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Can\'t sign in? Forgot your username? Enter your email address below and we will send you your username If the address matches an existing account you will receive an email with instructions to retrieve your usernameCan\'t sign in? Forgot your password?Enter your email address below and we will send you the reset instructions If the address matches an existing account you will receive an email with instructions to reset your password. Close Dr. Gemma Reguera Editor in Chief (2026) | Michigan State University Gemma Reguera is a professor in the Department of Microbiology and Molecular Genetics at Michigan State University. Her work investigates energy conversion reactions catalyzed by microbes in natural and anthropogenic systems. Editorial Board Applied and Environmental MicrobiologyArticleJuly 2016Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes Florence Mus, Matthew B. Crook, Kevin Garcia, Amaya Garcia Costas, Barney A. Geddes, Evangelia D. Kouri, Ponraj Paramasivan, Min-Hyung Ryu, Giles E. D. Oldroyd, Philip S. Poole, Michael K. Udvardi, Christopher A. Voigt, Jean-Michel Anéand John W. PetersSymbiotic Nitrogen Fixation and the Challenges to Its Extension to NonlegumesAuthors: Florence Mus, Matthew B. Crook, Kevin Garcia, Amaya Garcia Costas, Barney A. Geddes, Evangelia D. Kouri, Ponraj Paramasivan, … Show All … , Min-Hyung Ryu, Giles E. D. Oldroyd, Philip S. Poole, Michael K. Udvardi, Christopher A. Voigt, Jean-Michel Ané, and John W. Peters Show FewerDOI: https://doi.org/10.1128/AEM.01055-16Volume 82, Number 131 July 2016ABSTRACTREFERENCESABSTRACTAccess to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.REFERENCES1.Boyd ES, Peters JW. 2013. New insights into the evolutionary history of biological nitrogen fixation. Front Microbiol 4:201.CrossrefPubMedGoogle Scholar2.Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. 2015. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320.CrossrefPubMedGoogle Scholar3.Santi C, Bogusz D, Franche C. 2013. Biological nitrogen fixation in non-legume plants. 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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsFlorence MusDepartment of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USAView all articles by this authorMatthew B. CrookDepartment of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAView all articles by this authorKevin GarciaDepartment of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAView all articles by this authorAmaya Garcia CostasDepartment of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USAView all articles by this authorBarney A. GeddesDepartment of Plant Sciences, University of Oxford, Oxford, United KingdomView all articles by this authorEvangelia D. KouriPlant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USAView all articles by this authorPonraj ParamasivanJohn Innes Centre, Norwich Research Park, Norwich, United KingdomView all articles by this authorMin-Hyung RyuDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USAView all articles by this authorGiles E. D. OldroydJohn Innes Centre, Norwich Research Park, Norwich, United KingdomView all articles by this authorPhilip S. PooleDepartment of Plant Sciences, University of Oxford, Oxford, United KingdomView all articles by this authorMichael K. UdvardiPlant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USAView all articles by this authorChristopher A. VoigtDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USAView all articles by this authorJean-Michel AnéDepartment of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAView all articles by this authorJohn W. PetersDepartment of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USAView all articles by this authorEditorR. M. KellyEditorNorth Carolina State UniversityNotesAddress correspondence to Jean-Michel Ané, [email protected], or John W. Peters, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleFebruary 2013Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities Barbara J. MacGregor, Jennifer F. Biddle, Jason R. Siebert, Eric Staunton, Eric L. Hegg, Ann G. Matthysseand Andreas TeskeWhy Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase ActivitiesAuthors: Barbara J. MacGregor, Jennifer F. Biddle, Jason R. Siebert, Eric Staunton, Eric L. Hegg, Ann G. Matthysse, and Andreas TeskeDOI: https://doi.org/10.1128/AEM.02538-12Volume 79, Number 415 February 2013ABSTRACTREFERENCESABSTRACTOrange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange Beggiatoa (\"Candidatus Maribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.REFERENCES1.Jannasch HW, Nelson DC, and Wirsen CO. 1989. Massive natural occurrence of unusually large bacteria (Beggiatoa sp.) at a hydrothermal deep-sea vent site.Nature 342:834–836.Google Scholar2.Albertin ML. 1989. Interpretations and analysis of Guaymas Basin multi-channel seismic reflection profiles: implications for tectonic history. M.A. thesis. University of Texas at Austin, Austin, TX.Google Scholar3.Aragón-Arreola M, Morandi M, Martín-Barajas A, Delgado-Argote L, and González-Fernández A. 2005. 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Biotechnol. 4:287–294.PubMedGoogle ScholarInformation ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 79 • Number 4 • 15 February 2013Pages: 1183 - 1190HistoryReceived: 17 August 2012Accepted: 3 December 2012Published online: 4 February 2013Copyright© 2013 American Society for Microbiology.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsBarbara J. MacGregorDepartment of Marine Sciences, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USAView all articles by this authorJennifer F. BiddleCollege of Earth, Ocean, and the Environment, University of Delaware, Lewes, Delaware, USAView all articles by this authorJason R. SiebertDepartment of Biochemistry Molecular Biology, Michigan State University, East Lansing, Michigan, USAView all articles by this authorEric StauntonDepartment of Environmental and Health Sciences, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USAView all articles by this authorEric L. HeggDepartment of Biochemistry Molecular Biology, Michigan State University, East Lansing, Michigan, USAView all articles by this authorAnn G. MatthysseDepartment of Biology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USAView all articles by this authorAndreas TeskeDepartment of Marine Sciences, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USAView all articles by this authorNotesAddress correspondence to Barbara J. MacGregor, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleOctober 2019Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation Dominik Danso, Jennifer Chowand Wolfgang R. StreitPlastics: Environmental and Biotechnological Perspectives on Microbial DegradationAuthors: Dominik Danso https://orcid.org/0000-0003-2214-2002, Jennifer Chow https://orcid.org/0000-0002-7499-5325, and Wolfgang R. Streit https://orcid.org/0000-0001-7617-7396DOI: https://doi.org/10.1128/AEM.01095-19Volume 85, Number 191 October 2019ABSTRACTREFERENCESABSTRACTPlastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.REFERENCES1.Geyer R, Jambeck JR, Law KL. 2017. Production, use, and fate of all plastics ever made. Sci Adv 3:e1700782.CrossrefPubMedGoogle Scholar2.PlasticsEurope. 