[ { "id": "authors:5hcmg-zsr04", "collection": "authors", "collection_id": "5hcmg-zsr04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170518-163637436", "type": "book_section", "title": "Molecular Methods in Geomicrobiology", "book_title": "Ehrlich's Geomicrobiology, Sixth Edition", "author": [ { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Ehrlich", "given_name": "Henry Lutz", "clpid": "Ehrlich-H-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "clpid": "Newman-D-K" }, { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" } ], "abstract": "In addition to the techniques described in Chapter 8, molecular tools have become increasingly important in the study of the presence, activity, and mechanisms of catalysis by geomicrobial organisms. Today, various molecules (deoxyribonucleic acid [DNA], ribonucleic acid [RNA], protein, and lipids) are used to detect specific geomicrobial agents in situ and make inferences about their metabolic activity. DNA sequencing has become routine, expanding our appreciation of the genetic potential of uncultivated organisms and complex natural communities from the environment. Isotope labeling approaches allow us to measure metabolic activity more directly and to specifically link organisms with geochemical fluxes. Finally, the application of molecular genetic, cell biological, and biochemical techniques to study the genes and gene products that catalyze geochemically significant reactions is unraveling the mechanisms underlying these processes. Together, these molecular approaches provide a window into the interactions between microorganisms and their geochemical environment and enable predictions about how these geomicrobial processes may be altered in response to environmental perturbations.", "doi": "10.1201/b19121-10", "isbn": "9781466592407", "publisher": "CRC Press", "place_of_publication": "Boca Raton, FL", "publication_date": "2015-10", "pages": "187-207" }, { "id": "authors:m0f29-kqv05", "collection": "authors", "collection_id": "m0f29-kqv05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170518-165224584", "type": "book_section", "title": "Extraction and Measurement of NAD(P)+ and NAD(P)H", "book_title": "Pseudomonas Methods and Protocols", "author": [ { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Filloux", "given_name": "Alain", "clpid": "Filloux-A" }, { "family_name": "Ramos", "given_name": "Juan-Luis", "clpid": "Ramos-J-L" } ], "abstract": "Nicotinamide adenine dinucleotides are critical redox-active substrates for countless catabolic and anabolic reactions. Ratios of NAD+ to NADH and NADP+ to NADPH are therefore considered key indicators of the overall intracellular redox potential and metabolic state. These ratios can be measured in bulk conditions using a highly sensitive enzyme cycling-based colorimetric assay (detection limit at or below 0.05 \u03bcM or 1 pmol) following a simple extraction procedure involving solutions of acid and base. Special considerations are necessary to avoid measurement artifacts caused by the presence of endogenous redox-active metabolites, such as phenazines made by diverse Pseudomonas species (see Chapter 25).", "doi": "10.1007/978-1-4939-0473-0_26", "isbn": "9781493904723", "publisher": "Humana Press", "place_of_publication": "New York, NY", "publication_date": "2014-06-04", "pages": "311-323" }, { "id": "authors:6c0bf-d7z50", "collection": "authors", "collection_id": "6c0bf-d7z50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170522-090349682", "type": "book_section", "title": "Measurement of Phenazines in Bacterial Cultures", "book_title": "Pseudomonas Methods and Protocols", "author": [ { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Filloux", "given_name": "Alain", "clpid": "Filloux-A" }, { "family_name": "Ramos", "given_name": "Juan-Luis", "clpid": "Ramos-J-L" } ], "abstract": "Certain pseudomonads are capable of producing phenazines\u2014pigmented, reversibly redox-active metabolites that induce a variety of physiological effects on the producing organism as well as others in their vicinity. Environmental conditions and the specific physiological state of cells can dramatically affect the absolute amounts and relative proportions of the various phenazines produced. The method detailed here\u2014high-performance liquid chromatography coupled to detection by UV\u2013Vis absorption\u2014can be used to separate and quantify the amount of phenazines in a Pseudomonas culture. Simple spectrophotometric measurements of filtered