Microbial Community Analysis, Influence of Reactor Hybridation and Effect of the Proportion of Glycol Ethers/Ethanol Mixtures in Egsb Reactors
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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 -
1 Microbial Transformations of Organic Chemicals in Produced Fluid From
Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem. -
1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds. -
Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol
Journal of Water and Environment Technology, Vol.13, No.2, 2015 Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol Takahiro WATARI 1), Daisuke TANIKAWA2), Kyohei KURODA1), Akinobu NAKAMURA1), Nanako FUJII3), Fuminori YONEYAMA3), Osamu WAKISAKA3), Masashi HATAMOTO1), Takashi YAMAGUCHI 1) 1) Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan 2) Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-1-11 Agaminami, Kure, Hiroshima 737-8506, Japan 3) Fundamental Material Laboratory Office, Material Technology Research and Development Laboratory, Research and Development Headquarters, Sumitomo Riko Company Limited, 3-1 Higashi, Komaki, Aichi 485-8550, Japan ABSTRACT This study evaluated the performance of a novel treatment system consisting of an upflow anaerobic sludge blanket (UASB) and a downflow hanging sponge (DHS) for the treatment of industrial wastewater containing 8% ethylene glycol and 2% propylene glycol discharged from a rubber production unit. The system achieved high COD removal (91 ± 4.3%) and methane recovery (82 ± 20%) at an organic loading rate of 8.5 kg-COD/(m3·day). The UASB allowed an organic loading rate of 14 kg-COD/(m3·day) with a constant hydraulic retention time of 24 h. The COD of DHS effluent was 370 ± 250 mg-COD/L during the entire experimental period. Thus, the proposed system could be applicable for treating industrial wastewater containing ethylene glycol. Massively parallel 16S rRNA gene sequencing elucidated the microbial community structure of the UASB. The dominant family Pelobacteriaceae could mainly degrade the organic compounds of ethylene glycol and decomposed products of ethanol. -
(Pelobacter) and Methanococcoides Are Responsible for Choline-Dependent Methanogenesis in a Coastal Saltmarsh Sediment
The ISME Journal https://doi.org/10.1038/s41396-018-0269-8 ARTICLE Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment 1 1 1 2 3 1 Eleanor Jameson ● Jason Stephenson ● Helen Jones ● Andrew Millard ● Anne-Kristin Kaster ● Kevin J. Purdy ● 4 5 1 Ruth Airs ● J. Colin Murrell ● Yin Chen Received: 22 January 2018 / Revised: 11 June 2018 / Accepted: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope 13 probing with high throughput sequencing of 16S rRNA genes and C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm 13 incubation with C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that 1234567890();,: 1234567890();,: choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. -
Disentangling Syntrophic Electron Transfer Mechanisms in Methanogenesis Through Electrochemical Stimulation, Omics, and Machine Learning
Disentangling Syntrophic Electron Transfer Mechanisms in Methanogenesis Through Electrochemical Stimulation, Omics, and Machine Learning Heyang Yuan ( [email protected] ) Temple University https://orcid.org/0000-0003-1146-2430 Xuehao Wang University of Illinois at Urbana-Champaign Tzu-Yu Lin University of Illinois at Urbana-Champaign Jinha Kim University of Illinois at Urbana-Champaign Wen-Tso Liu University of Illinois at Urbana-Champaign Research Keywords: Direct interspecies electron transfer, Extracellular electron transfer, Interspecies hydrogen transfer, Geobacter, Methanogenesis, Omics, Machine learning Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-288821/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/25 Abstract Background: Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. Results: To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, acetate accumulated in all reactors, while propionate was detected only in the electrochemical reactors. Four dominant fermentative bacteria were identied in the core population, and metatranscriptomics analysis suggested that they were responsible for the degradation of fructose and ethanol to propionate, propanol, acetate, and H2. -