2018. PlasticsEurope, plastics—the facts 2018: an analysis of European plastics production, demand and waste data. PlasticsEurope, Brussels, Belgium.Google Scholar3.Ellen MacArthur Foundation. 2017. The new plastics economy: rethinking the future of plastics and catalysing action. 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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSPETcutinasemicrobial plastic degradationpolyamidespolyethylenepolyethylene terephthalatepolypropylenepolystyrenepolyurethanepolyvinylchlorideContributorsAuthorsDominik Danso https://orcid.org/0000-0003-2214-2002Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, GermanyView all articles by this authorJennifer Chow https://orcid.org/0000-0002-7499-5325Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, GermanyView all articles by this authorWolfgang R. Streit https://orcid.org/0000-0001-7617-7396Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, GermanyView all articles by this authorEditorHarold L. DrakeEditorUniversity of BayreuthNotesAddress correspondence to Wolfgang R. Streit, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleDecember 2009Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Hornand Carolyn F. WeberIntroducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial CommunitiesAuthors: Patrick D. Schloss [email protected], Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, … Show All … , Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Horn, and Carolyn F. Weber Show FewerDOI: https://doi.org/10.1128/AEM.01541-09Volume 75, Number 231 December 2009ABSTRACTREFERENCESABSTRACTmothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.REFERENCES1.Antonopoulos, D. A., S. M. Huse, H. G. Morrison, T. M. Schmidt, M. L. Sogin, and V. B. Young.2009. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. 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L., H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, et al.2006. Microbial diversity in the deep sea and the underexplored \"rare biosphere.” Proc. Natl. Acad. Sci. USA103:12115-12120.PubMedGoogle Scholar28.Turnbaugh, P. J., M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, et al.2009. A core gut microbiome in obese and lean twins. Nature457:480-484.PubMedGoogle Scholar29.Turnbaugh, P. J., R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, et al.2007. The human microbiome project. Nature449:804-810.CrossrefPubMedGoogle ScholarInformation ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 75 • Number 23 • 1 December 2009Pages: 7537 - 7541HistoryReceived: 30 June 2009Accepted: 26 September 2009Published online: 2 October 2009Copyright© 2009.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsPatrick D. Schloss [email protected]Department of Microbiology, University of Massachusetts, Amherst, MassachusettsDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, MichiganView all articles by this authorSarah L. WestcottDepartment of Microbiology, University of Massachusetts, Amherst, MassachusettsDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, MichiganView all articles by this authorThomas RyabinDepartment of Microbiology, University of Massachusetts, Amherst, MassachusettsView all articles by this authorJustine R. HallDepartment of Biology, University of New Mexico, Albuquerque, New MexicoView all articles by this authorMartin HartmannDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, BC, CanadaView all articles by this authorEmily B. HollisterDepartment of Soil and Crop Sciences, Texas A M University, College Station, TexasView all articles by this authorRyan A. LesniewskiDepartment of Soil, Water, and Climate, University of Minnesota, St. Paul, MinnesotaView all articles by this authorBrian B. OakleyDepartment of Biological Sciences, University of Warwick, Coventry, United KingdomView all articles by this authorDonovan H. ParksFaculty of Computer Science, Dalhousie University, Halifax, NS, CanadaView all articles by this authorCourtney J. RobinsonDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, MichiganView all articles by this authorJason W. SahlEnvironmental Science and Engineering, Colorado School of Mines, Golden, ColoradoView all articles by this authorBlaz StresDepartment of Animal Science, University of Ljubljana, Ljubljana, SloveniaView all articles by this authorGerhard G. ThallingerInstitute for Genomics and Bioinformatics, Graz University of Technology, Graz, AustriaView all articles by this authorDavid J. Van HornDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, MichiganView all articles by this authorCarolyn F. WeberDepartment of Biological Sciences, Louisiana State University, Baton Rouge, LousianaView all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleMay 2010Effects of Air Temperature and Relative Humidity on Coronavirus Survival on Surfaces Lisa M. Casanova, Soyoung Jeon, William A. Rutala, David J. Weberand Mark D. SobseyEffects of Air Temperature and Relative Humidity on Coronavirus Survival on SurfacesAuthors: Lisa M. Casanova [email protected], Soyoung Jeon, William A. Rutala, David J. Weber, and Mark D. SobseyDOI: https://doi.org/10.1128/AEM.02291-09Volume 76, Number 91 May 2010ABSTRACTREFERENCESABSTRACTAssessment of the risks posed by severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) on surfaces requires data on survival of this virus on environmental surfaces and on how survival is affected by environmental variables, such as air temperature (AT) and relative humidity (RH). The use of surrogate viruses has the potential to overcome the challenges of working with SARS-CoV and to increase the available data on coronavirus survival on surfaces. Two potential surrogates were evaluated in this study; transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHV) were used to determine effects of AT and RH on the survival of coronaviruses on stainless steel. At 4°C, infectious virus persisted for as long as 28 days, and the lowest level of inactivation occurred at 20% RH. Inactivation was more rapid at 20°C than at 4°C at all humidity levels; the viruses persisted for 5 to 28 days, and the slowest inactivation occurred at low RH. Both viruses were inactivated more rapidly at 40°C than at 20°C. The relationship between inactivation and RH was not monotonic, and there was greater survival or a greater protective effect at low RH (20%) and high RH (80%) than at moderate RH (50%). There was also evidence of an interaction between AT and RH. The results show that when high numbers of viruses are deposited, TGEV and MHV may survive for days on surfaces at ATs and RHs typical of indoor environments. TGEV and MHV could serve as conservative surrogates for modeling exposure, the risk of transmission, and control measures for pathogenic enveloped viruses, such as SARS-CoV and influenza virus, on health care surfaces.REFERENCES1.Abad, F., R. Pinto, and A. Bosch.1994. Survival of enteric viruses on environmental fomites. Appl. Environ. 