Fluctuation and Re-Establishment of Aerobic Granules Properties During the Long-Term Operation Period with Low-Strength and Low C/N Ratio Wastewater
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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Leadbetterella Byssophila Type Strain (4M15)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Leadbetterella byssophila type strain (4M15). Permalink https://escholarship.org/uc/item/907989cw Journal Standards in genomic sciences, 4(1) ISSN 1944-3277 Authors Abt, Birte Teshima, Hazuki Lucas, Susan et al. Publication Date 2011-03-04 DOI 10.4056/sigs.1413518 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:2-12 DOI:10.4056/sigs.1413518 Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Birte Abt1, Hazuki Teshima2,3, Susan Lucas2, Alla Lapidus2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Amrita Pati2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Brian J. Tindall1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk1, and Nikos C. Kyrpides2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 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 Lawrence Livermore National Laboratory, Livermore, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C. -
Taxonomy JN869023
Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075 -
Metabarcoding for Bacterial Diversity Assessment: Looking Inside Didymosphenia Geminata Mats in Patagonian Aquatic Ecosystems
Aquatic Invasions (2021) Volume 16, Issue 1: 43–61 Special Issue: Proceedings of the 21st International Conference on Aquatic Invasive Species Guest editors: Sarah Bailey, Bonnie Holmes and Oscar Casas-Monroy CORRECTED PROOF Research Article Metabarcoding for bacterial diversity assessment: looking inside Didymosphenia geminata mats in Patagonian aquatic ecosystems Ana Victoria Suescún1,*, Karla Martinez-Cruz2, Maialen Barret3 and Leyla Cárdenas1,4 1Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile 2Environmental Biogeochemistry in Extreme Ecosystems Laboratory, Universidad de Magallanes, Punta Arenas, Chile 3Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France 4Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Chile Author e-mails: [email protected] (AVS), [email protected] (KM), [email protected] (MB), [email protected] (LC) *Corresponding author Co-Editors’ Note: This study was contributed in relation to the 21st International Conference Abstract on Aquatic Invasive Species held in Montreal, Canada, October 27–31, 2019 (http://www.icais. The number of organisms that spread and invade new habitats has increased in recent org/html/previous21.html). This conference has decades as a result of drastic environmental changes such as climate change and provided a venue for the exchange of anthropogenic activities. Microbial species invasions occur worldwide in terrestrial information on various aspects of aquatic and aquatic systems and represent an emerging challenge to our understanding of invasive species since its inception in 1990. The conference continues to provide an the interplay between biodiversity and ecosystem functioning. Due to the difficulty opportunity for dialog between academia, of detecting and evaluating non-indigenous microorganisms, little is known about industry and environmental regulators. -
Innovative Process for Granulation of Continuous Flow Conventional Activated Sludge
Innovative Process for Granulation of Continuous Flow Conventional Activated Sludge Bev Stinson, Ph.D AECOM, Global Wastewater Technology Leader May 9th 2019 2 2Introduction The objective of this presentation is to: • Introduce Aerobic Granular Sludge (AGS), including mechanisms for formation and benefits • Present performance data for a Nereda® SBR pilot • AECOM’s continuous-flow granular sludge process for BNR infra-stretching or footprint reductions 3 3What is Granular Sludge? – Sludge granule is a tightly aggregated mass of microorganisms in a matrix of extra polymeric substances (EPS) – A cross between floc and fixed film growth – Their large size (>0.2mm) and density allow for excellent settling characteristics = more compact WWTPs Reference: Sarma, S.J. et al., 2017. Finding knowledge gaps in aerobic granulation technology 4 4Granular Sludge Relies on Dominance Slow Growing Microorganisms – Treatment processes that rely on slow-growing bacteria are better at granulation – Anaerobic systems were the first granular sludge processes developed (Biothane™, Biobed™) to treat high strength soluble COD waste Anaerobic granules supporting acid formers & methanogen growth Reference: van Lier, J.B. et al., 2015. Celebrating 40 years anaerobic sludge bed reactors for industrial wastewater treatment 5 5 Granular ANAMMOX – The first Anaerobic Oxidizing Ammonia (ANAMMOX™) process was based on a granular sludge approach 6 6 Aerobic Granular Sludge – Developing aerobic granular sludge (AGS) for treating domestic wastewater has been more challenging -
Architecture, Component, and Microbiome of Biofilm Involved In
