Insights Into the Bacterial Species and Communities of a Full-Scale Anaerobic/ Anoxic/Oxic Wastewater Treatment Plant by Using Third-Generation Sequencing
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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 -
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure Authors: Suzanne L. Ishaq, Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled The final publication is available at Springer via http://dx.doi.org/10.1007/s00248-016-0861-2. Ishaq, Suzanne L. , Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled. "Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure." Microbial Ecology 73, no. 2 (February 2017): 417-434. DOI: 10.1007/s00248-016-0861-2. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure 1,2 & 2 & 3 & 4 & Suzanne L. Ishaq Stephen P. Johnson Zach J. Miller Erik A. Lehnhoff 1 1 2 Sarah Olivo & Carl J. Yeoman & Fabian D. Menalled 1 Department of Animal and Range Sciences, Montana State University, P.O. Box 172900, Bozeman, MT 59717, USA 2 Department of Land Resources and Environmental Sciences, Montana State University, P.O. Box 173120, Bozeman, MT 59717, USA 3 Western Agriculture Research Center, Montana State University, Bozeman, MT, USA 4 Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, USA Abstract Farming practices affect the soil microbial commu- then individual farm. Living inoculum-treated soil had greater nity, which in turn impacts crop growth and crop-weed inter- species richness and was more diverse than sterile inoculum- actions. -
Molecular and Kinetic Characterization of Anammox Bacteria Enrichments and Determination of the Suitability of Anammox for Landfill Leachate Treatment
AN ABSTRACT OF THE THESIS OF Sharmin Sultana for the degree of Master of Science in Environmental Engineering presented on December 1, 2016 Title: Molecular and Kinetic Characterization of Anammox Bacteria Enrichments and Determination of the Suitability of Anammox for Landfill Leachate Treatment Abstract approved: ______________________________________________________ Tyler S. Radniecki Anaerobic ammonium oxidation (anammox) has recently appeared as a promising approach for removing nitrogen from landfill leachates because it requires less oxygen and no organic carbon compared to traditional nitrification-denitrification system, and it produces low sludge volumes, thereby reducing operating and biological sludge disposal costs by over 60%. Anammox bacteria anaerobically oxidize ammonia with nitrite to form dinitrogen gas, which is bubbled out of the system. When combined with partial nitrification (the aerobic oxidation of half the ammonia to nitrite), anammox bacteria can be an efficient and sustainable solution to treat landfill leachate. However, leachate loading rates to the anammox reactor are critical due to the high concentrations of potential anammox inhibitors, including heterogenous organic carbon, heavy metals, pesticides and nitrite. In this study, anammox bacteria were enriched from two sources; sludge from the world’s first full-scale anammox plant (Dokhaven wastewater treatment plant) in Rotterdam, Netherlands and sludge from the Virginia Hampton Roads Sanitation District (HRSD) wastewater treatment facility, the first full-scale anammox plant in the United States. The sludge was enriched over 14 months in two sequencing batch reactors (SBR) and about a year period in a novel carbon nanotube membrane upflow anaerobic sludge blanket (MUASB) reactor. Of the two systems, SBR and MUASB, the MUASB was much more effective at enriching anammox bacteria due to its ability to capture planktonic anammox cells and enhance the anammox granulation process. -
Shifts in Soil Bacterial Communities Associated with the Potato
Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments Caroline Sablayrolles, Jan Dirk van Elsas, Joana Falcão Salles To cite this version: Caroline Sablayrolles, Jan Dirk van Elsas, Joana Falcão Salles. Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments. Applied Soil Ecology, Elsevier, 2013, 63, pp.78-87. 10.1016/j.apsoil.2012.09.004. hal-02147674 HAL Id: hal-02147674 https://hal.archives-ouvertes.fr/hal-02147674 Submitted on 4 Jun 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible This is an author’s version published in: http://oatao.univ-toulouse.fr/23717 Official URL: https://doi.org/10.1016/j.apsoil.2012.09.004 To cite this version: İnceoğlu, Özgül and Sablayrolles, Caroline and van Elsas, Jan Dirk and Falcão Salles, Joana Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments. (2013) Applied Soil Ecology, 63. 78-87. -
Impact of Plant Species, N Fertilization and Ecosystem Engineers on the Structure and Function of Soil Microbial Communities
