Metagenomic Views of Microbial Dynamics Influenced By
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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. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
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. -
Tree Scale: 1 D Bacteria P Desulfobacterota C Jdfr-97 O Jdfr-97 F Jdfr-97 G Jdfr-97 S Jdfr-97 Sp002010915 WGS ID MTPG01
d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermodesulfobacterium s Thermodesulfobacterium commune WGS ID JQLF01 d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermosulfurimonas s Thermosulfurimonas dismutans WGS ID LWLG01 d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f DG-60 g DG-60 s DG-60 sp001304365 WGS ID LJNA01 ID WGS sp001304365 DG-60 s DG-60 g DG-60 f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f Desulfofervidaceae g Desulfofervidus s Desulfofervidus auxilii RS GCF 001577525 1 001577525 GCF RS auxilii Desulfofervidus s Desulfofervidus g Desulfofervidaceae f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfatatoraceae g Thermodesulfatator s Thermodesulfatator atlanticus WGS ID ATXH01 d Bacteria p Desulfobacterota c Desulfobacteria o Desulfatiglandales f NaphS2 g 4484-190-2 s 4484-190-2 sp002050025 WGS ID MVDB01 ID WGS sp002050025 4484-190-2 s 4484-190-2 g NaphS2 f Desulfatiglandales o Desulfobacteria c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g QOAM01 s QOAM01 sp003978075 WGS ID QOAM01 d Bacteria p Desulfobacterota c BSN033 o UBA8473 f UBA8473 g UBA8473 s UBA8473 sp002782605 WGS -
Impacts of Desulfobacterales and Chromatiales on Sulfate Reduction in The
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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-NC-ND 4.0 International license. 1 Impacts of Desulfobacterales and Chromatiales on sulfate reduction in the 2 subtropical mangrove ecosystem as revealed by SMDB analysis 3 Shuming Mo 1, †, Jinhui Li 1, †, Bin Li 2, Ran Yu 1, Shiqing Nie 1, Zufan Zhang 1, Jianping 4 Liao 3, Qiong Jiang 1, Bing Yan 2, *, and Chengjian Jiang 1, 2 * 5 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro- 6 bioresources, Guangxi Research Center for Microbial and Enzyme Engineering 7 Technology, College of Life Science and Technology, Guangxi University, Nanning 8 530004, China. 9 2 Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove 10 Research Center, Guangxi Academy of Sciences, Beihai 536000, China. 11 3 School of Computer and Information Engineering, Nanning Normal University, 12 Nanning 530299, China. 13 † These authors contributed equally to this work. 14 *: Corresponding Author: 15 Tel: +86-771-3270736; Fax: +86-771-3237873 16 Email: [email protected] (CJ); [email protected] (BY) 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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. -
Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. .................................................................... -
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 -
Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities
Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use. This chapter was originally published in the book Advances in Applied Microbiology, Vol 66, published by Elsevier, and the attached copy is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who know you, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier's permissions site at: http://www.elsevier.com/locate/permissionusematerial From: Noha Youssef, Mostafa S. Elshahed, and Michael J. McInerney, Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities. In Allen I. Laskin, Sima Sariaslani, and Geoffrey M. Gadd, editors: Advances in Applied Microbiology, Vol 66, Burlington: Academic Press, 2009, pp. 141-251. ISBN: 978-0-12-374788-4 © Copyright 2009 Elsevier Inc. Academic Press. Author's personal copy CHAPTER 6 Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities Noha Youssef, Mostafa S. Elshahed, and Michael J. McInerney1 Contents I. Introduction 142 II. Factors Governing Oil Recovery 144 III. Microbial Ecology of Oil Reservoirs 147 A. Origins of microorganisms recovered from oil reservoirs 147 B. Microorganisms isolated from oil reservoirs 148 C. Culture-independent analysis of microbial communities in oil reservoirs 155 IV. -
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. -
Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones
International Journal of Environmental Research and Public Health Article Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones Yongkui Yang 1,2 , Longfei Wang 1, Feng Xiang 1, Lin Zhao 1,2 and Zhi Qiao 1,2,* 1 School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; [email protected] (Y.Y.); [email protected] (L.W.); [email protected] (F.X.); [email protected] (L.Z.) 2 China-Singapore Joint Center for Sustainable Water Management, Tianjin University, Tianjin 300350, China * Correspondence: [email protected]; Tel.: +86-22-87402072 Received: 14 November 2019; Accepted: 7 January 2020; Published: 9 January 2020 Abstract: Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs. Keywords: activated sludge; industrial zone; metabolic function; microbial community; wastewater treatment 1.