www.nature.com/npjbiofilms ARTICLE OPEN Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors Tomohiro Inaba1, Tomoyuki Hori1, Hidenobu Aizawa1, Atsushi Ogata1 and Hiroshi Habe1 Biofilm formation on the filtration membrane and the subsequent clogging of membrane pores (called biofouling) is one of the most persistent problems in membrane bioreactors for wastewater treatment and reclamation. Here, we investigated the structure and microbiome of fouling-related biofilms in the membrane bioreactor using non-destructive confocal reflection microscopy and high-throughput Illumina sequencing of 16S rRNA genes. Direct confocal reflection microscopy indicated that the thin biofilms were formed and maintained regardless of the increasing transmembrane pressure, which is a common indicator of membrane fouling, at low organic-loading rates. Their solid components were primarily extracellular polysaccharides and microbial cells. In contrast, high organic-loading rates resulted in a rapid increase in the transmembrane pressure and the development of the thick biofilms mainly composed of extracellular lipids. High-throughput sequencing revealed that the biofilm microbiomes, including major and minor microorganisms, substantially changed in response to the organic-loading rates and biofilm development. These results demonstrated for the first time that the architectures, chemical components, and microbiomes of the biofilms on fouled membranes were tightly associated with one another and differed considerably depending on the organic-loading conditions in the membrane bioreactor, emphasizing the significance of alternative indicators other than the transmembrane pressure for membrane biofouling. npj Biofilms and Microbiomes (2017) 3:5 ; doi:10.1038/s41522-016-0010-1 INTRODUCTION improvement of confocal reflection microscopy (CRM).9, 10 This Membrane bioreactors (MBRs) have been broadly exploited for the unique analytical technique uses a special installed beam splitter treatment of municipal and industrial wastewaters. -
Targeting of Flavobacterium Johnsoniae Proteins for Secretion by the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations May 2017 Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Microbiology Commons Recommended Citation Kulkarni, Surashree Sunil, "Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System" (2017). Theses and Dissertations. 1501. https://dc.uwm.edu/etd/1501 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee May 2017 ABSTRACT TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni The University of Wisconsin-Milwaukee, 2017 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae and many related bacteria secrete proteins across the outer membrane using the type IX secretion system (T9SS). Proteins secreted by T9SSs have amino-terminal signal peptides for export across the cytoplasmic membrane by the Sec system and carboxy-terminal domains (CTDs) targeting them for secretion across the outer membrane by the T9SS. Most but not all T9SS CTDs belong to family TIGR04183 (type A CTDs). -
Aerobic Granulation in a Sequencing Batch Reactor for the Treatment of Piggery Wastewater
Aerobic Granulation in a Sequencing Batch Reactor for the Treatment of Piggery Wastewater Dalei Zhang1*, Yanan Wang1, Hongwei Li1, Shaoran Wang2, Yumei Jing3 ABSTRACT: This study investigated the formation of aerobic granules strategy on the treatment of swine wastewater and found that fed with digested piggery wastewater. After 42 days of cultivation, small feeding ratio had a more significant effect on the removal of yellow granules with mean diameter of 0.4 mm were first observed in the phosphorus and nitrogen than on the removal of chemical reactor. Scanning electron microscope pictures showed the granules oxygen demand (COD). Huang et al. (2011) found that high were compact, round structures with clear outer shapes and mainly 2þ 2þ composed of filamentous bacteria. Maximum chemical oxygen demand concentrations of K and Ca would be helpful for removing and ammonia removal ratios were 90.1 and 91.7%, respectively. The nutrients in piggery wastewater. Previous studies have shown Monod equation, which was used to describe ammonium utilization, great improvements in treating piggery wastewater, but there are yielded a maximum rate of 6.25 mg (g volatile suspended solids)À1 hÀ1. still some problems that hinder treatment (Latif et al., 2011). The measurement of extracellular polymeric substances (EPS) content Rich nitrogenous compounds in the wastewater make active and three-dimensional excitation and emission matrix results showed biomass densification, granular processes, and, consequently, that the EPS concentration increased during the granulation process. microorganism retention in the reactor difficult, limiting the use Fluorescence in situ hybridization analysis showed significant amounts of upflow anaerobic sludge blanket (UASB) reactors. -
Influence of Host Plants on the Diversity of Gut Microbiota
