The impact of immigration on microbial community composition in full-scale anaerobic digesters
暂无分享,去创建一个
Marta Nierychlo | Mads Albertsen | M. Nierychlo | S. McIlroy | P. Nielsen | R. Kirkegaard | M. Dueholm | J. M. Kristensen | M. Albertsen | Rasmus H. Kirkegaard | Simon J. McIlroy | Jannie M. Kristensen | Søren M. Karst | Morten S. Dueholm | Per H. Nielsen | P. Nielsen | S. Karst | Morten S. Dueholm
[1] M. Manefield. The ecology of RNA , 2008, The ISME Journal.
[2] Anne K Camper,et al. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. , 2006, Journal of microbiological methods.
[3] Mark Hernandez,et al. Quantification of Gordona amarae Strains in Foaming Activated Sludge and Anaerobic Digester Systems with Oligonucleotide Hybridization Probes , 1998, Applied and Environmental Microbiology.
[4] H. Dahle,et al. Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. , 2006, International journal of systematic and evolutionary microbiology.
[5] Sean Tyrrel,et al. Anaerobic digestion foaming causes--a review. , 2009, Bioresource technology.
[6] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[7] Eric P. Nawrocki,et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.
[8] Steven Salzberg,et al. BIOINFORMATICS ORIGINAL PAPER , 2004 .
[9] S. Sørensen,et al. 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. , 2013, FEMS microbiology ecology.
[10] Sang-Hoon Lee,et al. Influence of influent wastewater communities on temporal variation of activated sludge communities. , 2015, Water research.
[11] B. Birren,et al. The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing , 2012, PloS one.
[12] L. T. Angenent,et al. Bacterial community structures are unique and resilient in full-scale bioenergy systems , 2011, Proceedings of the National Academy of Sciences.
[13] Å. Westlund,et al. Operational aspects on foaming in digesters caused by , 1998 .
[14] Hadley Wickham,et al. Reshaping Data with the reshape Package , 2007 .
[15] Susan Holmes,et al. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.
[16] S. McIlroy,et al. Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life , 2016, bioRxiv.
[17] D. Zitomer,et al. Influent wastewater microbiota and temperature influence anaerobic membrane bioreactor microbial community. , 2016, Bioresource technology.
[18] P. Weiland. Biogas production: current state and perspectives , 2009, Applied Microbiology and Biotechnology.
[19] Jianhua Guo,et al. Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing , 2015, Microbial Cell Factories.
[20] J. Stewart,et al. A real‐time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution , 2010, Journal of applied microbiology.
[21] A. Uitterlinden,et al. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.
[22] H. Wickham. Simple, Consistent Wrappers for Common String Operations , 2015 .
[23] C. Etchebehere,et al. Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge. , 1998, International journal of systematic bacteriology.
[24] S. Kleinsteuber,et al. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials , 2013, Applied Microbiology and Biotechnology.
[25] Donovan H. Parks,et al. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking , 2015, PeerJ.
[26] Yihui Xie,et al. A General-Purpose Package for Dynamic Report Generation in R , 2016 .
[27] Lieve Helsen,et al. Anaerobic digestion in global bio-energy production: Potential and research challenges , 2011 .
[28] Aaron Marc Saunders,et al. A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. , 2010, Water research.
[29] Aaron Marc Saunders,et al. Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome. , 2015, Water research.
[30] M. Carballa,et al. Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus. , 2015, Current opinion in biotechnology.
[31] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[32] M. C. Tomei,et al. "Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge. , 2005, FEMS microbiology reviews.
[33] Mads Albertsen,et al. Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities , 2015, PloS one.
[34] E. Zoetendal,et al. Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe. , 2002, International journal of systematic and evolutionary microbiology.
[35] Hideki Harada,et al. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. , 2006, International journal of systematic and evolutionary microbiology.
[36] J. Nielsen,et al. Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics , 2016, The ISME Journal.
[37] Peter Dalgaard,et al. R Development Core Team (2010): R: A language and environment for statistical computing , 2010 .
[38] Aviaja Anna Hansen,et al. MiDAS: the field guide to the microbes of activated sludge , 2015, Database J. Biol. Databases Curation.
[39] Se Jin Song,et al. Tiny microbes, enormous impacts: what matters in gut microbiome studies? , 2016, Genome Biology.
[40] S. Campanaro,et al. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy , 2016, Biotechnology for Biofuels.
[41] Gergely Maróti,et al. Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing , 2012, Biotechnology for Biofuels.
[42] Willy Verstraete,et al. Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. , 2012, Bioresource technology.
[43] D. Lane. 16S/23S rRNA sequencing , 1991 .
[44] Wen-Tso Liu,et al. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity , 2016, Scientific Reports.
[45] E. Pelletier,et al. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge , 2009, The ISME Journal.
[46] M. Nierychlo,et al. Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters , 2016, The ISME Journal.
[47] I. Head,et al. Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants. , 2002, Environmental microbiology.
[48] J. Tiedje,et al. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.
[49] Anne Gunn Rike,et al. A metagenomic study of the microbial communities in four parallel biogas reactors , 2014, Biotechnology for Biofuels.
[50] G. Pusch,et al. Phylogenetic conservatism of functional traits in microorganisms , 2012, The ISME Journal.
[51] George M. Weinstock,et al. Genomic approaches to studying the human microbiota , 2012, Nature.
[52] A. Macario,et al. Isolation of Methanobrevibacter smithii from human feces , 1982, Applied and environmental microbiology.
[53] Per Halkjær Nielsen,et al. MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups , 2017, Database J. Biol. Databases Curation.
[54] James R. Cole,et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..
[55] B. Patel,et al. Anaerobaculum thermoterrenum gen. nov., sp. nov., a novel, thermophilic bacterium which ferments citrate. , 1997, International journal of systematic bacteriology.
[56] Brian D. Ripley,et al. Create Dendrograms and Tree Diagrams Using 'ggplot2' , 2015 .
[57] H. Aldrich,et al. Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. , 1999, International journal of systematic bacteriology.
[58] Birgitte K. Ahring,et al. Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria , 1987, Applied and environmental microbiology.
[59] L. Raskin,et al. PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets , 2012, PloS one.
[60] Wen-Tso Liu,et al. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen , 2016, The ISME Journal.
[61] Aaron Marc Saunders,et al. The activated sludge ecosystem contains a core community of abundant organisms , 2015, The ISME Journal.
[62] I. Angelidaki,et al. Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis , 2016, Biotechnology for Biofuels.
[63] Pelin Yilmaz,et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..
[64] B. Knapp,et al. Removal of Free Extracellular DNA from Environmental Samples by Ethidium Monoazide and Propidium Monoazide , 2008, Applied and Environmental Microbiology.
[65] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[66] Tanja Woyke,et al. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity , 2016, Nature Microbiology.