Bacterial Community Change Through Drinking Water Treatment Processes
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The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of
Gohli et al. Microbiome (2019) 7:160 https://doi.org/10.1186/s40168-019-0772-9 RESEARCH Open Access The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Jostein Gohli1* , Kari Oline Bøifot1,2, Line Victoria Moen1, Paulina Pastuszek3, Gunnar Skogan1, Klas I. Udekwu4 and Marius Dybwad1,2 Abstract Background: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. Methods: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. Results: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer. -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
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. -
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Vol. 648: 79–94, 2020 MARINE ECOLOGY PROGRESS SERIES Published August 27 https://doi.org/10.3354/meps13421 Mar Ecol Prog Ser OPEN ACCESS Microbiome analyses and presence of cable bacteria in the burrow sediment of Upogebia pugettensis Cheng Li1,*, Clare E. Reimers1, John W. Chapman2 1College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon 97331, USA 2Department of Fisheries and Wildlife, Oregon State University, Hatfield Marine Science Center, 2030 SE Marine Science Dr. Newport, Oregon 97365, USA ABSTRACT: We utilized methods of sediment cultivation, catalyzed reporter deposition− fluorescence in situ hybridization, scanning electron microscopy, and 16s rRNA gene sequencing to investigate the presence of novel filamentous cable bacteria (CB) in estuarine sediments bioturbated by the mud shrimp Upogebia pugettensis Dana and also to test for trophic connections between the shrimp, its commensal bivalve (Neaeromya rugifera), and the sediment. Agglutinated sediments from the linings of shrimp burrows exhibited higher abundances of CB compared to surrounding suboxic and anoxic sediments. Furthermore, CB abundance and activity increased in these sedi- ments when they were incubated under oxygenated seawater. Through core microbiome analy- sis, we found that the microbiomes of the shrimp and bivalve shared 181 taxa with the sediment bacterial community, and that these shared taxa represented 17.9% of all reads. Therefore, bac- terial biomass in the burrow sediment lining is likely a major food source for both the shrimp and the bivalve. The biogeochemical conditions created by shrimp burrows and other irrigators may help promote the growth of CB and select for other dominant members of the bacterial commu- nity, particularly a variety of members of the Proteobacteria. -
A Snapshot on Prokaryotic Diversity of the Solimões River Basin (Amazon, Brazil)
A snapshot on prokaryotic diversity of the Solimões River basin (Amazon, Brazil) D. Toyama1, C.D. Santos-Júnior1, L.T. Kishi1, T.C.S. Oliveira2, J.W. Garcia3, H. Sarmento4, F.P. Miranda5 and F. Henrique-Silva1 1Laboratório de Biologia Molecular, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil 2Departamento de Química, Universidade Federal do Amazonas, Manaus, AM, Brasil 3Noosfera Projetos Especiais Ltda., São Paulo, SP, Brasil 4Laboratório de Biodiversidade e Processos Microbianos, Departamento de Hidrobiologia, Universidade Federal de São Carlos, São Carlos, SP, Brasil 5Petróleo Brasileiro S.A., Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil Corresponding author: F. Henrique-Silva E-mail: [email protected] Genet. Mol. Res. 16 (2): gmr16029567 Received December 8, 2016 Accepted April 7, 2017 Published May 18, 2017 DOI http://dx.doi.org/10.4238/gmr16029567 Copyright © 2017 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution ShareAlike (CC BY-SA) 4.0 License. ABSTRACT. The Amazon region has the largest hydrographic basin on the planet and is well known for its huge biodiversity of plants and animals. However, there is a lack of studies on aquatic microbial biodiversity in the Solimões River, one of its main water courses. To investigate the microbial biodiversity of this region, we performed 16S rRNA gene clone libraries from Solimões River and adjacent rivers and lakes. Our question was which microorganisms inhabit the different types of aquatic environments in this part of the basin, and how diversity varies among these environments (rivers and lakes). -
The Influence of Bacteria on the Adaptation to Changing Environments in Ectocarpus : a Systems Biology Approach Hetty Kleinjan
The influence of bacteria on the adaptation to changing environments in Ectocarpus : a systems biology approach Hetty Kleinjan To cite this version: Hetty Kleinjan. The influence of bacteria on the adaptation to changing environments in Ectocar- pus : a systems biology approach. Molecular biology. Sorbonne Université, 2018. English. NNT : 2018SORUS267. tel-02868508 HAL Id: tel-02868508 https://tel.archives-ouvertes.fr/tel-02868508 Submitted on 15 Jun 2020 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. Sorbonne Université ED 227 - Sciences de la Nature et de l'Homme : écologie & évolution Laboratoire de Biologie Intégrative des Modèles Marins Equipe Biologie des algues et interactions avec l'environnement The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach Par Hetty KleinJan Thèse de doctorat en Biologie Marine Dirigée par Simon Dittami et Catherine Boyen Présentée et soutenue publiquement le 24 septembre 2018 Devant un jury composé de : Pr. Ute Hentschel Humeida, Rapportrice GEOMAR, Kiel, Germany Dr. Suhelen Egan, Rapportrice UNSW Sydney, Australia Dr. Fabrice Not, Examinateur Sorbonne Université – CNRS Dr. David Green, Examinateur SAMS, Oban, UK Dr. Aschwin Engelen, Examinateur CCMAR, Faro, Portugal Dr. -
