DOCSLIB.ORG

Mechanisms of Diversity Maintenance, Resilience, and Niche Differentiation in Activated Sludge Microbial Communities

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mechanisms of Diversity Maintenance, Resilience, and Niche Differentiation in Activated Sludge Microbial Communities MECHANISMS OF DIVERSITY MAINTENANCE, RESILIENCE, AND NICHE DIFFERENTIATION IN ACTIVATED SLUDGE MICROBIAL COMMUNITIES By David Charles Vuono A thesis submitted to the Faculty and Board of Trustees of the Colorado School of Mines in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Environmental Science and Engineering). Golden, Colorado Date __________________ Signed:___________________ David C. Vuono Signed:___________________ Dr. Jörg E. Drewes Thesis Advisor Signed:___________________ Dr. Junko Munakata Marr Thesis Co-Advisor Golden, Colorado Date __________________ Signed:___________________ Dr. John E. McCray Professor and Department Head Department of Civil and Environmental Engineering ii 1 ABSTRACT Scarcity of potable water is a major threat to human civilization, particularly in semi-arid and arid regions of the world. As a consequence, water reclamation and reuse of treated wastewater has received more attention. Local reuse of reclaimed water that is tailored to local needs will be essential in cities because of greater population densities. Because it has been applied under many operational configurations, the activated sludge process was chosen to investigate if new operational strategies could facilitate tailored reuse of reclaimed water. However, alterations of operational conditions within the same biological nutrient removal treatment plant have not been tested for the intentional retention of nutrients in treated wastewater. Thus, the consequences of changing treatment conditions on biological and engineered operational parameters in a treatment plant are unknown, specifically the resilience of functionally important microorganisms involved in the removal of nutrients or trace organic chemicals. This dissertation describes the use of a variety of genomic molecular techniques such as massively parallel DNA/RNA sequencing to phylogenetically reconstruct activated sludge microbial community assemblages in a full-scale active sludge wastewater treatment bioreactor that is configured as a sequencing batch membrane bioreactor (SBMBR). The SBMBR system, located at the Colorado School of Mines’ Water Reclamation Test Site, was operated under different bioreactor set-points through time to investigate fundamental and applied questions in the fields of microbial ecology and environmental engineering. The key findings of each research chapter are as follows: Chapter 2) Adjustments in aeration strategy can be used to elevate nutrient concentrations in the effluent of an SBMBR without adverse effects on bioreactor operation. Chapter 3) Bioreactor performance in an SBMBR is resilient to long-term disturbances. Abundant bacterial populations recover from the disturbance more than rare populations. Chapter 4) A long-term disturbance allows for immigrating bacteria to colonize and establish into an activated sludge community. In some cases, newly established colonizers become abundant community members post disturbance. Chapter 5) Bacterial populations within a stable treatment process exhibit distinct activity signatures that correspond to fluctuations in redox conditions. iii 2 TABLE OF CONTENTS 1 ABSTRACT ............................................................................................................................. iii 3 LIST OF FIGURES ............................................................................................................... viii 4 LIST OF TABLES .................................................................................................................... x 5 ACKNOWLEDGEMENTS ..................................................................................................... xi 6 DEDICATION ........................................................................................................................ xii 1 CHAPTER 1 ............................................................................................................................. 1 1.1 Background ................................................................................................................... 1 1.2 Research Motivation ..................................................................................................... 3 1.3 Research Objectives ...................................................................................................... 4 2 CHAPTER 2 – ENGINEERING AND OPERATIONAL CHALLENGES FOR FLEXIBLE HYBRID TREATMENT SYSTEMS ............................................................................................. 6 2.1 Abstract ......................................................................................................................... 6 2.2 Introduction ................................................................................................................... 6 2.3 Materials and Methods .................................................................................................. 8 2.3.1 Site layout and SBMBR process description .................................................... 9 2.3.2 Description of treatment strategies. ................................................................ 11 2.3.3 Data acquisition and analytical procedures ..................................................... 11 2.3.4 Statistical Analysis .......................................................................................... 