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Casanova [email protected]Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North CarolinaView all articles by this authorSoyoung JeonDepartment of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North CarolinaView all articles by this authorWilliam A. RutalaDepartment of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North CarolinaView all articles by this authorDavid J. WeberDepartment of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North CarolinaView all articles by this authorMark D. SobseyDepartment of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North CarolinaView all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleFebruary 2006Comparative Genomics of DNA Fragments from Six Antarctic Marine Planktonic Bacteria Joseph J. Grzymski, Brandon J. Carter, Edward F. DeLong, Robert A. Feldman, Amir Ghadiriand Alison E. MurrayComparative Genomics of DNA Fragments from Six Antarctic Marine Planktonic BacteriaAuthors: Joseph J. Grzymski, Brandon J. Carter, Edward F. DeLong, Robert A. Feldman, Amir Ghadiri, and Alison E. Murray [email protected]DOI: https://doi.org/10.1128/AEM.72.2.1532-1541.2006Volume 72, Number 2February 2006ABSTRACTREFERENCESABSTRACTSixenvironmental fosmid clones from Antarctic coastal waterbacterioplankton were completely sequenced. The genome fragmentsharbored small-subunit rRNA genes that were between 85 and 91% similarto those of their nearest cultivated relatives. The six fragments spanfour phyla, including the Gemmatimonadetes,Proteobacteria (α and γ),Bacteroidetes, and high-G+C gram-positive bacteria.Gene-finding and annotation analyses identified 244 total open readingframes. Amino acid comparisons of 123 and 113 Antarcticbacterial amino acid sequences to mesophilic homologs fromG+C-specific and SwissProt/UniProt databases, respectively,revealed widespread adaptation to the cold. The most significantchanges in these Antarctic bacterial protein sequences included areduction in salt-bridge-forming residues such as arginine, glutamicacid, and aspartic acid, reduced proline contents, and a reduction instabilizing hydrophobic clusters. Stretches of disordered amino acidswere significantly longer in the Antarctic sequences than in themesophilic sequences. 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Evol.Microbiol.53:1155-1163.PubMedGoogle ScholarInformation ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 72 • Number 2 • February 2006Pages: 1532 - 1541HistoryReceived: 25 April 2005Accepted: 8 November 2005Copyright© 2006.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsJoseph J. GrzymskiDesert Research Institute, 2215 Raggio Parkway, Reno, Nevada 89512View all articles by this authorBrandon J. CarterDesert Research Institute, 2215 Raggio Parkway, Reno, Nevada 89512View all articles by this authorEdward F. DeLongMassachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139View all articles by this authorRobert A. FeldmanAmersham Biosciences, 928 E. Argues Avenue, Sunnyvale, California 94086Present address: Symbio Corporation, 1455 Adams Dr., Menlo Park, CA 94025.View all articles by this authorAmir GhadiriAmersham Biosciences, 928 E. Argues Avenue, Sunnyvale, California 94086View all articles by this authorAlison E. Murray [email protected]Desert Research Institute, 2215 Raggio Parkway, Reno, Nevada 89512View all articles by this authorNotes†Supplemental material for this article may be found at http://aem.asm.org/.Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleDecember 2005UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Catherine Lozuponeand Rob KnightUniFrac: a New Phylogenetic Method for Comparing Microbial CommunitiesAuthors: Catherine Lozupone and Rob Knight [email protected]DOI: https://doi.org/10.1128/AEM.71.12.8228-8235.2005Volume 71, Number 12December 2005ABSTRACTREFERENCESABSTRACTWe introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. 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Microbiol.21:546-556.PubMedGoogle ScholarInformation ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 71 • Number 12 • December 2005Pages: 8228 - 8235HistoryReceived: 3 May 2005Accepted: 26 August 2005Copyright© 2005.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsCatherine LozuponeDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309View all articles by this authorRob Knight [email protected]Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309View all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleSeptember 2011Biodegradation of Polyester Polyurethane by Endophytic Fungi Jonathan R. Russell, Jeffrey Huang, Pria Anand, Kaury Kucera, Amanda G. Sandoval, Kathleen W. Dantzler, DaShawn Hickman, Justin Jee, Farrah M. Kimovec, David Koppstein, Daniel H. Marks, Paul A. Mittermiller, Salvador Joel Núñez, Marina Santiago, Maria A. Townes, Michael Vishnevetsky, Neely E. Williams, Mario Percy Núñez Vargas, Lori-Ann Boulanger, Carol Bascom-Slackand Scott A. StrobelBiodegradation of Polyester Polyurethane by Endophytic FungiAuthors: Jonathan R. Russell, Jeffrey Huang, Pria Anand, Kaury Kucera, Amanda G. Sandoval, Kathleen W. Dantzler, DaShawn Hickman, … Show All … , Justin Jee, Farrah M. Kimovec, David Koppstein, Daniel H. Marks, Paul A. Mittermiller, Salvador Joel Núñez, Marina Santiago, Maria A. Townes, Michael Vishnevetsky, Neely E. Williams, Mario Percy Núñez Vargas, Lori-Ann Boulanger, Carol Bascom-Slack, and Scott A. Strobel [email protected] Show FewerDOI: https://doi.org/10.1128/AEM.00521-11Volume 77, Number 171 September 2011ABSTRACTREFERENCESABSTRACTBioremediation is an important approach to waste reduction that relies on biological processes to break down a variety of pollutants. This is made possible by the vast metabolic diversity of the microbial world. To explore this diversity for the breakdown of plastic, we screened several dozen endophytic fungi for their ability to degrade the synthetic polymer polyester polyurethane (PUR). Several organisms demonstrated the ability to efficiently degrade PUR in both solid and liquid suspensions. Particularly robust activity was observed among several isolates in the genus Pestalotiopsis, although it was not a universal feature of this genus. Two Pestalotiopsis microspora isolates were uniquely able to grow on PUR as the sole carbon source under both aerobic and anaerobic conditions. Molecular characterization of this activity suggests that a serine hydrolase is responsible for degradation of PUR. 