The Influence of Invasive Jellyfish Blooms on The
Biol Invasions DOI 10.1007/s10530-014-0810-2 MOLECULAR TOOLS The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy Caterina Manzari • Bruno Fosso • Marinella Marzano • Anita Annese • Rosa Caprioli • Anna Maria D’Erchia • Carmela Gissi • Marianna Intranuovo • Ernesto Picardi • Monica Santamaria • Simonetta Scorrano • Giuseppe Sgaramella • Loredana Stabili • Stefano Piraino • Graziano Pesole Received: 14 November 2013 / Accepted: 31 October 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract The rapid expansion of multicellular microbial taxonomic and functional diversity. Here native and alien species outbreaks in aquatic and we used an effective and highly sensitive experimental terrestrial ecosystems (bioinvasions) may produce strategy, bypassing the efficiency bottleneck of the significant impacts on bacterial community dynamics traditional bacterial isolation and culturing method, to and nutrient pathways with major ecological implica- identify changes of the planktonic microbial commu- tions. In aquatic ecosystems, bioinvasions may cause nity inhabiting a marine coastal lagoon (Varano, adverse effects on the water quality resulting from Adriatic Sea) under the influence of an outbreak- changes in biological, chemical and physical proper- forming alien jellyfish species. Water samples were ties linked to significant transformations of the collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m-3; E, up to 0.03 medusae Caterina Manzari, Bruno Fosso and Marinella Marzano have -3 contributed equally to this work. m ) to conduct a snapshot microbiome analysis by a metagenomic approach. -
Tochko Colostate 0053N 15136.Pdf (4.934Mb)
THESIS PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Submitted by Laura Tochko Department of Civil and Environmental Engineering In partial fulfillment of the requirements For the Degree of Master of Science Colorado State University Fort Collins, Colorado Fall 2018 Master’s Committee: Advisor: Tom Sale Joe Scalia Sally Sutton Copyright by Laura Elizabeth Tochko 2018 All Rights Reserved ABSTRACT PROCESSES GOVERNING THE PERFORMANCE OF OLEOPHILIC BIO-BARRIERS (OBBS) – LABORATORY AND FIELD STUDIES Petroleum sheens, a potential Clean Water Act violation, can occur at petroleum refining, distribution, and storage facilities located near surface water. In general, sheen remedies can be prone to failure due to the complex processes controlling the flow of light non-aqueous phase liquid (LNAPL) at groundwater/surface water interfaces (GSIs). Even a small gap in a barrier designed to resist the movement of LNAPL can result in a sheen of large areal extent. The cost of sheen remedies, exacerbated by failure, has led to research into processes governing sheens and development of the oleophilic bio-barrier (OBB). OBBs involve 1) an oleophilic (oil-loving) plastic geocomposite which intercepts and retains LNAPL and 2) cyclic delivery of oxygen and nutrients via tidally driven water level fluctuations. The OBB retains LNAPL that escapes the natural attenuation system through oleophilic retention and enhances the natural biodegradation capacity such that LNAPL is retained or degraded instead of discharging to form a sheen. Sand tank experiments were conducted to visualize the movement of LNAPL as a wetting and non-wetting fluid in a water-saturated tank. -
Diversity and Activity of Aerobic Thermophilic Carbon Monoxide-Oxidizing Bacteria on Kilauea Volcano, Hawaii
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2013 Diversity and activity of aerobic thermophilic carbon monoxide-oxidizing bacteria on Kilauea Volcano, Hawaii Caitlin Elizabeth King Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation King, Caitlin Elizabeth, "Diversity and activity of aerobic thermophilic carbon monoxide-oxidizing bacteria on Kilauea Volcano, Hawaii" (2013). LSU Doctoral Dissertations. 690. https://digitalcommons.lsu.edu/gradschool_dissertations/690 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. DIVERSITY AND ACTIVITY OF AEROBIC THERMOPHILIC CARBON MONOXIDE- OXIDIZING BACTERIA ON KILAUEA VOLCANO, HAWAII A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Caitlin E. King B.S., Louisiana State University, 2008 December 2013 ACKNOWLEDGEMENTS First and foremost, I would like to thank my advisor Dr. Gary King for his guidance, flexibility, and emotional and financial support over the past 5 years. I am fortunate that I was able to accompany Dr. King on two field excursions to Hawaii. Dr. King also went on additional field trips on behalf of my project and initiated our metagenomic work. Dr. King made this project possible and taught me the important skills of troubleshooting and writing critically, which have prepared me for success in both my professional and personal life. -