13 2.4 Results and Discussion ............................................................................................... 13 2.4.1 Start up ............................................................................................................ 13 2.4.2 Treatment Performance under Strategies 1 and 2 ........................................... 14 2.4.3 Membrane performance .................................................................................. 17 2.4.4 Conclusion ...................................................................................................... 21 2.5 Acknowledgments ....................................................................................................... 21 3 CHAPTER 3 – PHYLOGENETIC RECONSTRUCTION OF AN ACTIVATED SLUDGE COMMUNITY UNDER DIFFERENT SOLIDS RETENTION TIMES ..................................... 22 3.1 Abstract ....................................................................................................................... 22 3.2 Introduction ................................................................................................................. 23 3.3 Materials and Methods ................................................................................................ 25 iv 3.3.1 Sampling, Amplification, and Sequencing ..................................................... 25 3.3.2 SSU rRNA processing pipeline and quality control ....................................... 25 3.4 Results ......................................................................................................................... 26 3.4.1 Analysis of Ecosystem Function ..................................................................... 26 3.4.2 Effects of SRT on Bacterial Diversity ............................................................ 27 3.4.3 Effects of SRT on Community Composition .................................................. 30 3.4.4 Bacterial Dynamics/Response During Selective Enrichment of r-K Strategists 31 3.5 Discussion ................................................................................................................... 34 3.5.1 Microbial Diversity is Not Resilient to All Types of Disturbance ................. 34 3.5.2 Improved Methods of Comparing Microbial Diversity .................................. 36 3.5.3 Prediction of Ecosystem Health Based on Indicator Species ......................... 36 3.5.4 Merging Ecology and Environmental Engineering ........................................ 37 3.6 Acknowledgments ....................................................................................................... 37 4 CHAPTER 4 – IMMIGRATION AND MECHANISMS OF MICROBIAL DIVERSITY MAINTENANCE IN ACTIVATED SLUDGE ........................................................................... 37 4.1 Abstract ....................................................................................................................... 38 4.2 Introduction ................................................................................................................. 38 4.3 Materials and Methods ................................................................................................ 40 4.3.1 Bioreactor operation ........................................................................................ 40 4.3.2 Sampling, Amplification, and Sequencing ..................................................... 40 4.3.3 SSU rRNA processing and quality control ..................................................... 41 4.3.4 Biodiversity analysis, null model consideration and network analysis .......... 41 4.4 Results ......................................................................................................................... 43 4.4.1 Bacterial composition and diversity of sewage-derived and sludge communities ................................................................................................................ 44 4.4.2 Disturbance drives phylogenetic community structure ................................... 45 4.4.3 Activated sludge communities become more similar to influent during disturbance .................................................................................................................
Load more

Recommended publications
  • The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
    The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • Consortia of Anti-Nematode Fungi and Bacteria in the Rhizosphere Of
    bioRxiv preprint doi: https://doi.org/10.1101/332403; this version posted May 28, 2018. 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 Consortia of anti-nematode fungi and bacteria in the 2 rhizosphere of soybean plants attacked by root-knot 3 nematodes 4 5 Hirokazu Toju1,2* and Yu Tanaka2,3 6 7 1Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan 8 2Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and 9 Technology Agency, Kawaguchi, Saitama 332-0012, Japan 10 3Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto, 11 606-8502, Japan 12 13 *Correspondence: Hirokazu Toju ([email protected]). 14 15 This article includes 5 Figures, 4 Tables, 5 Supplementary Figures, and 5 Supplementary 16 Data. 17 Running head: Anti-nematode microbiomes 18 bioRxiv preprint doi: https://doi.org/10.1101/332403; this version posted May 28, 2018. 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. 19 Abstract. 20 Cyst and root-knot nematodes are major risk factors of agroecosystem management, often 21 causing devastating impacts on crop production. The use of microbes that parasitize or prey 22 on nematodes has been considered as a promising approach for suppressing phytopathogenic 23 nematode populations.