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RussellDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorJeffrey HuangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorPria AnandDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorKaury KuceraDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorAmanda G. SandovalDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorKathleen W. DantzlerDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorDaShawn HickmanDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorJustin JeeDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorFarrah M. KimovecDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorDavid KoppsteinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorDaniel H. MarksDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorPaul A. MittermillerDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorSalvador Joel NúñezDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorMarina SantiagoDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorMaria A. TownesDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorMichael VishnevetskyDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorNeely E. WilliamsDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorMario Percy Núñez VargasUniversidad Nacional San Antõnio Abad del Cusco, Peru Escuela Post Grado, Facultad de Biologia, Andes Amazon Guianas Herbario Vargas (CUZ), Cusco, PeruView all articles by this authorLori-Ann BoulangerDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorCarol Bascom-SlackDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorScott A. Strobel [email protected]Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520View all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleMay 2021Determining Gut Microbial Dysbiosis: a Review of Applied Indexes for Assessment of Intestinal Microbiota Imbalances Shaodong Wei, Martin Iain Bahl, Simon Mark Dahl Baunwall, Christian Lodberg Hvasand Tine Rask LichtDetermining Gut Microbial Dysbiosis: a Review of Applied Indexes for Assessment of Intestinal Microbiota ImbalancesAuthors: Shaodong Wei, Martin Iain Bahl, Simon Mark Dahl Baunwall, Christian Lodberg Hvas, and Tine Rask Licht https://orcid.org/0000-0002-6399-9574 [email protected]DOI: https://doi.org/10.1128/AEM.00395-21Volume 87, Number 1111 May 2021ABSTRACTREFERENCESABSTRACTAssessing \"dysbiosis” in intestinal microbial communities is increasingly considered a routine analysis in microbiota studies, and it has added relevant information to the prediction and characterization of diseases and other adverse conditions. 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DrakeUniversity of BayreuthHistoryPublished online: 19 March 2021Copyright© 2021 Wei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSdysbiosisdysbiosis indexgutimbalanceintestinemicrobiomemicrobiotaContributorsAuthorsShaodong WeiNational Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkView all articles by this authorMartin Iain BahlNational Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkView all articles by this authorSimon Mark Dahl BaunwallDepartment of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, DenmarkView all articles by this authorChristian Lodberg HvasDepartment of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, DenmarkView all articles by this authorTine Rask Licht https://orcid.org/0000-0002-6399-9574 [email protected]National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkView all articles by this authorEditorHarold L. DrakeEditorUniversity of BayreuthMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied MicrobiologyArticleNovember 1956Analytical Microbiology John J. GavinAnalytical Microbiology: I. The Test OrganismAuthor: John J. GavinDOI: https://doi.org/10.1128/am.4.6.323-331.1956Volume 4, Number 6November 1956Information ContributorsInformationPublished InApplied MicrobiologyVolume 4 • Number 6 • November 1956Pages: 323 - 331PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorJohn J. GavinFood Research Laboratories, Inc., Long Island City, N. Y.View all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleJune 2005Inactivation of Enteric Adenovirus and Feline Calicivirus by Chlorine Dioxide Jeanette A. Thurston-Enriquez, Charles N. Haas, Joseph Jacangeloand Charles P. GerbaInactivation of Enteric Adenovirus and Feline Calicivirus by Chlorine DioxideAuthors: Jeanette A. Thurston-Enriquez [email protected], Charles N. Haas, Joseph Jacangelo, and Charles P. GerbaDOI: https://doi.org/10.1128/AEM.71.6.3100-3105.2005Volume 71, Number 6June 2005ABSTRACTREFERENCESABSTRACTChlorine dioxide (ClO2) inactivation experiments were conducted with adenovirus type 40 (AD40) and feline calicivirus (FCV). Experiments were carried out in buffered, disinfectant demand-free water under high- and low-pH and -temperature conditions. Ct values (the concentration of ClO2 multiplied by contact time with the virus) were calculated directly from bench-scale experiments and from application of the efficiency factor Hom (EFH) model. AD40 Ct ranges for 4-log inactivation (Ct99.99%) at 5°C were 0.77 to 1.53 mg/liter × min and 0.80 to 1.59 mg/liter × min for pH 6 and 8, respectively. For 15°C AD40 experiments, 0.49 to 0.74 mg/liter × min and 0.12 mg/liter × min Ct99.99% ranges were observed for pH 6 and 8, respectively. FCV Ct99.99% ranges for 5°C experiments were 20.20 to 30.30 mg/liter × min and 0.68 mg/liter × min for pH 6 and 8, respectively. For 15°C FCV experiments, Ct99.99% ranges were 4.20 to 6.72 and 0.18 mg/liter × min for pH 6 and 8, respectively. Viral inactivation was higher at pH 8 than at pH 6 and at 15°C than at 5°C. Comparison of Ct values and inactivation curves demonstrated that the EFH model described bench-scale experiment data very well. Observed bench-scale Ct99.99% ranges and EFH model Ct99.99% values demonstrated that FCV is more resistant to ClO2 than AD40 for the conditions studied. U.S. Environmental Protection Agency guidance manual Ct99.99% values are higher than Ct99.99% values calculated from bench-scale experiments and from EFH model application.REFERENCES1.Aieta, E. M., and J. D. Berg.1986. 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Thurston-Enriquez [email protected]U.S. Department of Agriculture-Agricultural Research Service, 120 Keim Hall, University of Nebraska East Campus, Lincoln, Nebraska 68583-0934View all articles by this authorCharles N. HaasSchool of Environmental Science, Engineering, and Policy, Drexel University, Philadelphia, Pennsylvania 19104View all articles by this authorJoseph JacangeloMontgomery Watson Harza, Lovettsville, Virginia 20180View all articles by this authorCharles P. GerbaDepartment of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721View all articles by this authorMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleApril 2015Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System Yu Jiang, Biao Chen, Chunlan Duan, Bingbing Sun, Junjie Yangand Sheng YangMultigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 SystemAuthors: Yu Jiang, Biao Chen, Chunlan Duan, Bingbing Sun, Junjie Yang, and Sheng YangDOI: https://doi.org/10.1128/AEM.04023-14Volume 81, Number 71 April 2015ABSTRACTREFERENCESABSTRACTAn efficient genome-scale editing tool is required for construction of industrially useful microbes. 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KellyHistoryReceived: 10 December 2014Accepted: 17 January 2015Published online: 30 January 2015Copyright© 2015 American Society for Microbiology.