culture supernatants can be used to quantify certain oxidized phenazines, such as pyocyanin, in cultures. For cases where the conditions under study are not planktonic cultures (e.g., soil or biofilms) extracting the phenazines may be a necessary first step.", "doi": "10.1007/978-1-4939-0473-0_25", "isbn": "9781493904723", "publisher": "Springer", "place_of_publication": "New York", "publication_date": "2014-03-29", "pages": "303-310" }, { "id": "authors:vth3k-1d892", "collection": "authors", "collection_id": "vth3k-1d892", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180516-113554814", "type": "book_section", "title": "The Yin and Yang of Phenazine Physiology", "book_title": "Microbial Phenazines: Biosynthesis, Agriculture and Health", "author": [ { "family_name": "Grahl", "given_name": "Nora", "clpid": "Grahl-N" }, { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Hogan", "given_name": "Deborah A.", "orcid": "0000-0002-6366-2971", "clpid": "Hogan-D-A" } ], "contributor": [ { "family_name": "Chincholkar", "given_name": "Sudhir", "clpid": "Chincholkar-S" }, { "family_name": "Thomashow", "given_name": "Linda", "clpid": "Thomashow-L" } ], "abstract": "Microorganisms are seldom solitary. They are surrounded by both clonal cells and other members of the local microbial community, and they often exist in, on, or in close proximity to multi-cellular host organisms like plants and humans. Whether in vivo during infection or in situ in the nutrient rich rhizosphere, microorganisms affect each other and the host. Phenazines, a class of secondary metabolites secreted by diverse bacteria, are best known for their antibiotic properties and have been shown to affect a broad spectrum of organisms ranging from bacteria over fungi, plants, nematodes, parasites, and humans. However, phenazines are also involved in numerous aspects of bacterial physiology like survival, iron acquisition, signaling, and biofilm formation in ways that have the potential to increase the fitness of both the phenazine-producing strain and non-producers alike. The overarching theme of this chapter is that phenazines can be beneficial or detrimental to organisms, depending on the milieu and one's perspective. In this chapter, we will highlight specific examples to discuss the yin and yang of phenazine physiology.", "doi": "10.1007/978-3-642-40573-0_3", "isbn": "9783642405730", "publisher": "Springer", "place_of_publication": "Berlin", "publication_date": "2013-12-06", "pages": "43-69" }, { "id": "authors:vkdjt-py709", "collection": "authors", "collection_id": "vkdjt-py709", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130410-131113193", "type": "book_section", "title": "In Pursuit of Billion-Year-Old Rosetta Stones", "book_title": "Microbes and Evolution: The World That Darwin Never Saw", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Kolter", "given_name": "Roberto", "clpid": "Kolter-R" }, { "family_name": "Maloy", "given_name": "Stanley R.", "clpid": "Maloy-S-R" } ], "abstract": "If I have learned anything about evolution, it is that the path life takes moves in mysterious ways. If someone had told me 20 years ago that I would wind up a professor of geobiology, I would have laughed. It certainly wasn't something I aspired to in college, where, as a German studies major, I didn't take a single biology class and took only one geology class. I didn't even know that\ngeobiology existed as a discipline at the time!", "doi": "10.1128/9781555818470.ch29", "isbn": "978-1-55581-540-0", "publisher": "ASM Press", "place_of_publication": "Washington, DC", "publication_date": "2012", "pages": "209-215" }, { "id": "authors:n7g2e-cr643", "collection": "authors", "collection_id": "n7g2e-cr643", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121106-134254144", "type": "book_section", "title": "Molecular biology's contributions to geobiology", "book_title": "Fundamentals of Geobiology", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Reysenbach", "given_name": "Anna-Louise", "clpid": "Reysenbach-A-L" } ], "contributor": [ { "family_name": "Knoll", "given_name": "Andrew H.", "clpid": "Knoll-A-H" }, { "family_name": "Canfield", "given_name": "Donald E.", "clpid": "Canfield-D-E" }, { "family_name": "Konhauser", "given_name": "Kurt O.", "clpid": "Konhauser-K-O" } ], "abstract": "On August 7, 1996, US President Bill Clinton held a press conference to announce the possibility that the Allan Hills 84001 meteorite might provide insight into ancient life on Mars. With