The Genome of Pelobacter Carbinolicus Reveals
Aklujkar et al. BMC Genomics 2012, 13:690 http://www.biomedcentral.com/1471-2164/13/690 RESEARCH ARTICLE Open Access The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features Muktak Aklujkar1*, Shelley A Haveman1, Raymond DiDonato Jr1, Olga Chertkov2, Cliff S Han2, Miriam L Land3, Peter Brown1 and Derek R Lovley1 Abstract Background: The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results: Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. -
Bacterial Communities in Manganese Nodules in Rice Field Subsoils: Estimation Using PCR-DGGE and Sequencing Analyses
Soil Science and Plant Nutrition (2007) 53, 575–584 doi: 10.1111/j.1747-0765.2007.00176.x ORIGINALBlackwell Publishing Ltd ARTICLE BacterialORIGINAL communities ARTICLE in manganese nodules Bacterial communities in manganese nodules in rice field subsoils: Estimation using PCR-DGGE and sequencing analyses Vita Ratri CAHYANI1,3, Jun MURASE1, Eiji ISHIBASHI2, Susumu ASAKAWA1 and Makoto KIMURA1 1Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, 2Agricultural Experiment Station, Okayama Prefectural General Agricultural Center, Okayama 709-0801, Japan; and 3Faculty of Agriculture, Sebelas Maret University, Surakarta 57126, Indonesia Abstract The phylogenetic positions of bacterial communities in manganese (Mn) nodules from subsoils of two Japanese rice fields were estimated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR- DGGE) analysis followed by sequencing of 16S rDNA. The DGGE band patterns and sequencing analysis of characteristic DGGE bands revealed that the bacterial communities in Mn nodules were markedly different from those in the plow layer and subsoils. Three out of four common bands found in Mn nodules from two sites corresponded to Deltaproteobacteria and were characterized as sulfate-reducing and iron-reducing bacteria. The other DGGE bands of Mn nodules corresponded to sulfate and iron reducers (Deltaproteo- bacteria), methane-oxidizing bacteria (Gamma and Alphaproteobacteria), nitrite-oxidizing bacteria (Nitrospirae) and Actinobacteria. In addition, some DGGE bands of Mn nodules showed no clear affiliation to any known bacteria. The present study indicates that members involved in the reduction of Mn nodules dominate the bacterial communities in Mn nodules in rice field subsoils. Key words: bacteria, manganese nodule, manganese reduction, phylogeny, rice field. INTRODUCTION The sites of Fe and Mn accumulation in the subsoil layer are termed Fe and Mn illuvial horizons, and the Rice is a staple crop in Asian countries. -
Disentangling the Syntrophic Electron Transfer Mechanisms of Candidatus Geobacter Eutrophica Through Electrochemical Stimulation
www.nature.com/scientificreports OPEN Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning Heyang Yuan1,2*, Xuehao Wang1, Tzu‑Yu Lin1, Jinha Kim1 & Wen‑Tso Liu1* Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica‑dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica’s EET ability. The high‑quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics‑enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET. Anaerobic digestion is widely used to convert high-strength waste streams to biogas. -
Syntrophics Bridging the Gap of Methanogenesis in the Jharia Coal
g in Geno nin m i ic M s ta & a P Jha et al., J Data Mining Genomics Proteomics 2015, 6:3 D r f o Journal of o t e l DOI: 10.4172/2153-0602.1000177 o a m n r i c u s o J ISSN: 2153-0602 Data Mining in Genomics & Proteomics Short Communication Open Access Syntrophics Bridging the Gap of Methanogenesis in the Jharia Coal Bed Basin Priyanka Jha1,5*, Sujit Ghosh1,2 $, Kunal Mukhopadhyay1, Ashish Sachan1 and Ambarish S Vidyarthi 3,4 1Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India– 835215 2Department of Botany, J.K. College, Purulia, West Bengal, India– 723101 3Department of Biotechnology, Birla Institute of Technology, Mesra, Patna Extension, Bihar, India– 800014 4Institute of Engineering and Technology, Sitapur Road, Lucknow, India– 226021 5Discipline of Microbiology, School of Life Sciences, University of KwaZulu Natal, Pietermaritzburg Campus, Pietermaritzburg– 