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsYu JiangKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaShanghai Research Center of Industrial Biotechnology, Shanghai, ChinaView all articles by this authorBiao ChenKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaShanghai Research Center of Industrial Biotechnology, Shanghai, ChinaView all articles by this authorChunlan DuanKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaView all articles by this authorBingbing SunKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaShanghai Research Center of Industrial Biotechnology, Shanghai, ChinaView all articles by this authorJunjie YangKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaShanghai Research Center of Industrial Biotechnology, Shanghai, ChinaView all articles by this authorSheng YangKey Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, ChinaShanghai Research Center of Industrial Biotechnology, Shanghai, ChinaShanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, ChinaView all articles by this authorEditorR. M. KellyEditorNotesAddress correspondence to Sheng Yang, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleNovember 2016Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food Robyn C. Mirandaand Donald W. SchaffnerLonger Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to FoodAuthors: Robyn C. Miranda and Donald W. Schaffner https://orcid.org/0000-0001-9200-0400DOI: https://doi.org/10.1128/AEM.01838-16Volume 82, Number 211 November 2016ABSTRACTREFERENCESABSTRACTBacterial cross-contamination from surfaces to food can contribute to foodborne disease. The cross-contamination rate of Enterobacter aerogenes on household surfaces was evaluated by using scenarios that differed by surface type, food type, contact time ( 1, 5, 30, and 300 s), and inoculum matrix (tryptic soy broth or peptone buffer). The surfaces used were stainless steel, tile, wood, and carpet. The food types were watermelon, bread, bread with butter, and gummy candy. Surfaces (25 cm2) were spot inoculated with 1 ml of inoculum and allowed to dry for 5 h, yielding an approximate concentration of 107 CFU/surface. Foods (with a 16-cm2 contact area) were dropped onto the surfaces from a height of 12.5 cm and left to rest as appropriate. Posttransfer, surfaces and foods were placed in sterile filter bags and homogenized or massaged, diluted, and plated on tryptic soy agar. The transfer rate was quantified as the log percent transfer from the surface to the food. Contact time, food, and surface type all had highly significant effects (P 0.000001) on the log percent transfer of bacteria. The inoculum matrix (tryptic soy broth or peptone buffer) also had a significant effect on transfer (P = 0.013), and most interaction terms were significant. More bacteria transferred to watermelon (∼0.2 to 97%) than to any other food, while the least bacteria transferred to gummy candy (∼0.1 to 62%). Transfer of bacteria to bread (∼0.02 to 94%) was similar to transfer of bacteria to bread with butter (∼0.02 to 82%), and these transfer rates under a given set of conditions were more variable than with watermelon and gummy candy.IMPORTANCE The popular notion of the \"five-second rule” is that food dropped on the floor and left there for 5 s is \"safe” because bacteria need time to transfer. The rule has been explored by a single study in the published literature and on at least two television shows. Results from two academic laboratories have been shared through press releases but remain unpublished. We explored this topic by using four different surfaces (stainless steel, ceramic tile, wood, and carpet), four different foods (watermelon, bread, bread with butter, and gummy candy), four different contact times ( 1, 5, 30, and 300 s), and two bacterial preparation methods. Although we found that longer contact times result in more transfer, we also found that other factors, including the nature of the food and the surface, are of equal or greater importance. Some transfer takes place \"instantaneously,” at times of 1 s, disproving the five-second rule.REFERENCES1.Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States–major pathogens. Emerg Infect Dis 17:7–15.CrossrefPubMedGoogle Scholar2.Gould LH, Walsh KA, Vieira AR, Herman K, Williams IT, Hall AJ, Cole D. 2013. Surveillance for foodborne disease outbreaks—United States, 1998–2008. 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A. ElkinsFDA Center for Food Safety and Applied NutritionHistoryReceived: 16 June 2016Accepted: 16 August 2016Published online: 2 September 2016Copyright© 2016 American Society for Microbiology.PermissionsRequest permissions for this article.Request PermissionsContributorsAuthorsRobyn C. MirandaRutgers, The State University of New Jersey, New Brunswick, New Jersey, USAView all articles by this authorDonald W. Schaffner https://orcid.org/0000-0001-9200-0400Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USAView all articles by this authorEditorC. A. ElkinsEditorFDA Center for Food Safety and Applied NutritionNotesAddress correspondence to Donald W. Schaffner, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleApril 2021Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities Caroline S. Fortunato, David A. Butterfield, Benjamin Larson, Noah Lawrence-Slavas, Christopher K. Algar, Lisa Zeigler Allen, James F. Holden, Giora Proskurowski, Emily Reddington, Lucy C. Stewart, Begüm D. Topçuoğlu, Joseph J. Vallinoand Julie A. HuberSeafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial CommunitiesAuthors: Caroline S. Fortunato, David A. Butterfield, Benjamin Larson https://orcid.org/0000-0002-1007-1684, Noah Lawrence-Slavas, Christopher K. Algar, Lisa Zeigler Allen, James F. Holden https://orcid.org/0000-0002-4343-2378, … Show All … , Giora Proskurowski, Emily Reddington, Lucy C. Stewart, Begüm D. Topçuoğlu, Joseph J. Vallino, and Julie A. Huber https://orcid.org/0000-0002-4790-7633 [email protected] Show FewerDOI: https://doi.org/10.1128/AEM.00078-21Volume 87, Number 913 April 2021ABSTRACTREFERENCESABSTRACTDepressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.REFERENCES1.Butterfield DA, Roe KK, Lilley MD, Huber JA, Baross JA, Embley RW, Massoth GJ. 2004. 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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSRNA-SIPautotrophydeep seahydrothermal ventinstrumentationmetagenomicsmetatranscriptomicsContributorsAuthorsCaroline S. FortunatoDepartment of Biology, Widener University, Chester, Pennsylvania, USAView all articles by this authorDavid A. ButterfieldJoint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USAView all articles by this authorBenjamin Larson https://orcid.org/0000-0002-1007-1684NOAA/PMEL, Seattle, Washington, USAView all articles by this authorNoah Lawrence-SlavasJoint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USAView all articles by this authorChristopher K. AlgarDepartment of Oceanography, Dalhousie University, Halifax, Nova Scotia, CanadaView all articles by this authorLisa Zeigler AllenMicrobial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USAView all articles by this authorJames F. Holden https://orcid.org/0000-0002-4343-2378Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USAView all articles by this authorGiora ProskurowskiMarqMetrix, Inc., Seattle, Washington, USAView all articles by this authorEmily ReddingtonGreat Pond Foundation, Edgartown, Massachusetts, USAView all articles by this authorLucy C. StewartDepartment of Microbiology, University of Massachusetts, Amherst, Massachusetts, USAPresent address: Lucy C. Stewart, Toha Science, Wellington, New Zealand; Begüm D. Topçuoğlu, Merck Exploratory Science Center, Cambridge, Massachusetts, USA.View all articles by this authorBegüm D. TopçuoğluDepartment of