterial cell wall. The cell wall binding domains were from C. perfringens prophage endolysins (Phage LYtic enzymes; Ply): PlyCP18, PlyCP10, PlyCP33, PlyCP41, and PlyCP26F. The resulting fifteen chimeric proteins were more thermostable than the native C. perfringens endolysins, and killed swine and poultry disease-associated strains of C. perfringens.
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Affiliation(s)
- Steven M. Swift
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agricultural (USDA), Agricultural Research Service, Baltimore Avenue, Beltsville, MD 10300, USA or (S.M.S.); (K.P.R.); (D.M.D.)
- Contrafect Corporation., Yonkers, NY 10701, USA
| | - Kevin P. Reid
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agricultural (USDA), Agricultural Research Service, Baltimore Avenue, Beltsville, MD 10300, USA or (S.M.S.); (K.P.R.); (D.M.D.)
| | - David M. Donovan
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agricultural (USDA), Agricultural Research Service, Baltimore Avenue, Beltsville, MD 10300, USA or (S.M.S.); (K.P.R.); (D.M.D.)
- Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Timothy G. Ramsay
- Animal Biosciences and Biotechnology Laboratory, United States Department of Agricultural (USDA), Agricultural Research Service, Baltimore Avenue, Beltsville, MD 10300, USA or (S.M.S.); (K.P.R.); (D.M.D.)
- Correspondence: or
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Benavides A, Isaza JP, Niño-García JP, Alzate JF, Cabarcas F. CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes. BMC Genomics 2018; 19:858. [PMID: 30537931 PMCID: PMC6288851 DOI: 10.1186/s12864-018-5191-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome. Results We present a proteobacteria draft genome reconstructed from a Colombian’s Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish “CLAsificador MEtagenomico”, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome. Conclusions We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome. Electronic supplementary material The online version of this article (10.1186/s12864-018-5191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andres Benavides
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.
| | - Juan Pablo Isaza
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Grupo de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Juan Pablo Niño-García
- Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Grupo de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Felipe Cabarcas
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
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5
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Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, Chan KG. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. Microbiologyopen 2018; 7:e00615. [PMID: 29602271 PMCID: PMC6291792 DOI: 10.1002/mbo3.615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
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Affiliation(s)
- Li Sin Lee
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Geok Yuan Annie Tan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia.,Jiangsu University, Zhenjiang, China
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6
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Burgess SA, Flint SH, Lindsay D, Cox MP, Biggs PJ. Insights into the Geobacillus stearothermophilus species based on phylogenomic principles. BMC Microbiol 2017; 17:140. [PMID: 28651524 PMCID: PMC5485677 DOI: 10.1186/s12866-017-1047-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/13/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise lactose, but the ability of dairy strains of G. stearothermophilus to use lactose has now been well established. RESULTS This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative lac operon in four dairy strains. CONCLUSIONS The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative lac operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.
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Affiliation(s)
- S A Burgess
- School of Food and Nutrition, Massey University, Palmerston North, New Zealand.
- Infectious Disease Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
| | - S H Flint
- School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | - D Lindsay
- Fonterra Research Institute, Palmerston North, New Zealand
| | - M P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - P J Biggs
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
- Infectious Disease Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
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7
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Padilla-Del Valle R, Morales-Vale LR, Ríos-Velázquez C. Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing. GENOMICS DATA 2016; 11:98-101. [PMID: 28070487 PMCID: PMC5219636 DOI: 10.1016/j.gdata.2016.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/17/2016] [Indexed: 11/17/2022]
Abstract
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages. The library consisted of approximately 6000 clones, 90% containing metagenomic DNA. Next-Generation-Sequencing technology (Illumina MiSeq) was used to process the ThS metagenome. After removing the cloning vector, 122,026 sequences with 33.10 Mbps size and 64% of G + C content were annotated and analyzed using the MG-RAST online server. Bacteria showed to be the most abundant domain (95.84%) followed by unidentified sequences (2.28%), viruses (1.67%), eukaryotes (0.15%), and archaea (0.01%). The most abundant phyla were Proteobacteria (95.03%), followed by unidentified (2.28%), unclassified from viruses (1.74%), Firmicutes (0.20%) and Actinobacteria (0.18%). The most abundant species were Escherichia coli, Polaromonas naphthalenivorans, Albidiferax ferrireducens and Acidovorax sp. Subsystem functional analysis showed that 20% of genes belong to transposable elements, 10% to clustering-based subsystems, and 8% to the production of cofactors. Functional analysis using NOG annotation showed that 82.79% of proteins are poorly characterized indicating the possibility of novel microbial functions and with potential biomedical and biotechnological applications. Metagenomic data was deposited into the NCBI database under the accession number SAMN06131862.
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Affiliation(s)
- Ricky Padilla-Del Valle
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
| | - Luis R Morales-Vale
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
| | - Carlos Ríos-Velázquez
- Biology Department, University of Puerto Rico at Mayaguez, 108 Street Bo. Miradero Km 1.3, Zoo Entrance, Mayagüez 00680, Puerto Rico
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8
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Brumm P, Land ML, Hauser LJ, Jeffries CD, Chang YJ, Mead DA. Erratum to: Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 2016; 11:10. [PMID: 26819654 PMCID: PMC4729149 DOI: 10.1186/s40793-016-0133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/07/2016] [Indexed: 11/15/2022] Open
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9
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Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01065-16. [PMID: 27688322 PMCID: PMC5043570 DOI: 10.1128/genomea.01065-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The industrially important thermophile Geobacillus thermoglucosidasius has the potential to produce chemicals and fuels from biomass-derived sugar feedstocks. Here, we present the genome sequence of strain NCIMB 11955, the progenitor of an ethanologenic industrial strain, revealing 11 single-nucleotide polymorphisms and 2 indels compared to strain DSM 2542 and two novel plasmids.
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10
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Bezuidt OK, Pierneef R, Gomri AM, Adesioye F, Makhalanyane TP, Kharroub K, Cowan DA. The Geobacillus Pan-Genome: Implications for the Evolution of the Genus. Front Microbiol 2016; 7:723. [PMID: 27252683 PMCID: PMC4878294 DOI: 10.3389/fmicb.2016.00723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/02/2016] [Indexed: 11/13/2022] Open
Abstract
The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.
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Affiliation(s)
- Oliver K Bezuidt
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa
| | - Rian Pierneef
- Department of Biochemistry, Centre for Bioinformatics and Computational Biology, University of Pretoria Pretoria, South Africa
| | - Amin M Gomri
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, Institut de la Nutrition de l'Alimentation et des Technologies Agro-Alimentaire, Université des Frères Mentouri Constantine, Algeria
| | - Fiyin Adesioye
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa
| | - Thulani P Makhalanyane
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa
| | - Karima Kharroub
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, Institut de la Nutrition de l'Alimentation et des Technologies Agro-Alimentaire, Université des Frères Mentouri Constantine, Algeria
| | - Don A Cowan
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa
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