soaring rhetoric, he declared: 'Today, rock 84001 speaks to us across all those billions of years and millions of miles. It speaks of the possibility of life. If this discovery is confirmed, it will surely be one of the most stunning insights into our universe that science has ever uncovered. Its implications are as far-reaching and awe-inspiring as can be imagined. Even as it promises answers to some of our oldest questions, it poses still others even more fundamental.' Shortly thereafter, NASA expanded its support for astro-and geobiological research, which marked the beginning of a renaissance in geobiology. Seemingly overnight, geobiology was transformed from a somewhat arcane discipline to a glamorous field that promised to reveal the secrets of life. While today, most geobiologists would agree that the evidence for past life in AH84001 is inconclusive at best, and find the hype surrounding its discovery to be comical, nonetheless, the excitement it engendered has had a long-lasting and positive impact on our science. The enduring consequence of Clinton's press conference was that it called attention to the fact that life has been leaving signatures in its environment (be it earthly or extraterrestrial) for billions of years. In the years following the meteorite's discovery, it has become clear that to understand life's traces and-more importantly---effects on its environment, it is necessary to understand how life leaves its imprint and whether this can be distinguished from similar imprints left by abiotic processes. This is a central challenge in geobiology.", "isbn": "9781118280812", "publisher": "Wiley-Blackwell", "place_of_publication": "Hoboken, NJ", "publication_date": "2012", "pages": "228-249" }, { "id": "authors:mnn0f-zaw48", "collection": "authors", "collection_id": "mnn0f-zaw48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130403-084205757", "type": "book_section", "title": "From Geocycles to Genomes and Back", "book_title": "Microbial metal and metalloid metabolism: advances and applications", "author": [ { "family_name": "Bose", "given_name": "Arpita", "clpid": "Bose-A" }, { "family_name": "Kopf", "given_name": "Sebastian", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Stolz", "given_name": "John F.", "clpid": "Stolz-J-F" }, { "family_name": "Oremland", "given_name": "Ronald S.", "clpid": "Oremland-R-S" } ], "abstract": "A holy grail for environmental microbiologists\nis being able to predict the effects of any given\nmicrobial community on a particular environment.\nIn an era of increasingly dramatic\nchanges in global climate, this goal is becoming\nevermore important. It is now well accepted\nthat microorganisms have had and continue\nto have a profound influence on shaping the\nchemistry of the Earth. It would thus be both\nintellectually satisfying and practically useful if\nwe could enumerate the microbial players in a\nspecific locale, and, knowing their metabolic\npotential and how they regulate their various\nmetabolisms, make predictions about how\ntheir presence would shape the geochemistry\nof that locale as it evolves in time.", "isbn": "9781613444030", "publisher": "ASM Press", "place_of_publication": "Washington, D.C.", "publication_date": "2011", "pages": "13-38" }, { "id": "authors:m6esb-zcw51", "collection": "authors", "collection_id": "m6esb-zcw51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-074631357", "type": "book_section", "title": "What Genetics Offers Geobiology", "book_title": "Molecular Geomicrobiology", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" } ], "contributor": [ { "family_name": "Banfield", "given_name": "Jillian F.", "clpid": "Banfield-J-F" }, { "family_name": "Cervini-Silva", "given_name": "Javiera", "clpid": "Cervini-Silva-J" }, { "family_name": "Nealson", "given_name": "Kenneth H.", "clpid": "Nealson-K-H" } ], "abstract": "For over 50 years, the Parker Brothers' board game \"Clue\" has maintained its position as the classic family detective game. A murder has been committed in the mansion, but we don't know where, by whom, or how. Was it Professor Plum in the study with a knife, or Miss Scarlett in the ballroom with a candlestick? Through rolls of the dice, fragments of information patiently accumulated piece-by-piece, and the application of logic, players construct a case to figure out \"whodunit\". Because there are several potential solutions to the problem, the key challenge is to figure out what happened by understanding how it