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Detection of a Bacterial Group Within the Phylum Chloroflexi And
Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases. -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
1471-2164-13-670.Pdf
Hobley et al. BMC Genomics 2012, 13:670 http://www.biomedcentral.com/1471-2164/13/670 RESEARCH ARTICLE Open Access Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria Laura Hobley1,3, Thomas R Lerner1,4, Laura E Williams2, Carey Lambert1, Rob Till1, David S Milner1, Sarah M Basford1, Michael J Capeness1, Andrew K Fenton1,5, Robert J Atterbury1,6, Maximilian ATS Harris1 and R Elizabeth Sockett1* Abstract Background: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. Results: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. -
Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. -
Petroleum Hydrocarbon Rich Oil Refinery Sludge of North-East India
Roy et al. BMC Microbiology (2018) 18:151 https://doi.org/10.1186/s12866-018-1275-8 RESEARCHARTICLE Open Access Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations Ajoy Roy1, Pinaki Sar2, Jayeeta Sarkar2, Avishek Dutta2,3, Poulomi Sarkar2, Abhishek Gupta2, Balaram Mohapatra2, Siddhartha Pal1 and Sufia K Kazy1* Abstract Background: Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on- site bioremediation. Results: All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea -
Comparative Analyses of Whole-Genome Protein Sequences
www.nature.com/scientificreports OPEN Comparative analyses of whole- genome protein sequences from multiple organisms Received: 7 June 2017 Makio Yokono 1,2, Soichirou Satoh3 & Ayumi Tanaka1 Accepted: 16 April 2018 Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several Published: xx xx xxxx methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are diferent than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufcient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms. Te reconstruction of phylogenetic trees is a powerful tool for understanding organismal evolutionary processes. Molecular phylogenetic analysis using ribosomal RNA (rRNA) clarifed the phylogenetic relationship of the three domains, bacterial, archaeal, and eukaryotic1. -
Microbial Community Composition of Two Environmentally Conserved Estuaries in the Midorikawa River and Shirakawa River
Microbial Community Composition in Midorikawa and Shirakawa River 63 (Liem et al.) Microbial Community Composition of Two Environmentally Conserved Estuaries in the Midorikawa River and Shirakawa River Tran Thanh Liem1*, Mitsuaki Nakano1, Hiroto Ohta1, Takuro Niidome1, Tatsuya Masuda2, Kiyoshi Takikawa3, Shigeru Morimura1 1Graduate School of Science and Technology, Kumamoto University, Kumamoto City, Japan 2Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto City, Japan 3Center for Marine Environment Studies, Kumamoto University, Kumamoto City, Japan Abstract To provide a general overview of the microbial communities in environmentally conserved estuaries, the top 5 cm of sediment was sampled from the sandy estuary of the Shirakawa River and from the muddy estuary of the Midorikawa River. Higher amounts of organic matter were detected in the Midorikawa estuary sample than in the Shirakawa estuary sample. Measurement of redox potential revealed that the Shirakawa estuary was aerobic and the Midorikawa estuary was much less aerobic. Clone analysis was performed by targeting partial 16S rRNA gene sequences and using extracted DNA from the samples as a template. Various bacteria were detected, among which Gammaproteobacteria was dominant at both estuaries. Unclassified clones were detected in the Gammaproteobacteria group, mainly among samples from the Midorikawa estuary. Other detected bacterial groups were Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. All the Deltaproteobacteria clones were anaerobic sulfate-reducing bacteria. Those aerobic and anaerobic bacteria coexisted in the top 5 cm of the estuary sediments indicating the surface layer have active sulfur and carbon cycle. Abundance of aerobic Gammaproteobacteria may be an indicator for conserved estuaries. Keywords: conserved environment, clone analysis, estuary, microbial community, 16S rRNA gene. -
Metagenomic Views of Microbial Dynamics Influenced By
www.nature.com/scientificreports OPEN Metagenomic views of microbial dynamics infuenced by hydrocarbon seepage in sediments of the Gulf of Mexico Rui Zhao1, Zarath M. Summers2, Glenn D. Christman1, Kristin M. Yoshimura1 & Jennifer F. Biddle1* Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafoor hydrocarbon seeps have been demonstrated to signifcantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10–15 cm below seafoor) were collected from fve natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chlorofexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fxation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. -
Microbial Diversity of Thermophiles with Biomass Deconstruction Potential in a Foliage-Rich Hot Spring
