Anaerobic and Microaerobic Pretreatment for Improving Methane Production from Paper Waste in Anaerobic Digestion
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Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. -
Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis
GBE Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis Ciaran O’Flynn1,*, Oliver Deusch1, Aaron E. Darling2, Jonathan A. Eisen3,4,5, Corrin Wallis1,IanJ.Davis1,and Stephen J. Harris1 1 The WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, United Kingdom Downloaded from 2The ithree Institute, University of Technology Sydney, Ultimo, New South Wales, Australia 3Department of Evolution and Ecology, University of California, Davis 4Department of Medical Microbiology and Immunology, University of California, Davis 5UC Davis Genome Center, University of California, Davis http://gbe.oxfordjournals.org/ *Corresponding author: E-mail: ciaran.ofl[email protected]. Accepted: November 6, 2015 Abstract Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and at University of Technology, Sydney on January 17, 2016 plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions char- acterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to syn- thesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. -
Sequencing Batch Reactor and Bacterial Community in Aerobic Granular Sludge for Wastewater Treatment of Noodle-Manufacturing Sector
applied sciences Article Sequencing Batch Reactor and Bacterial Community in Aerobic Granular Sludge for Wastewater Treatment of Noodle-Manufacturing Sector Tang Thi Chinh 1,3,*, Phung Duc Hieu 1, Bui Van Cuong 1, Nguyen Nhat Linh 2, Nguyen Ngoc Lan 2,3, Nguyen Sy Nguyen 1, Nguyen Quang Hung 1,3 and Le Thi Thu Hien 2,3,* ID 1 Institute of Environmental Technology (IET), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam; [email protected] (P.D.H.); [email protected] (B.V.C.); [email protected] (N.S.N.); [email protected] (N.Q.H.) 2 Institute of Genome Research (IGR), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam; [email protected] (N.N.L.); [email protected] (N.N.L.) 3 Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam * Correspondence: [email protected] (T.T.C.); [email protected] (L.T.T.H.); Tel.: +84-904-187-106 (T.T.C.); +84-989-019-691 (L.T.T.H.) Received: 1 March 2018; Accepted: 26 March 2018; Published: 27 March 2018 Abstract: The sequencing batch reactor (SBR) has been increasingly applied in the control of high organic wastewater. In this study, SBR with aerobic granular sludge was used for wastewater treatment in a noodle-manufacturing village in Vietnam. The results showed that after two months of operation, the chemical oxygen demand, total nitrogen and total phosphorous removal efficiency of aerobic granular SBR reached 92%, 83% and 75%, respectively. -
Electronic Supplementary Information
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information Microbial community and antibiotic resistance profiles of biomass and effluent are distinctly affected by antibiotic addition to an anaerobic membrane bioreactor Ali Zarei-Baygi*, Moustapha Harb#,*, Phillip Wang*, Lauren Stadler^, and Adam L. Smith*† * Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA # Department of Civil and Environmental Engineering, Lebanese American University, 309 Bassil Building, Byblos, Lebanon ^ Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA †Corresponding author (Adam L. Smith) Phone: +1 213.740.0473 Email: [email protected] Number of pages: 15 Number of figures: 6 Number of tables: 6 S1 Quantification of antibiotics by LC-MS For antibiotics quantification, 10 mL samples were collected for each sampling time point from the influent and effluent of the AnMBR. Both collected samples and standard solutions were filtered through 0.2 µm PTFE syringe filters (Whatman) using 10 mL syringes with Luer lock tips and stored in certified 2 mL amber LC vials (Agilent) at 4 ºC refrigerator for no more than 3 days prior to analysis. Stock solutions of sulfamethoxazole and erythromycin were prepared in HPLC-grade methanol at concentrations of 20 mg/L and stored at -20 ºC. Ampicillin stock solution was prepared in HPLC-grade water at 4 mg/L due to its lack of solubility in methanol and stored at 4 ºC. For each antibiotic, a six-point standard calibration curve was constructed within the appropriate range (i.e., 0.1-30 µg/L to target effluent antibiotics and 30- 400 µg/L to target influent antibiotics). -
Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility. -