Microbiology, University of Massachusetts, Amherst, Massachusetts, USAPresent address: Lucy C. Stewart, Toha Science, Wellington, New Zealand; Begüm D. Topçuoğlu, Merck Exploratory Science Center, Cambridge, Massachusetts, USA.View all articles by this authorJoseph J. VallinoEcosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USAView all articles by this authorJulie A. Huber https://orcid.org/0000-0002-4790-7633 [email protected]Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USAView all articles by this authorEditorShuang-Jiang LiuEditorChinese Academy of SciencesMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleSeptember 2013Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform James J. Kozich, Sarah L. Westcott, Nielson T. Baxter, Sarah K. Highlanderand Patrick D. SchlossDevelopment of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing PlatformAuthors: James J. Kozich, Sarah L. Westcott, Nielson T. Baxter, Sarah K. Highlander, and Patrick D. SchlossDOI: https://doi.org/10.1128/AEM.01043-13Volume 79, Number 171 September 2013ABSTRACTREFERENCESABSTRACTRapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical to assess the strengths, weaknesses, and overall suitability of these platforms for the interrogation of microbial communities. Here, we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina\'s MiSeq platform, which is currently capable of producing paired 250-nucleotide reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in length (i.e., V34, V4, and V45) by resequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we reprocessed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.REFERENCES1.Hugenholtz P, Pitulle C, Hershberger KL, and Pace NR. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366–376.CrossrefPubMedGoogle Scholar2.The Human Microbiome Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–214.PubMedGoogle Scholar3.Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, and Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored \"rare biosphere.”. Proc. Natl. Acad. Sci. U. S. A. 103:12115–12120.CrossrefPubMedGoogle Scholar4.Junemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, and Harmsen D. 2012. 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ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117–1123.CrossrefPubMedGoogle Scholar22.Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, and Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537–7541.CrossrefPubMedGoogle Scholar23.Schloss PD. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol. 6:e1000844.CrossrefPubMedGoogle Scholar24.Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One 4:e8230.CrossrefPubMedGoogle Scholar25.Schloss PD. 2013. Secondary structure improves OTU assignments of 16S rRNA gene sequences. 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KozichDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USAView all articles by this authorSarah L. WestcottDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USAView all articles by this authorNielson T. BaxterDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USAView all articles by this authorSarah K. HighlanderDepartment of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USAView all articles by this authorPatrick D. SchlossDepartment of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USAView all articles by this authorNotesAddress correspondence to Patrick D. Schloss, [email protected].Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleMarch 2021Time Evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Wastewater during the First Pandemic Wave of COVID-19 in the Metropolitan Area of Barcelona, Spain Gemma Chavarria-Miró, Eduard Anfruns-Estrada, Adán Martínez-Velázquez, Mario Vázquez-Portero, Susana Guix, Miquel Paraira, Belén Galofré, Gloria Sánchez, Rosa M. Pintóand Albert BoschTime Evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Wastewater during the First Pandemic Wave of COVID-19 in the Metropolitan Area of Barcelona, SpainAuthors: Gemma Chavarria-Miró, Eduard Anfruns-Estrada, Adán Martínez-Velázquez, Mario Vázquez-Portero, Susana Guix https://orcid.org/0000-0002-1588-3198, Miquel Paraira, Belén Galofré, Gloria Sánchez, Rosa M. Pintó https://orcid.org/0000-0003-1382-6648 [email protected], and Albert Bosch https://orcid.org/0000-0002-8111-9059 [email protected]DOI: https://doi.org/10.1128/AEM.02750-20Volume 87, Number 711 March 2021ABSTRACTREFERENCESABSTRACTTwo large wastewater treatment plants (WWTP), covering around 2.7 million inhabitants, which represents around 85% of the metropolitan area of Barcelona, were sampled before, during, and after the implementation of a complete lockdown. Five one-step reverse transcriptase quantitative PCR (RT-qPCR) assays, targeting the polymerase (IP2 and IP4), the envelope (E), and the nucleoprotein (N1 and N2) genome regions, were employed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detection in 24-h composite wastewater samples concentrated by polyethylene glycol (PEG) precipitation. SARS-CoV-2 was detected in a sewage sample collected 41 days ahead of the declaration of the first COVID-19 case. The evolution of SARS-CoV-2 genome copies in wastewater evidenced the validity of water-based epidemiology (WBE) to anticipate COVID-19 outbreaks, to evaluate the impact of control measures, and even to estimate the burden of shedders, including presymptomatic, asymptomatic, symptomatic, and undiagnosed cases. For the latter objective, a model was applied for the estimation of the total number of shedders, evidencing a high proportion of asymptomatic infected individuals. In this way, an infection prevalence of 2.0 to 6.5% was figured. On the other hand, proportions of around 0.12% and 0.09% of the total population were determined to be required for positive detection in the two WWTPs. At the end of the lockdown, SARS-CoV-2 RNA apparently disappeared in the WWTPs but could still be detected in grab samples from four urban sewers. Sewer monitoring allowed for location of specific hot spots of COVID-19, enabling the rapid adoption of appropriate mitigation measures.IMPORTANCE Water-based epidemiology (WBE) is a valuable early warning tool for tracking the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among the population, including not only symptomatic patients but also asymptomatic, presymptomatic, and misdiagnosed carriers, which represent a high proportion of the infected population. In the specific case of Barcelona, wastewater surveillance anticipated by several weeks not only the original COVID-19 pandemic wave but also the onset of the second wave. In addition, SARS-CoV-2 occurrence in wastewater evidenced the efficacy of the adopted lockdown measures on the circulation of the virus. Health authorities profited from WBE to complement other inputs and adopt rapid and adequate measures to mitigate the effects of the pandemic. 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All Rights Reserved.