Inuence of Host Plants on the Diversity of Gut Microbiota Communities of Fall Armyworm Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae) Juliana Amaka Ugwu ( [email protected] ) Forestry Research Institute of Nigeria https://orcid.org/0000-0003-1862-6864 Fred Asiegbu Department of Forest sciences, University of Helsinki, P.O Box 27, FIN-00014 Helsinki, Finland. Research Article Keywords: host plants, microbial variability, fall armyworm, larvae, bacteria Posted Date: June 30th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-657579/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract The gut bacteria of insects inuence their host physiology positively, although their mechanism is not yet understood. This study characterized the microbiome of the gut of Spodoptera frugiperda larvae fed with nine different host plants; sugar cane (M1), maize (M2), onion (M3), cucumber (R1), tomato (R2), sweet potato (R3), cabbage L1), green amaranth (L2), and celocia (L3) by sequencing the theV3-V4 hypervariable region of the 16S rRNA gene using Illumina PE250 NovaSeq system. The results revealed that gut bacterial composition varied among larvae samples fed on different host plants. Three alpha diversity indices revealed highly signicant differences on the gut bacterial diversity of S. frugiperda fed with different host plants.. Analysis of Molecular Variance (AMOVA) and Analysis of Similarity (ANOSIM) also revealed signicant variations on the bacterial communities among the various host plants. Five bacteria phyla (Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria and Bacteroidetes) were prevalent across the larvae samples. Firmicutes (44.1%) was the most dominant phylum followed by Proteobacteria (28.5%). -
Flavobacterium Gliding Motility: from Protein Secretion to Cell Surface Adhesin Movements
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations August 2019 Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements Joseph Johnston University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Biology Commons, Microbiology Commons, and the Molecular Biology Commons Recommended Citation Johnston, Joseph, "Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements" (2019). Theses and Dissertations. 2202. https://dc.uwm.edu/etd/2202 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee August 2019 ABSTRACT FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston The University of Wisconsin-Milwaukee, 2019 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae exhibits rapid gliding motility over surfaces. At least twenty genes are involved in this process. Seven of these, gldK, gldL, gldM, gldN, sprA, sprE, and sprT encode proteins of the type IX protein secretion system (T9SS). The T9SS is required for surface localization of the motility adhesins SprB and RemA, and for secretion of the soluble chitinase ChiA. This thesis demonstrates that the gliding motility proteins GldA, GldB, GldD, GldF, GldH, GldI and GldJ are also essential for secretion. -
Defining Functional Diversity for Lignocellulose Degradation in a Microbial Community Using Multi-Omics Studies
Alessi et al. Biotechnol Biofuels (2018) 11:166 https://doi.org/10.1186/s13068-018-1164-2 Biotechnology for Biofuels RESEARCH Open Access Defning functional diversity for lignocellulose degradation in a microbial community using multi‑omics studies Anna M. Alessi1, Susannah M. Bird1, Nicola C. Oates1, Yi Li1, Adam A. Dowle2, Etelvino H. Novotny3, Eduardo R. deAzevedo4, Joseph P. Bennett1, Igor Polikarpov4, J. Peter W. Young5, Simon J. McQueen‑Mason1 and Neil C. Bruce1* Abstract Background: Lignocellulose is one of the most abundant forms of fxed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only efective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial commu‑ nities that efciently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform “community-level” metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. Results: Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre- treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. -
Granular Biofilms: Formation, Function, Application
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 7 June 2019 doi:10.20944/preprints201906.0053.v1 1 Review 2 Granular biofilms: formation, function, application, 3 and new trends as model microbial communities 4 Anna Christine Trego, Simon Mills and Gavin Collins 5 Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland 6 Galway, University Road, Galway, H91 TK33, Ireland. 7 Corresponding author: 8 Tel: 00353 (0) 91 49 31 63 9 e-mail: [email protected] 10 11 KEYWORDS: Anammox; Biofilms; Granulation; Methanogens; Microbial ecology; Sludge 12 granules; Wastewater 13 14 LIST OF ABBREVIATIONS 15 AD – Anaerobic digestion 16 AHL – N-acetyl-homoserine-lactone 17 Anammox – Anaerobic ammonium oxidation 18 AOB – Ammonia oxidising bacteria 19 cDNA – Complementary DNA 20 COD – Chemical oxygen demand 21 EGSB – Expanded granular sludge bed 22 EPS – Extracellular polymeric substances 23 FISH – Fluorescence in situ hybridization 24 HRT – Hydraulic retention time 25 HTS – High-throughput sequencing Page 1 © 2019 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 7 June 2019 doi:10.20944/preprints201906.0053.v1 1 mRNA – Messenger RNA 2 MS – Mass spectrometry 3 NMR – Nuclear magnetic resonance 4 NOB – Nitrite-oxidising bacteria 5 OLR – Organic loading rate 6 OTU – Operational taxonomic unit 7 PAO – Polyphosphate-accumulating organism(s) 8 qPCR – Quantitative PCR 9 rRNA – Ribosomal RNA 10 SBR – Sequencing batch reactor 11