Endosymbiont Diversity and Evolution Across Weevil Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/171181; this version posted August 1, 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. Endosymbiont diversity and evolution across weevil tree of life Guanyang Zhang1#, Patrick Browne1,2#, Geng Zhen1#, Andrew Johnston4, Hinsby Cadillo-Quiroz5, and Nico Franz1 1 School of Life Sciences, Arizona State University, Tempe, Arizona, USA 2 Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark # These authors contributed equally to this work ABSTRACT As early as the time of Paul Buchner, a pioneer of endosymbionts research, it was shown that weevils host diverse bacterial endosymbionts, probably only second to the hemipteran insects. To date, there is no taxonomically broad survey of endosymbionts in weevils, which preclude any systematic understanding of the diversity and evolution of endosymbionts in this large group of insects, which comprise nearly 7% of described diversity of all insects. We gathered the largest known taxonomic sample of weevils representing four families and 17 subfamilies to perform a study of weevil endosymbionts. We found that the diversity of endosymbionts is exceedingly high, with as many as 44 distinct kinds of endosymbionts detected. We recovered an ancient origin of association of Nardonella with weevils, dating back to 124 MYA. We found repeated losses of this endosymbionts, but also cophylogeny with weevils. We also investigated patterns of coexistence and coexclusion. INTRODUCTION Weevils (Insecta: Coleoptera: Curculionoidea) host diverse bacterial endosymbionts. -
Research Article Review Jmb
J. Microbiol. Biotechnol. (2017), 27(0), 1–7 https://doi.org/10.4014/jmb.1707.07027 Research Article Review jmb Methods 20,546 sequences and all the archaeal datasets were normalized to 21,154 sequences by the “sub.sample” Bioinformatics Analysis command. The filtered sequences were classified against The raw read1 and read2 datasets was demultiplexed by the SILVA 16S reference database (Release 119) using a trimming the barcode sequences with no more than 1 naïve Bayesian classifier built in Mothur with an 80% mismatch. Then the sequences with the same ID were confidence score [5]. Sequences passing through all the picked from the remaining read1 and read2 datasets by a filtration were also clustered into OTUs at 6% dissimilarity self-written python script. Bases with average quality score level. Then a “classify.otu” function was utilized to assign lower than 25 over a 25 bases sliding window were the phylogenetic information to each OTU. excluded and sequences which contained any ambiguous base or had a final length shorter than 200 bases were Reference abandoned using Sickle [1]. The paired reads were assembled into contigs and any contigs with an ambiguous 1. Joshi NA, FJ. 2011. Sickle: A sliding-window, adaptive, base, more than 8 homopolymeric bases and fewer than 10 quality-based trimming tool for FastQ files (Version 1.33) bp overlaps were culled. After that, the contigs were [Software]. further trimmed to get rid of the contigs that have more 2. Schloss PD. 2010. The Effects of Alignment Quality, than 1 forward primer mismatch and 2 reverse primer Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies. -
Page 1 of 41 RSC Advances
RSC Advances This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. This Accepted Manuscript will be replaced by the edited, formatted and paginated article as soon as this is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/advances Page 1 of 41 RSC Advances 1 Regulation of acidogenic metabolism towards enhanced short chain fatty acids biosynthesis 2 from waste: Metagenomic Profiling 3 4 Omprakash Sarkar, A. Naresh Kumar, Shikha Dahiya, K.Vamshi Krishna, Dileep Kumar 5 Yeruva, S.Venkata Mohan* 6 Bioengineering and Environmental Sciences (BEES), CSIR-Indian Institute of Chemical 7 Technology (CSIR-IICT), Hyderabad 500 007, India 8 *E-mail: [email protected]; Tel: 0091-40-27161765 9 10 Abstract 11 Short chain carboxylic (volatile fatty) acids (VFA) production in mixed microbiomes is majorly 12 limited by the prevalence of the methanogenic bacteria and availability of substrate from waste 13 to the biocatalyst during the fermentation process. -
The Microbiome of the Footrot Lesion in Merino Sheep Is Characterized by a Persistent Bacterial Dysbiosis T ⁎ Andrew S