IMPACT OF PLANT SPECIES, N FERTILIZATION AND ECOSYSTEM ENGINEERS ON THE STRUCTURE AND FUNCTION OF SOIL MICROBIAL COMMUNITIES Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades "Doctor rerum naturalium" der Georg-August-Universität Göttingen im Promotionsprogramm Biologie der Georg-August University School of Science (GAUSS) vorgelegt von Birgit Pfeiffer aus Forst/ Lausitz Göttingen 2013 Betreuungsausschuss Prof. Dr. Rolf Daniel, Genomische und angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik; Georg-August-Universität Göttingen PD Dr. Michael Hoppert, Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik; Georg-August-Universität Göttingen Mitglieder der Prüfungskommission Referent/in: Prof. Dr. Rolf Daniel, Genomische und angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik; Georg-August-Universität Göttingen Korreferent/in: PD Dr. Michael Hoppert, Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik; Georg-August-Universität Göttingen Weitere Mitglieder der Prüfungskommission: Prof. Dr. Hermann F. Jungkunst, Geoökologie / Physische Geographie, Institut für Umweltwissenschaften, Universität Koblenz-Landau Prof. Dr. Stefanie Pöggeler, Genetik eukaryotischer Mikroorganismen, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen Prof. Dr. Stefan Irniger, Molekulare Mikrobiologie und Genetik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen Jun.-Prof. Dr. Kai Heimel, Molekulare Mikrobiologie und Genetik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen Tag der mündlichen Prüfung: 20.12.2013 Two things are necessary for our work: unresting patience and the willingness to abandon something in which a lot of time and effort has been put. Albert Einstein, (Free translation from German to English) Dedicated to my family. Table of contents Table of contents Table of contents I List of publications III A. GENERAL INTRODUCTION 1 1. BIODIVERSITY AND ECOSYSTEM FUNCTIONING AS IMPORTANT GLOBAL ISSUES 1 2. -
Comparison of Methods to Identify Pathogens and Associated Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada
RESEARCH ARTICLE Comparison of Methods to Identify Pathogens and Associated Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada Etienne Yergeau1*, Luke Masson2, Miria Elias1, Shurong Xiang3, Ewa Madey4, a11111 Hongsheng Huang5, Brian Brooks5, Lee A. Beaudette3 1 National Research Council Canada, Energy Mining and Environment, Montreal, Qc, Canada, 2 National Research Council Canada, Human Health Therapeutics, Montreal, Qc, Canada, 3 Environment Canada, Biological Assessment and Standardization Section, Ottawa, On, Canada, 4 Canadian Food Inspection Agency, Fertilizer Safety Office, Plant Health & Biosecurity Directorate, Ottawa, On, Canada, 5 Canadian Food Inspection Agency, Ottawa Laboratory – Fallowfield, Ottawa, On, Canada OPEN ACCESS * [email protected] Citation: Yergeau E, Masson L, Elias M, Xiang S, Madey E, Huang H, et al. (2016) Comparison of Methods to Identify Pathogens and Associated Abstract Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada. The use of treated municipal wastewater residues (biosolids) as fertilizers is an attractive, PLoS ONE 11(4): e0153554. doi:10.1371/journal. inexpensive option for growers and farmers. Various regulatory bodies typically employ pone.0153554 indicator organisms (fecal coliforms, E. coli and Salmonella) to assess the adequacy and Editor: Leonard Simon van Overbeek, Wageningen efficiency of the wastewater treatment process in reducing pathogen loads in the final University and Research Centre, NETHERLANDS product. Molecular detection approaches can offer some advantages over culture-based Received: October 28, 2015 methods as they can simultaneously detect a wider microbial species range, including Accepted: March 31, 2016 non-cultivable microorganisms. However, they cannot directly assess the viability of the Published: April 18, 2016 pathogens. -
Identification of Novel Betaproteobacteria in a Succinate-Assimilating Population in Denitrifying Rice Paddy Soil by Using Stable Isotope Probing
Microbes Environ. Vol. 23, No. 3, 192–200, 2008 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.23.192 Identification of Novel Betaproteobacteria in a Succinate-Assimilating Population in Denitrifying Rice Paddy Soil by Using Stable Isotope Probing TAKAYUKI SAITO1,†, SATOSHI ISHII1,†,*, SHIGETO OTSUKA1, MASAYA NISHIYAMA2, and KEISHI SENOO1 1Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan; and 2Faculty of Environmental Studies, Nagasaki University, 1–14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852–8521, Japan (Received April 8, 2008—Accepted May 24, 2008) Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for the denitrification have not been well characterized. In this study, we employed Stable Isotope Probing (SIP) to study succinate-assimilating denitrifiers in soil microcosms amended with nitrate and 13C-succinate. Microbial popula- tions represented in 12C- and 13C-DNA fractions were different based on denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified 16S rRNA gene fragment. A nearly full-length 16S rRNA gene was also amplified, cloned, and sequenced from 13C-DNA fraction. Both PCR-DGGE and clone library analyses revealed that Burkholderi- ales and Rhodocyclales dominated the succinate-assimilating population in denitrifying soil after 24 h incubation. Among these, novel Betaproteobacteria, possibly within the order Rhodocyclales, represented 43% of the clones obtained. Nitrite reductase genes, nirS and nirK, were also amplified and cloned from the 13C-DNA fraction. While most nirK clones in this study were similar to the nirK sequences from Rhizobiales, a majority of the nirS clones were similar to the nirS sequences from Burkholderiales and Rhodocyclales, consistent with the 16S rRNA gene analysis. -