happened.", "doi": "10.2138/rmg.2005.59.2", "isbn": "9780939950713", "publisher": "Mineralogical Society of America", "place_of_publication": "Chantilly, VA", "publication_date": "2005", "pages": "9-26" }, { "id": "authors:rymn1-w2g21", "collection": "authors", "collection_id": "rymn1-w2g21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130502-115233969", "type": "book_section", "title": "Isotopic Constraints on Biogeochemical Cycling of Fe", "book_title": "Geochemistry of Non-Traditional Stable Isotopes", "author": [ { "family_name": "Johnson", "given_name": "Clark M.", "clpid": "Johnson-C-M" }, { "family_name": "Beard", "given_name": "Brian L.", "clpid": "Beard-B-L" }, { "family_name": "Roden", "given_name": "Eric E.", "clpid": "Roden-E-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Nealson", "given_name": "Kenneth H.", "orcid": "0000-0001-5189-3732", "clpid": "Nealson-K-H" } ], "contributor": [ { "family_name": "Johnson", "given_name": "Clark M.", "clpid": "Johnson-C-M" }, { "family_name": "Beard", "given_name": "Brian L.", "clpid": "Beard-B-L" }, { "family_name": "Albar\u00e8de", "given_name": "Francis", "clpid": "Albar\u00e8de-F" } ], "abstract": "Cycling of redox-sensitive elements such as Fe is affected by not only ambient Eh-pH conditions, but also by a significant biomass that may derive energy through changes in redox state (e.g., Nealson 1983; Lovely et al. 1987; Myers and Nealson 1988; Ghiorse 1989). The evidence now seems overwhelming that biological processing of redox-sensitive metals is likely to be the rule in surface- and near-surface environments, rather than the exception. The Fe redox cycle of the Earth fundamentally begins with tectonic processes, where \"juvenile\" crust (high-temperature metamorphic and igneous rocks) that contains Fe which is largely in the divalent state is continuously exposed on the surface. If the surface is oxidizing, which is likely for the Earth over at least the last two billion years (e.g., Holland 1984), exposure of large quantities of Fe(II) at the surface represents a tremendous redox disequilibrium. Oxidation of Fe(II) early in Earth's history may have occurred through increases in ambient O2 contents through photosynthesis (e.g., Cloud 1965, 1968), UV-photo oxidation (e.g., Braterman and Cairns-Smith 1987), or anaerobic photosynthetic Fe(II) oxidation (e.g., Hartman 1984; Widdel et al. 1993; Ehrenreich and Widdel 1994). Iron oxides produced by oxidation of Fe(II) represent an important sink for Fe released by terrestrial weathering processes, which will generally be quite reactive. In turn, dissimilatory microbial reduction of ferric oxides, coupled to oxidation of organic carbon and/or H2, is an important process by which Fe(III) is reduced in both modern and ancient sedimentary environments (Lovley 1991; Nealson and Saffarini 1994). Recent microbiological evidence (Vargas et al. 1998), together with a wealth of geochemical information, suggests that microbial Fe(III) reduction may have been one of the earliest forms of respiration on Earth. It therefore seems inescapable that biological redox cycling of Fe has occurred for at least several billion years of Earth's history.", "doi": "10.2138/gsrmg.55.1.359", "isbn": "0-939950-67-7", "publisher": "Mineralogical Society of America", "place_of_publication": "Washington, DC", "publication_date": "2004-01", "pages": "359-408" }, { "id": "authors:k2req-pky63", "collection": "authors", "collection_id": "k2req-pky63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130326-102905673", "type": "book_section", "title": "Planar Array REDOX Cells and pH Sensors for ISS Water Quality and Microbe Detection", "author": [ { "family_name": "Buehler", "given_name": "Martin G.", "clpid": "Buehler-M-G" }, { "family_name": "Kuhlman", "given_name": "Gregory M.", "clpid": "Kuhlman-G-M" }, { "family_name": "Myung", "given_name": "Nosang V.", "clpid": "Myung-N-V" }, { "family_name": "Keymeulen", "given_name": "Didier", "clpid": "Keymeulen-D" }, { "family_name": "Kounaves", "given_name": "Samuel P.", "clpid": "Kounaves-S-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Lies", "given_name": "Douglas", "clpid": "Lies-D-P" } ], "abstract": "This paper describes results acquired from E-Tongue 2 and E-Tongue 3 which are arrays of planar three-element electrochemical cells and pH sensors. The approach uses ASV (Anodic Stripping Voltammery) to achieve a detection limit, which in the case of Pb, is below one \u03bcM which is needed for water quality measurements. The richness