    [Show full text]
  • Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
    bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. 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 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017.
    [Show full text]
  • Analysis of the Genome and Metabolome of Marine
    www.nature.com/scientificreports OPEN Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Received: 15 June 2018 Accepted: 29 October 2018 Potential for Biosynthesis of Novel Published: xx xx xxxx Specialized Metabolites Jamshid Amiri Moghaddam 1, Max Crüsemann1, Mohammad Alanjary2, Henrik Harms3,4, Antonio Dávila-Céspedes1, Jochen Blom 5, Anja Poehlein6, Nadine Ziemert2, Gabriele M. König1 & Till F. Schäberle 3,4,7 Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scafolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifca DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modifed peptides (RiPPs) were mostly strain specifc.
    [Show full text]
  • Exploring the Diversity and Antimicrobial Potential of Predatory Bacteria from Indonesian Mangroves
    Exploring the diversity and antimicrobial potential of predatory bacteria from Indonesian mangroves Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades einer Doktorin der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n Von Senlie Octaviana Aus Salatiga / Indonesien 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent. Dr. Joachim Wink eingereicht am: 22.02.2021 mündliche Prüfung (Disputation) am: 05.05.2021 Druckjahr 2021 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Senlie Octaviana, Tjandrawati Mozef, and Joachim Wink. Taxonomy and antimicrobial activity of gliding bacterium from Indonesian Mangroves. Submitted to Hayati Journal of Biosciences (2020). Senlie Octaviana, Gian Primahana, Tjandrawati Mozef, Luiz G. A. Borges, Dietmar H. Pieper and Joachim Wink. Antimicrobial Potential of Myxobacteria from Indonesian Mangroves. Submitted to Current Microbiology Journal (2021). Tagungsbeiträge Diversity and antimicrobial potential of myxobacteria from Indonesian Mangroves (2020). Retreat of the Helmholtz Centre for Infection Research Graduate School, Braunschweig, Germany (Mündlicher Vortrag). Posterbeiträge Myxobacteria from Coastal Area in Indonesia as a source of novel anti-infective. June 2018. HIPS-Symposium, Saarbrücken, Germany. A gliding
    [Show full text]
  • Aquaculture Environment Interactions 10:413
    Vol. 10: 413–427, 2018 AQUACULTURE ENVIRONMENT INTERACTIONS Published September 27 https://doi.org/10.3354/aei00278 Aquacult Environ Interact OPENPEN ACCESSCCESS Effects of finfish aquaculture on biogeochemistry and bacterial communities associated with sulfur cycles in highly sulfidic sediments Ayeon Choi1, Hyeyoun Cho1, Bomina Kim1, Hyung Chul Kim2, Rae-Hong Jung2, Won-Chan Lee2, Jung-Ho Hyun1,* 1Department of Marine Science and Convergent Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, Republic of Korea 2Marine Environment Research Division, National Institute of Fisheries Science (NIFS), Busan 46083, Republic of Korea ABSTRACT: A combination of biogeochemical analyses and molecular microbiological analyses were conducted to assess the environmental impact of finfish aquaculture and to elucidate the major microbial assemblages responsible for the production and removal of reduced sulfur com- + pounds in fish-farm sediments. The average concentrations of H2S (123 µM) and NH4 (1310 µM) and the dissimilatory sulfite reductase (dsr) gene copy number (1.9 × 109 copies cm−3) in the sedi- ments at the farm site were 15-, 1.5- and 2-fold higher, respectively, than those measured at the less-impacted reference site. Accordingly, the sulfate reduction rate (SRR) at the farm site (118 mmol m−2 d−1) was 19-fold higher than that measured at the reference site (6.2 mmol m−2 d−1). Analyses of dsrA and 16S rRNA gene sequences revealed that the Syntrophobacteraceae and Desulfobulbaceae groups are the major sulfate-reducing bacteria around the fish-farm sediment. −2 −1 Interestingly, despite the high SRR (12.2−19.6 mmol m d ), the H2S concentration was low (<8 µM) in the top 0−2 cm of the fish-farm sediments.