Veterinary Microbiology 236 (2019) 108378 Contents lists available at ScienceDirect Veterinary Microbiology journal homepage: www.elsevier.com/locate/vetmic The microbiome of the footrot lesion in Merino sheep is characterized by a persistent bacterial dysbiosis T ⁎ Andrew S. McPherson, Om P. Dhungyel, Richard J. Whittington Farm Animal Health, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, 425 Werombi Rd, Camden, New South Wales, 2570, Australia ARTICLE INFO ABSTRACT Keywords: Footrot is prevalent in most sheep-producing countries; the disease compromises sheep health and welfare and Footrot has a considerable economic impact. The disease is the result of interactions between the essential causative Merino agent, Dichelobacter nodosus, and the bacterial community of the foot, with the pasture environment and host Sheep resistance influencing disease expression. The Merino, which is the main wool sheep breed in Australia, is Microbiome particularly susceptible to footrot. We characterised the bacterial communities on the feet of healthy and footrot- Dichelobacter nodosus affected Merino sheep across a 10-month period via sequencing and analysis of the V3-V4 regions of the bacterial 16S ribosomal RNA gene. Distinct bacterial communities were associated with the feet of healthy and footrot- affected sheep. Infection with D. nodosus appeared to trigger a shift in the composition of the bacterial com- munity from predominantly Gram-positive, aerobic taxa to predominantly Gram-negative, anaerobic taxa. A total of 15 bacterial genera were preferentially abundant on the feet of footrot-affected sheep, several of which have previously been implicated in footrot and other mixed bacterial diseases of the epidermis of ruminants. -
Type of the Paper (Article
Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland). -
The Human Gut Virome Is Highly Diverse, Stable and Individual-Specific
bioRxiv preprint doi: https://doi.org/10.1101/657528; this version posted June 3, 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-NC-ND 4.0 International license. 1 The human gut virome is highly diverse, stable and individual-specific. 2 3 Andrey N. Shkoporov*†, Adam G. Clooney, Thomas D.S. Sutton, Feargal J. Ryan, 4 Karen M. Daly, James A. Nolan, Siobhan A. McDonnell, Ekaterina V. Khokhlova, Lorraine 5 A. Draper, Amanda Forde, Emma Guerin, Vimalkumar Velayudhan, R. Paul Ross., Colin 6 Hill.* 7 8 APC Microbiome Ireland & School of Microbiology, University College Cork, Cork 9 T12 YT20, Ireland 10 11 * Correspondence: [email protected], [email protected] 12 † Lead contact. 13 14 Summary 15 The human gut contains a vast array of viruses, mostly bacteriophages. The majority 16 remain uncharacterised and their roles in shaping the gut microbiome and in impacting on 17 human health remain poorly understood. Here we performed a longitudinal focused 18 metagenomic study of faecal bacteriophage populations in healthy adults. Our results reveal 19 high temporal stability and individual specificity of bacteriophage consortia which correlates 20 with the bacterial microbiome. We report the existence of a stable, numerically predominant 21 individual-specific persistent personal virome. Clustering of bacteriophage genomes and de 22 novo taxonomic annotation identified several groups of crAss-like and Microviridae 23 bacteriophages as the most stable colonizers of the human gut. -
Tenebrio Molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs
Tenebrio Molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs Sandra Meyer, Denise K. Gessner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis and Klaus Eder Table S1. Characteristics of gene-specific primers used for qPCR analysis in small intestinal mucosa. Annealing PCR Forward (5` to 3`) NCBI GeneBank Gene Temperature Product Slope R2 E Reverse (5` to 3`) Accession No. (°C) Size (bp) Reference genes CAGTCACCTTGAGCCGGGCGA ATP5MC1 64 94 NM_001025218 -3.55 0.999 1.91 TAGCGCCCCGGTGGTTTGC AGGGGCTCTCCAGAACATCATCC GAPDH 60 446 NM_001206359 -3.33 1.000 2.00 TCGCGTGCTCTTGCTGGGGTTGG GTCGCAAGACTTATGTGACC RPS9 62 325 XM_021094878 -3.28 0.999 2.02 AGCTTAAAGACCTGGGTCTG CTACGCCCCCGTCGCAAAGG SDHA 64 380 XM_021076930 -3.32 1.000 2.00 AGTTTGCCCCCAGGCGGTTG Target genes GATCGGCTCCATCGTCAGCA CLDN1 60 115 NM_001244539 -3.54 0.994 1.92 CGACACGCAGGACATCCACA ACTTCCAAACTGGCTGTTGC CXCL8 59 120 NM_213867 -3.59 0.994 1.90 GGAATGCGTATTTATGCACTGG GTTCTCTGAGAAATGGGAGC IL1B 58 143 NM_214055 -3.51 0.997 1.93 CTGGTCATCATCACAGAAGG AAGGTGATGCCACCTCAGAC IL6 60 151 NM_001252429 -3.54 0.994 1.92 TCTGCCAGTACCTCCTTGCT MUC1 CGGGCTTCTGGGACTCTTTT 58 312 XM_021089728 -3.63 0.999 1.89 1 TTCTTTCGTCGGCACTGACA TGTGTTTTGCTTTGGGTCCAG MUC13 58 171 NM_001105293 -3.58 1.000 1.90 CACAGCCAACTCCACTGTAGC CTTCCAACCATCCTCCCACC MUC2 58 174 XM_021082584 -3.53 0.996 1.92 GCCGTCTTGAAATCATCGCC GCCTACTCGTCCAACGGGAA OCLN 60 246 NM_001163647 -3.60 0.999 1.90 GCCCGTCGTGTAGTCTGTCT CAGACTTCGACCACAACGGA SLC15A1 58 99 NM_214347 -3.52 0.998 1.93 TTATCCCGCCAGTACCCAGA CGCAACCATTGGAGTTGGCGC SLC2A2 63 122 NM_001097417 -3.37 0.997 1.98 TGGCACAAACAAACATCCCACTCA CTGACACTGGTGCTTGCTTT SLC2A5 57 156 XM_021095282 -3.45 0.989 1.95 TTCGCTCATGTATTCCCCGA GTGGCGGACAGTAGTGAACA SLC5A1 57 89 NM_001164021 -3.31 1.000 1.92 AGAAGGCAGGATTTCAGGCA GTCGTCCTGATCCTGACCCG TJP1 60 207 XM_021098827 -3.26 0.996 2.03 TGGTGGGTTTGGTGGGTTGA CCAAGGACTCAGATCATCGT TNF 58 146 NM_214022 -3.36 1.000 1.99 GCTGGTTGTCTTTCAGCTTC Table S2.