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSSARS-CoV-2COVID-19epidemiologysurveillanceearly warningsewageContributorsAuthorsGemma Chavarria-MiróEnteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorEduard Anfruns-EstradaEnteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorAdán Martínez-VelázquezEnteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorMario Vázquez-PorteroEnteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorSusana Guix https://orcid.org/0000-0002-1588-3198Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorMiquel ParairaAigües de Barcelona, Barcelona, SpainView all articles by this authorBelén GalofréAigües de Barcelona, Barcelona, SpainView all articles by this authorGloria SánchezDepartment of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna, Valencia, SpainView all articles by this authorRosa M. Pintó https://orcid.org/0000-0003-1382-6648 [email protected]Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorAlbert Bosch https://orcid.org/0000-0002-8111-9059 [email protected]Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, SpainInstitute of Nutrition and Food Safety, University of Barcelona, Barcelona, SpainView all articles by this authorEditorChristopher A. ElkinsEditorCenters for Disease Control and PreventionMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleJuly 2021A Bioengineered Nisin Derivative To Control Streptococcus uberis Biofilms Mariana Pérez-Ibarreche, Des Field, R. Paul Rossand Colin HillA Bioengineered Nisin Derivative To Control Streptococcus uberis BiofilmsAuthors: Mariana Pérez-Ibarreche, Des Field [email protected], R. Paul Ross, and Colin Hill https://orcid.org/0000-0002-8527-1445 [email protected]DOI: https://doi.org/10.1128/AEM.00391-21Volume 87, Number 1627 July 2021ABSTRACTREFERENCESABSTRACTAntimicrobial peptides are evolving as novel therapeutic options against the increasing problem of multidrug-resistant microorganisms, and nisin is one such avenue. However, some bacteria possess a specific nisin resistance system (NSR), which cleaves the peptide reducing its bactericidal efficacy. NSR-based resistance was identified in strains of Streptococcus uberis, a ubiquitous pathogen that causes mastitis in dairy cattle. Previous studies have demonstrated that a nisin A derivative termed nisin PV, featuring S29P and I30V, exhibits enhanced resistance to proteolytic cleavage by NSR. Our objective was to investigate the ability of this nisin derivative to eradicate and inhibit biofilms of S. uberis DPC 5344 and S. uberis ATCC 700407 (nsr+) using crystal violet (biomass), 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) (viability) assays, and confocal microscopy (viability and architecture). When preestablished biofilms were assessed, both peptides reduced biofilm biomass by over 60% compared to that of the untreated controls. However, a 42% higher reduction in viability was observed following treatment with nisin PV compared to that of nisin A. Accordingly, confocal microscopy analysis revealed significantly more dead cells on the biofilm upper surface and a reduced thickness following treatment with nisin PV. When biofilm inhibition was assessed, nisin PV inhibited biofilm formation and decreased viability up to 56% and 85% more than nisin A, respectively. Confocal microscopy analysis revealed a lack of biofilm for S. uberis ATCC 700407 and only dead cells for S. uberis DPC 5344. These results suggest that nisin PV is a promising alternative to effectively reduce the biofilm formation of S. uberis strains carrying NSR.IMPORTANCE One of the four most prevalent species of bovine mastitis-causing pathogens is S. uberis. Its ability to form biofilms confers on the bacteria greater resistance to antibiotics, requiring higher doses to be more effective. In a bid to limit antibiotic resistance development, the need for alternative antimicrobials is paramount. Bacteriocins such as nisin represent one such alternative that could alleviate the impact of mastitis caused by S. uberis. However, many strains of S. uberis have been shown to possess nisin resistance determinants, such as the nisin resistance protein (NSR). In this study, we demonstrate the ability of nisin and a nisin derivative termed PV that is insensitive to NSR to prevent and remove biofilms of NSR-producing S. uberis strains. These findings will add new information to the antimicrobial bacteriocins and control of S. uberis research fields specifically in relation to biofilms and nsr+ mastitis-associated strains.REFERENCES1.Dufour S, Labrie J, Jacques M. 2019. The mastitis pathogens culture collection. Microbiol Resour Announc 8:e00133-19.CrossrefPubMedGoogle Scholar2.Guimarães JLB, Brito MAVP, Lange CC, Silva MR, Ribeiro JB, Mendonça LC, Mendonça JFM, Souza GN. 2017. Estimate of the economic impact of mastitis: a case study in a Holstein dairy herd under tropical conditions. 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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSStreptococcus uberisbiofilmsNSRantimicrobial agentsnisin Anisin PVContributorsAuthorsMariana Pérez-IbarrecheAPC Microbiome Ireland, University College Cork, Cork, IrelandView all articles by this authorDes Field [email protected]APC Microbiome Ireland, University College Cork, Cork, IrelandView all articles by this authorR. Paul RossAPC Microbiome Ireland, University College Cork, Cork, IrelandView all articles by this authorColin Hill https://orcid.org/0000-0002-8527-1445 [email protected]APC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Microbiology, University College Cork, Cork, IrelandView all articles by this authorEditorM. Julia PettinariEditorUniversity of Buenos AiresMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleJanuary 2021Airborne Disinfection by Dry Fogging Efficiently Inactivates Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Mycobacteria, and Bacterial Spores and Shows Limitations of Commercial Spore Carriers Jan Schinköthe, Hendrik A. Scheinemann, Sandra Diederich, Holger Freese, Michael Eschbaumer, Jens P. Teifkeand Sven ReicheAirborne Disinfection by Dry Fogging Efficiently Inactivates Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Mycobacteria, and Bacterial Spores and Shows Limitations of Commercial Spore CarriersAuthors: Jan Schinköthe, Hendrik A. Scheinemann https://orcid.org/0000-0002-4275-7672, Sandra Diederich, Holger Freese, Michael Eschbaumer, Jens P. Teifke https://orcid.org/0000-0001-7168-4970, and Sven Reiche https://orcid.org/0000-0001-7575-2483DOI: https://doi.org/10.1128/AEM.02019-20Volume 87, Number 315 January 2021ABSTRACTREFERENCESABSTRACTAirborne disinfection of high-containment facilities before maintenance or between animal studies is crucial. Commercial spore carriers (CSC) coated with 106 spores of Geobacillus stearothermophilus are often used to assess the efficacy of disinfection. We used quantitative carrier testing (QCT) procedures to compare the sensitivity of CSC with that of surrogates for nonenveloped and enveloped viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mycobacteria, and spores, to an aerosolized mixture of peroxyacetic acid and hydrogen peroxide (aPAA-HP). We then used the QCT methodology to determine relevant process parameters to develop and validate effective disinfection protocols (≥4-log10 reduction) in various large and complex facilities. Our results demonstrate that aPAA-HP is a highly efficient procedure for airborne room