    [Show full text]
  • Downloaded from the Genebank
    bioRxiv preprint doi: https://doi.org/10.1101/401109; this version posted August 27, 2018. 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 Title: Differential amplicons for the evaluation of RNA integrity extracted from complex 2 environmental samples 3 4 Authors: Fabien Cholet#, Umer Z. Ijaz & Cindy J. Smith 5 6 Infrastructure and Environment Research Division, School of Engineering, University of 7 Glasgow, UK, G12 8LT 8 9 10 11 12 13 14 15 # Address correspondence to [email protected] 16 17 18 19 20 21 22 23 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/401109; this version posted August 27, 2018. 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. 26 Abstract 27 Background 28 Reliability and reproducibility of transcriptomics-based studies are highly dependent on the 29 integrity of RNA. Microfluidics-based techniques based on ribosomal RNA such as the RNA 30 Integrity Number (RIN) are currently the only approaches to evaluate RNA integrity. 31 However, it is not known if ribosomal RNA reflects the integrity of the meaningful part of the 32 sample, the mRNA. Here we test this assumption and present a new integrity index, the Ratio 33 amplicon, Ramp, to monitor mRNA integrity based on the differential amplification of long to 34 short RT-Q-PCR amplicons of the glutamine synthetase A (glnA) transcript.
    [Show full text]
  • Genome Relatedness and Evolutionary Changes David E
    Whitworth BMC Genomics (2015) 16:780 DOI 10.1186/s12864-015-2018-y RESEARCH ARTICLE Open Access Genome-wide analysis of myxobacterial two-component systems: genome relatedness and evolutionary changes David E. Whitworth Abstract Background: Two-component systems (TCSs) are abundant prokaryotic signaling pathways, whose evolution is of particular importance because of their role in bacterial pathogenicity. Comparative genomics can provide important insights into the evolution of these genes, but inferences are dependent on the relatedness of the compared genomes. This study investigated the relationship between evolutionary distance and TCS evolution in myxobacterial genomes, of which there are several sequenced examples, of varying relatedness, and which encode large numbers of TCSs. Methods: Myxobacterial TCS gene sets were compared, orthologues defined, and changes in TCS properties such as gene organisation, domain architecture and size identified. Results: Genome relatedness/evolutionary distance was found to have a large effect on the apparent frequency of evolutionary events affecting TCS genes, but not on the relative dominance of different types of mutations. Large (≥1 gene) indels were the most common changes, often giving rise to gene organisation changes. Smaller indels were also common, sometimes changing domain architecture, and/or leading to pseudogene formation. Individuality of myxobacterial TCS gene sets seems primarily due to lineage specific gene loss. However, there is also evidence of extensive acquisition of genes by lateral transfer, with gene duplication also creating new TCS genes. Conclusions: This study provides catalogues of myxobacterial TCS gene sets and their orthology relationships, benchmarked against genome relatedness. It also provides insights into the relationship between evolutionary distance and the inference of TCS estudies of TCS evolution beyond the myxobacteriavolution, which may be important for studies of TCS evolutiThe online version of this articleon beyond the myxobacteria.