Molecular Characterization of Bacterial Phylogenetic And
Environ & m m en u ta le l o B r t i o e t P e f c h Olapade, J Pet Environ Biotechnol 2013, 4:3 o Journal of Petroleum & n l a o l n o r DOI: 10.4172/2157-7463.1000144 g u y o J ISSN: 2157-7463 Environmental Biotechnology Research Article Open Access Molecular Characterization of Bacterial Phylogenetic and Functional Groups at Terrebonne Bay along the Coastline of the Gulf of Mexico Ola A Olapade* Department of Biology and the Center for Sustainability and the Environment, Albion College, 611 East Porter Street, Albion, MI 49224, USA Abstract The detection and quantification of bacterial phylogenetic and functional groups as well as community diversity at the site of the Deepwater Horizon oil spill in Terrebonne Bay along the Gulf of Mexico were carried out using nucleic acid staining, Fluorescence in situ Hybridization (FISH) and 16S rRNA gene cloning and sequencing approaches. Results from the 16S rRNA gene clone library analysis revealed high occurrences of bacterial members belonging to the Cyanobacteria (28%), β- Proteobacteria (21%), Bacteroidetes (17%), Actinobacteria (12%) and the α- Proteobacteria (10%). Particularly, bacterial members identified within the clone library as belonging to the β- Proteobacteria subclass were mostly hydrocarbon degraders, including Methylibium petroleiphilum, Burkholderia cepacia, Hydrogenophaga taeniospiralis and Methylobacillus flagellates. Simultaneous analyses of both planktonic and benthic bacterial communities by FISH revealed the numerical dominance of members of the type I Methanotrophic Bacteria (MB) over the type II populations. The results from the study clearly reveal a shift in the bacterial community structure and composition in response to the tragic methane and crude oil discharges from the Deepwater Horizon rig along the Gulf of Mexico. -
Effects of a Simulated Acute Oil Spillage on Bacterial Communities
microorganisms Article Effects of a Simulated Acute Oil Spillage on Bacterial Communities from Arctic and Antarctic Marine Sediments 1, 1, 2 3 2 Carmen Rizzo y , Roberta Malavenda y, Berna Gerçe , Maria Papale , Christoph Syldatk , 4 1, 1, 1,3, Rudolf Hausmann , Vivia Bruni z, Luigi Michaud z, Angelina Lo Giudice * and Stefano Amalfitano 5 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; [email protected] (C.R.); [email protected] (R.M.) 2 Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany; [email protected] (B.G.); [email protected] (C.S.) 3 Institute of Polar Sciences, National Research Council (CNR-ISP), 98122 Messina, Italy; [email protected] 4 Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; [email protected] 5 Water Research Institute, National Research Council (CNR-IRSA), 00015 Rome, Italy; amalfi[email protected] * Correspondence: [email protected]; Tel.: +00-3909-0601-5415 These authors contributed equally to this work. y Posthumous. z Received: 21 October 2019; Accepted: 28 November 2019; Published: 30 November 2019 Abstract: Background: The bacterial community responses to oil spill events are key elements to predict the fate of hydrocarbon pollution in receiving aquatic environments. In polar systems, cold temperatures and low irradiance levels can limit the effectiveness of contamination removal processes. In this study, the effects of a simulated acute oil spillage on bacterial communities from polar sediments were investigated, by assessing the role of hydrocarbon mixture, incubation time and source bacterial community in selecting oil-degrading bacterial phylotypes. -
Seasonal and Spatial Variations in Bacterial Communities from Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Clams
fmicb-11-01860 August 3, 2020 Time: 12:3 # 1 ORIGINAL RESEARCH published: 05 August 2020 doi: 10.3389/fmicb.2020.01860 Seasonal and Spatial Variations in Bacterial Communities From Tetrodotoxin-Bearing and Non-tetrodotoxin-Bearing Clams Laura Biessy1,2,3*, John K. Pearman1, Kirsty F. Smith1, Ian Hawes2 and Susanna A. Wood1 1 Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand, 2 Department of Biological Sciences, University of Waikato, Hamilton, New Zealand, 3 New Zealand Food Safety Science and Research Centre, Palmerston North, New Zealand Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, but the source remains uncertain. The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and Edited by: digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus Chris Dupont, stutchburyi that lives amongst toxic P.australis populations were also analyzed. Bacterial J. Craig Venter Institute, United States communities were characterized using 16S ribosomal RNA gene metabarcoding in Reviewed by: Maria Fátima Carvalho, P. australis sourced monthly from the Hokianga Harbor, a site known to have TTX- Universidade do Porto, Portugal bearing clams, for 1 year, from ten sites with varying TTX concentrations around Detmer Sipkema, Wageningen University & Research, New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was Netherlands detected in P.