disinfection. Relevant process parameters such as temperature and relative humidity can be wirelessly monitored. Furthermore, we found striking differences in inactivation efficacies against some of the tested microorganisms. Overall, we conclude that dry fogging a mixture of aPAA-HP is highly effective against a broad range of microorganisms as well as material compatible with relevant concentrations. Furthermore, CSC are artificial bioindicators with lower resistance and thus should not be used for validating airborne disinfection when microorganisms other than viruses have to be inactivated.IMPORTANCE Airborne disinfection is not only of crucial importance for the safe operation of laboratories and animal rooms where infectious agents are handled but also can be used in public health emergencies such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. We show that dry fogging an aerosolized mixture of peroxyacetic acid and hydrogen peroxide (aPAA-HP) is highly microbicidal, efficient, fast, robust, environmentally neutral, and a suitable airborne disinfection method. In addition, the low concentration of dispersed disinfectant, particularly for enveloped viral pathogens such as SARS-CoV-2, entails high material compatibility. For these reasons and due to the relative simplicity of the procedure, it is an ideal disinfection method for hospital wards, ambulances, public conveyances, and indoor community areas. Thus, we conclude that this method is an excellent choice for control of the current SARS-CoV-2 pandemic.REFERENCES1.Ackland NR, Hinton MR, Denmeade KR. 1980. Controlled formaldehyde fumigation system. Appl Environ Microbiol 39:480–487.CrossrefPubMedGoogle Scholar2.Lach VH. 1990. A study of conventional formaldehyde fumigation methods. 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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSairborne disinfectiondry fogroom disinfectionperoxyacetic acidsevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Indiana vesiculovirus (VSIV)murine norovirus (MNV)Mycobacterium senegalenseGeobacillus stearothermophilusBacillus subtilisContributorsAuthorsJan SchinkötheDepartment of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyPresent address: Jan Schinköthe, Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany.View all articles by this authorHendrik A. Scheinemann https://orcid.org/0000-0002-4275-7672Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorSandra DiederichInstitute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorHolger FreeseDepartment of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorMichael EschbaumerInstitute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorJens P. Teifke https://orcid.org/0000-0001-7168-4970Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorSven Reiche https://orcid.org/0000-0001-7575-2483Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, GermanyView all articles by this authorEditorHarold L. DrakeEditorUniversity of BayreuthNotesAddress correspondence to Sven Reiche, [email protected].Jan Schinköthe and Hendrik A. Scheinemann contributed equally to this work. Author order was determined on the basis of seniority in the project.Metrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleJuly 2021Articles of Significant Interest in This IssueArticles of Significant Interest in This IssueDOI: https://doi.org/10.1128/AEM.01182-21Volume 87, Number 1627 July 2021Information ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 87 • Number 16 • 27 July 2021eLocator: e01182-21HistoryPublished online: 27 July 2021Copyright© 2021 American Society for Microbiology. All Rights Reserved.PermissionsRequest permissions for this article.Request PermissionsContributorsMetrics CitationsMetricsCitationsView OptionsMediaFiguresOtherTablesShareApplied and Environmental MicrobiologyArticleMay 2021Saccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant Scale Taylor Reiter, Rachel Montpetit, Shelby Byer, Isadora Frias, Esmeralda Leon, Robert Viano, Michael Mcloughlin, Thomas Halligan, Desmon Hernandez, Ron Runnebaumand Ben MontpetitSaccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant ScaleAuthors: Taylor Reiter https://orcid.org/0000-0002-7388-421X, Rachel Montpetit, Shelby Byer, Isadora Frias, Esmeralda Leon, Robert Viano, Michael Mcloughlin, Thomas Halligan, Desmon Hernandez, Ron Runnebaum, and Ben Montpetit https://orcid.org/0000-0002-8317-983X [email protected]DOI: https://doi.org/10.1128/AEM.00036-21Volume 87, Number 1111 May 2021ABSTRACTREFERENCESABSTRACTSaccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns previously revealed genes that underlie cellular adaptation to the grape must and wine environments, involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage, similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions.IMPORTANCE This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). 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Appl Environ Microbiol 85:e00551-19.CrossrefPubMedGoogle ScholarInformation ContributorsInformationPublished InApplied and Environmental MicrobiologyVolume 87 • Number 11 • 11 May 2021eLocator: e00036-21Editor: Edward G. DudleyThe Pennsylvania State UniversityHistoryReceived: 8 January 2021Accepted: 15 March 2021Published online: 19 March 2021Copyright© 2021 Reiter et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.PermissionsRequest permissions for this article.Request PermissionsKEYWORDSSaccharomyces cerevisiaefermentationgene expressionContributorsAuthorsTaylor Reiter https://orcid.org/0000-0002-7388-421XFood Science Graduate Group, University of California, Davis, Davis, California, USADepartment of Viticulture and Enology, University of California, Davis, Davis, California, USADepartment of Population Health and Reproduction, University of California, Davis, Davis, California, USAView all articles by this authorRachel MontpetitDepartment of Viticulture and Enology, University of California, Davis, Davis, California, USAView all articles by this authorShelby ByerDepartment of Viticulture and Enology, University of California, Davis, Davis, California, USAView all articles by this authorIsadora FriasDepartment of Viticulture and Enology, University of California, Davis, Davis, California, USAView all articles by this authorEsmeralda LeonDepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorRobert VianoDepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorMichael McloughlinDepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorThomas HalliganDepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorDesmon HernandezDepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorRon RunnebaumDepartment of Viticulture and Enology, University of California, Davis, Davis, California, USADepartment of Chemical Engineering, University of California, Davis, Davis, California, USAView all articles by this authorBen Montpetit https://orcid.org/0000-0002-8317-983X [email protected]Food Science Graduate Group, University of California, Davis, Davis, California, USADepartment of Viticulture and Enology, University of California, Davis, Davis, California, USAView all articles by this authorEditorEdward G. 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