    [Show full text]
  • Haliangium Ochraceum Type Strain (SMP-2)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Permalink https://escholarship.org/uc/item/8t57s75h Journal Standards in genomic sciences, 2(1) ISSN 1944-3277 Authors Ivanova, Natalia Daum, Chris Lang, Elke et al. Publication Date 2010-01-28 DOI 10.4056/sigs.69.1277 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:96-106 DOI:10.4056/sigs.69.1277 Complete genome sequence of Haliangium ochraceum type strain (SMP-2T) Natalia Ivanova1, Chris Daum1, Elke Lang2, Birte Abt2, Markus Kopitz2, Elizabeth Saunders3, Alla Lapidus1, Susan Lucas1, Tijana Glavina Del Rio1, Matt Nolan1, Hope Tice1, Alex Copeland1, Jan-Fang Cheng1, Feng Chen1, David Bruce1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Mavromatis1, Amrita Pati1, Natalia Mikhailova1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1,3, Thomas Brettin1,3, Manfred Rohde6, Markus Göker2, Jim Bristow1, Victor Markowitz4, Jonathan A. Eisen1,7, Philip Hugenholtz1, Nikos C. Kyrpides1, and Hans-Peter Klenk2* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: aerobic, gliding, myxobacteria, fruiting bodies, moderately halophilic, mesophile, Gram-negative, decomposition of bacterial and yeast cells, Myxococcales, GEBA.
    [Show full text]
  • Functional Divergence and Potential Mechanisms of the Duplicate Reca Genes in Myxococcus Xanthus
    bioRxiv preprint doi: https://doi.org/10.1101/766055; this version posted September 11, 2019. 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. Functional divergence and potential mechanisms of the duplicate recA genes in Myxococcus xanthus Duo-hong Sheng§*, Yi-xue Wang§, Miao Qiu, Jin-yi Zhao, Xin-jing Yue, Yue-zhong Li* State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China E-mail addresses of the authors: Duo-hong Sheng, [email protected]；Tel. (+86) 532 58631538; ORCID ID, 0000-0002- 3044-8557. Yi-xue Wang, [email protected] Miao Qiu, [email protected] Jin-yi Zhao, [email protected] Xin-jing Yue, [email protected] Yue-zhong Li, [email protected]; Tel. (+86) 532 58631539; ORCID ID, 0000-0001-8336-6638. § These authors contribute equally to this paper. * The corresponding author. Author's contribution: DHS and YZL designed experiments; DHS, YXW, MQ and JYZ performed the experiments; DHS, XJY and YZL analyzed the data; DHS and YZL wrote the paper. Attach Files: 7 figures, 5 supplementary figures and 4 supplementary tables bioRxiv preprint doi: https://doi.org/10.1101/766055; this version posted September 11, 2019. 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.
    [Show full text]
  • Automated Identification of Myxobacterial Genera Using Convolutional Neural Network
    www.nature.com/scientificreports OPEN Automated identifcation of Myxobacterial genera using Convolutional Neural Network Hedieh Sajedi1*, Fatemeh Mohammadipanah2* & Ali Pashaei3 The Myxococcales order consist of eleven families comprising30 genera, and are featured by the formation of the highest level of diferential structure aggregations called fruiting bodies. These multicellular structures are essential for their resistance in ecosystems and is used in the primitive identifcation of these bacteria while their accurate taxonomic position is confrmed by the nucleotide sequence of 16SrRNA gene. Phenotypic classifcation of these structures is currently performed based on the stereomicroscopic observations that demand personal experience. The detailed phenotypic features of the genera with similar fruiting bodies are not readily distinctive by not particularly experienced researchers. The human examination of the fruiting bodies requires high skill and is error-prone. An image pattern analysis of schematic images of these structures conducted us to the construction of a database, which led to an extractable recognition of the unknown fruiting bodies. In this paper, Convolutional Neural Network (CNN) was considered as a baseline for recognition of fruiting bodies. In addition, to enhance the result the classifer, part of CNN is replaced with other classifers. By employing the introduced model, all 30 genera of this order could be recognized based on stereomicroscopic images of the fruiting bodies at the genus level that not only does not urge us to amplify and sequence gene but also can be attained without preparation of microscopic slides of the vegetative cells or myxospores. The accuracy of 77.24% in recognition of genera and accuracy of 88.92% in recognition of suborders illustrate the applicability property of the proposed machine learning model.
    [Show full text]