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. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Achieving Efficient and Stable Deammonification at Low
energies Article Achieving Efficient and Stable Deammonification at Low Temperatures—Experimental and Modeling Studies Hussein Al-Hazmi 1,* , Xi Lu 1,2, Dominika Grubba 1 , Joanna Majtacz 1, Przemysław Kowal 1 and Jacek M ˛akinia 1 1 Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza Street, 80-233 Gda´nsk,Poland; [email protected] (X.L.); [email protected] (D.G.); [email protected] (J.M.); [email protected] (P.K.); [email protected] (J.M.) 2 Institute of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China * Correspondence: [email protected] Abstract: The short-term effects of temperature on deammonification sludge were evaluated in a laboratory-scale sequencing batch reactor (SBR). Mathematical modeling was used for further evalu- ations of different intermittent aeration strategies for achieving high and stable deammonification performance at decreasing temperatures. As for the biomass cultivated at high temperatures (e.g., 30 ◦C), a higher temperature dependency (the adjusted Arrhenius coefficient θ for 11–17 ◦C = 1.71 vs. θ for 17–30 ◦C = 1.12) on the specific anammox growth rates was found at lower temperatures (11–17 ◦C) in comparison with higher temperatures (17–30 ◦C). Further evaluations of recovering the nitrogen removal efficiency at decreasing temperatures with the mathematical model by modifying the intermittent aeration strategies (aeration frequency (F) and the ratio (R) between non-aerated Citation: Al-Hazmi, H.; Lu, X.; (non-aer) phase and aerated (aer) phase durations) indicated that intermittent aeration with a pro- Grubba, D.; Majtacz, J.; Kowal, P.; longed non-aerated phase (e.g., R ≥ 4 regardless of F value) would help to maintain high and ◦ M ˛akinia,J. -
Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy
fmicb-10-01480 June 29, 2019 Time: 17:5 # 1 ORIGINAL RESEARCH published: 02 July 2019 doi: 10.3389/fmicb.2019.01480 Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy Lucia Cavalca1*, Sarah Zecchin1, Patrizia Zaccheo2, Ben Abbas3, Marco Rotiroti4, Tullia Bonomi4 and Gerard Muyzer5 1 Dipartimento di Scienze per gli Alimenti, la Nutrizione e l0Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy, 2 Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milan, Italy, 3 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 4 Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy, 5 Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Arsenic contamination of groundwater aquifers is an issue of global concern. Among the Edited by: affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits Qiaoyun Huang, for drinking water are present, with consequent issues of public concern. In this study, Huazhong Agricultural University, for the first time, the role of microbial communities in metalloid cycling in groundwater China samples from Northern Italy lying on Pleistocene sediments deriving from Alps Reviewed by: Ping Li, mountains has been investigated combining environmental genomics and cultivation China University of Geosciences, approaches. 16S rRNA gene libraries revealed a high number of yet uncultured China Santosh Kr. Karn, species, which in some of the study sites accounted for more of the 50% of the Sardar Bhagwan Singh Post total community. -
Anaerobic Degradation of Steroid Hormones by Novel Denitrifying Bacteria
Anaerobic degradation of steroid hormones by novel denitrifying bacteria Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der Rheinisch- Westfälischen Technischen Hochschule Aachen zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigte Dissertation vorgelegt von Diplom-Biologe Michael Fahrbach aus Bad Mergentheim (Baden-Württemberg) Berichter: Professor Dr. Juliane Hollender Professor Dr. Andreas Schäffer Tag der mündlichen Prüfung: 12. Dezember 2006 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfügbar. Table of Contents 1 Introduction.....................................................................................................................1 1.1 General information on steroids ...............................................................................1 1.2 Steroid hormones in the environment.......................................................................2 1.2.1 Natural and anthropogenic sources and deposits ............................................2 1.2.2 Potential impact on the environment ................................................................3 1.2.3 Fate of steroid hormones..................................................................................4 1.3 Microbial degradation of steroid hormones and sterols............................................5 1.3.1 Aerobic degradation..........................................................................................5 1.3.2 Anaerobic degradation......................................................................................7