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universiti Teknologi Malaysia Institutional Repository Received: 9 December 2017 | Revised: 29 January 2018 | Accepted: 12 February 2018 DOI: 10.1002/mbo3.615 ORIGINAL RESEARCH Microbial diversity of thermophiles with biomass deconstruction potential in a foliage- rich hot spring Li Sin Lee1 | Kian Mau Goh2 | Chia Sing Chan2 | Geok Yuan Annie Tan1 | Wai-Fong Yin1 | Chun Shiong Chong2 | Kok-Gan Chan1,3 1ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Abstract Lumpur, Malaysia The ability of thermophilic microorganisms and their enzymes to decompose biomass 2 Faculty of Biosciences and Medical have attracted attention due to their quick reaction time, thermostability, and de- Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia creased risk of contamination. Exploitation of efficient thermostable glycoside hy- 3Jiangsu University, Zhenjiang, China drolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for Correspondence Kok-Gan Chan, International Genome biomass degradation at high temperatures have not yet been thoroughly studied. We Centre, Jiangsu University, Zhenjiang, China. examined a Malaysian Y- shaped Sungai Klah hot spring located within a wooded area. Email: [email protected] The fallen foliage that formed a thick layer of biomass bed under the heated water of Funding information the Y- shaped Sungai Klah hot spring was an ideal environment for the discovery and Postgraduate Research Fund grant, Grant/ Award Number: PG124-2016A; University analysis of microbial biomass decay communities. We sequenced the hypervariable of Malaya, Grant/Award Number: GA001- regions of bacterial and archaeal 16S rRNA genes using total community DNA ex- 2016 and GA002-2016; Universiti Teknologi Malaysia GUP, Grant/Award Number: tracted from the hot spring. -
International Code of Nomenclature of Prokaryotes
2019, volume 69, issue 1A, pages S1–S111 International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision) Charles T. Parker1, Brian J. Tindall2 and George M. Garrity3 (Editors) 1NamesforLife, LLC (East Lansing, Michigan, United States) 2Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) 3Michigan State University (East Lansing, Michigan, United States) Corresponding Author: George M. Garrity ([email protected]) Table of Contents 1. Foreword to the First Edition S1–S1 2. Preface to the First Edition S2–S2 3. Preface to the 1975 Edition S3–S4 4. Preface to the 1990 Edition S5–S6 5. Preface to the Current Edition S7–S8 6. Memorial to Professor R. E. Buchanan S9–S12 7. Chapter 1. General Considerations S13–S14 8. Chapter 2. Principles S15–S16 9. Chapter 3. Rules of Nomenclature with Recommendations S17–S40 10. Chapter 4. Advisory Notes S41–S42 11. References S43–S44 12. Appendix 1. Codes of Nomenclature S45–S48 13. Appendix 2. Approved Lists of Bacterial Names S49–S49 14. Appendix 3. Published Sources for Names of Prokaryotic, Algal, Protozoal, Fungal, and Viral Taxa S50–S51 15. Appendix 4. Conserved and Rejected Names of Prokaryotic Taxa S52–S57 16. Appendix 5. Opinions Relating to the Nomenclature of Prokaryotes S58–S77 17. Appendix 6. Published Sources for Recommended Minimal Descriptions S78–S78 18. Appendix 7. Publication of a New Name S79–S80 19. Appendix 8. Preparation of a Request for an Opinion S81–S81 20. Appendix 9. Orthography S82–S89 21. Appendix 10. Infrasubspecific Subdivisions S90–S91 22. Appendix 11. The Provisional Status of Candidatus S92–S93 23. -
A Metagenomics Roadmap to the Uncultured Genome Diversity in Hypersaline Soda Lake Sediments Charlotte D
Vavourakis et al. Microbiome (2018) 6:168 https://doi.org/10.1186/s40168-018-0548-7 RESEARCH Open Access A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments Charlotte D. Vavourakis1 , Adrian-Stefan Andrei2†, Maliheh Mehrshad2†, Rohit Ghai2, Dimitry Y. Sorokin3,4 and Gerard Muyzer1* Abstract Background: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. Results: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria,evenin the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. -
Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria
Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria A Major Qualifying Report Submitted to the Faculty of Worcester Polytechnic Institute In Partial Fulfillment of the Requirements for the Degree of Bachelor of Science By: __________________________ Courtney McCann Date Approved: _______________________ Professor José M. Argüello Biochemistry WPI Project Advisor 1 Abstract Copper homeostasis is achieved in bacteria through a combination of copper chaperones and transporting and chelating proteins. Bioinformatic analyses were used to identify which of these proteins are present in Deltaproteobacteria. The genetic environment of the bacteria is affected by its lifestyle, as those that live in higher concentrations of copper have more of these proteins. Two major transport proteins, CopA and CusC, were found to cluster together frequently in the genomes and appear integral to copper homeostasis in Deltaproteobacteria. 2 Acknowledgements I would like to thank Professor José Argüello for giving me the opportunity to work in his lab and do some incredible research with some equally incredible scientists. I need to give all of my thanks to my supervisor, Dr. Teresita Padilla-Benavides, for having me as her student and teaching me not only lab techniques, but also how to be scientist. I would also like to thank Dr. Georgina Hernández-Montes and Dr. Brenda Valderrama from the Insituto de Biotecnología at Universidad Nacional Autónoma de México (IBT-UNAM), Campus Morelos for hosting me and giving me the opportunity to work in their lab. I would like to thank Sarju Patel, Evren Kocabas, and Jessica Collins, whom I’ve worked alongside in the lab. I owe so much to these people, and their support and guidance has and will be invaluable to me as I move forward in my education and career.