3201, South Africa $ - Authors contributed equally Abstract The bituminous and sub-bituminous rank of coals is being produced from the Jharia basin of Jharkhand which is the largest producer of CBM in India. Although there have been many reports on methanogenesis from Jharia, the present study deals with the special emphasis on the syntrophic microbes which can act as catalyst for the hydrogenotrophic methanogenesis. Using the metagenomic approach followed by 454 pyro sequencing, the presence of syntrophic community has been deciphered for the first time from the formation water samples of Jharia coal bed basin. The taxonomic assignment of unassembled clean metagenomic sequences was performed using BLASTX against the GenBank database through MG-RAST server. -
Th Annual Argonne National Laboratory Soil Metagenomics
th Annual 7Argonne National Laboratory Soil Metagenomics Meeting OCTOBER 21st- 23rd, 2015 Lisle/Naperville Hilton Hotel Lisle, IL Acknowledgements We would like to thank our sponsors for their generous support ArgonneSoilMetagenomicsMeeting2015 October 21, 2015 Welcome to the 7th Annual Argonne Soil Metagenomics Meeting! The aim of this series of meetings has been to incite discussion on the challenges and opportunities afforded by next-generation DNA sequencing and associated ‘omics approaches to understand the complex nature of soil microbial communities. This meeting aims to serve the research community by providing a venue for interaction among ecologists, microbiologists, bioinformaticists, and ‘omics enthusiasts — all focused on the wonders of life in soil. Through oral presentations, posters, discussion sessions, and participation by industry sponsors, the meeting will cover any aspect of soil metagenomics research, from technical development to data analysis to science breakthroughs. We hope you share your research, meet some new folks, learn something new, and enjoy the meeting! Sincerely, The Organizing Committee Sarah O’Brien, Chair Sarah Owens Darlyn Mishur Dionysios Antonopoulos Folker Meyer Will Trimble David Myrold 1 AGENDA Wednesday, October 21 7:30 Registration Continental breakfast 8:15 Introduction & announcements Session I: The Underexplored Biosphere 8:30 Ecological and evolutionary insight into the persistence of soil bacteria Jay T. Lennon, Stuart E. Jones 8:50 Phylogenetic distribution of resuscitation genes in soil microbes Fan Yang, Stuart E. Jones, Jay T. Lennon, Adina Howe 9:10 Moleculo hybrid synthetic long reads reconstruct full genomes from the rare biosphere with functional potential elucidated by high resolution mass spectrometry Richard Allen White III, Eric M. -
Supplementary Material
Supplementary Material 1 Supplementary Figures and Tables 1.1 Supplementary Figures Deltaproteobacterium PSCGC (2) Deltaproteobacteria Gammaproteobacteria bacterium isolate NP949 Gammaproteobacteria Deltaproteobacteria bacterium spp. (4) Deltaproteobacteria Streptomyces sp. CNQ-509 Actinobacteria candidate division KSB1 bacterium RBG_16_48_16 candidate division KSB1 Dethiobacter alkaliphilus AHT-1 Firmicutes-Clostridia Desulfuromonas sp. DDH-964 Deltaproteobacteria Desulfuromonas spp. (2) Deltaproteobacteria OTU-487 (Deltaproteobacteria bacterium 37-65-8) Spirochaetes bacterium (2) Spirochaetes Methanocella sp. RC-I Methanomicrobia Methanoregula boonei 6A8 Methanomicrobia candidate division OP9 bacterium SCGC AAA255-N14 Atribacteria Methanoregulace aearchaeon JGI M3C4D3-001-G22 Methanomicrobia Methanomicrobia (5) Methanofollis liminatans GKZPZ Methanomicrobia OTU-267 (uncultured microorganism) Candidatus Aminicenantes bacterium RBG_13_59_9 Aminicenantes Methanomassiliicoccus luminyensis B10 Thermoplasmata Anaerolineae bacterium CG_4_9_14_0_8 Chloroflexi Elusimicrobia bacterium GW (2) Elusimicrobia candidate division WOR-3 bacterium SM23_42 Methanomassiliicoccales archaeon RumEn M1 Thermoplasmata OTU-858 (uncultured microorganism) OTU-544 (uncultured bacterium) Theionarchaea archaeon DG-70-1 Theionarchaea Chloroflexi bacterium RIFOXYD12_FULL_57_15 Chloroflexi OTU-201 (uncultured bacterium) OTU-481 (uncultured bacterium) Methanomicrobia (6) Lentisphaerae bacterium (2) Lentisphaerae Fimicutes (5) Bdellovibrionales bacterium GWB1_55_8 Deltaproteobacteria