of the detectable species is illustrated with Fe where seven species are identified using the Pourbiax diagram. The detection of multiple species is illustrated using Pb and Cu. The apparatus was used to detect the electroactivity of the metabolic-surrogate, PMS (phenazine-methosulphate). Finally, four types of pH sensors were fabricated and characterized for linearity, sensitivity, and responsiveness.", "doi": "10.4271/2003-01-2553", "publisher": "SAE", "publication_date": "2003-07-07" }, { "id": "authors:b2erc-exn07", "collection": "authors", "collection_id": "b2erc-exn07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-123845559", "type": "book_section", "title": "Bacterial Respiration of Arsenate and Its Significance in the Environment", "book_title": "Environmental Chemistry of Arsenic", "author": [ { "family_name": "Oremland", "given_name": "Ronald S.", "clpid": "Oremland-R-S" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kail", "given_name": "Brian W.", "clpid": "Kail-B-W" }, { "family_name": "Stolz", "given_name": "John F.", "clpid": "Stolz-J-F" } ], "contributor": [ { "family_name": "Frankenberger", "given_name": "William T.", "clpid": "Frankenberger-W-T" } ], "abstract": "Although arsenic is a trace element in terms of its natural abundance, it nonetheless\nhas a common presence within the earth's crust. Because it is classified as a\ngroup VB element in the periodic table, it shares many chemical and biochemical\nproperties in common with its neighbors phosphorus and nitrogen. Indeed, in the\ncase of this element's most oxidized (+5) oxidation state, arsenate [HAsO_4^(2-) or\nAs (V)], its toxicity is based on its action as an analog of phosphate. Hence,\narsenate ions uncouple the oxidative phosphorylation normally associated with\nthe enzyme glyceraldehyde 3-phosphate dehydrogenase, thereby preventing the\nformation ofphosphoglyceroyl phosphate, a key high-energy intermediate in glycolysis.\nTo guard against this, a number of bacteria possess a detoxifying arsenate\nreductase pathway (the arsC system) whereby cytoplasmic enzymes remove internal\npools of arsenate by achieving its reduction to arsenite [H_2AsO_3- or As\n(III)]. However, because the arsenite product binds with internal sulfhydryl\ngroups that render it even more toxic than the original arsenate, efficient arsenite\nefflux from the cell is also required and is achieved by an active ion ''pumping'' system (1). The details of this bacterial arsenic detoxification phenomenon have\nbeen well established in the literature, and Chapter 10 in this volume provided\na thorough review. Here, we discuss bacterial respiration of arsenate and its significance\nin the environment. As a biological phenomenon, respiratory growth\non arsenate is quite remarkable, given the toxicity of the element. Moreover, the\nconsequences of microbial arsenate respiration may, at times, have a significant\nimpact on environmental chemistry.", "isbn": "9780824706760", "publisher": "Marcel Dekker", "place_of_publication": "New York", "publication_date": "2002", "pages": "273-295" }, { "id": "authors:gwj0x-nb211", "collection": "authors", "collection_id": "gwj0x-nb211", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130722-145408915", "type": "book_section", "title": "Arsenic", "book_title": "Encyclopedia of Microbiology, 2nd edition", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Lederberg", "given_name": "Joshua", "clpid": "Lederberg-J" } ], "abstract": "Arsenic is relatively abundant in the biosphere\nowing to contamination from a variety of anthropogenic\nsources in addition to its natural occurrence in\nminerals. Since the industrial revolution, arsenic has\nbeen discharged into waterways as a waste product\nof sulfuric acid manufacturing, sprayed onto soils as\na pesticide, dispersed into the air during ore smelting,\nand distributed over the Earth through mining activities.\nAlthough human activities are estimated to release 50,000 tons of arsenic per year, simple weathering\nof igneous and sedimentary rocks (including coal)\nnaturally releases nearly an equal amount of arsenic\ninto the environment. The geochemical cycle of arsenic\nis controlled by a variety of chemical reactions, including\noxidation-reduction, precipitation-dissolution,\nadsorption-desorption, and methylation. Strong evidence\nexists that microorganisms play an important\nrole in these reactions. This article will focus primarily\non the microbial contributions to the cycling of inorganic\narsenic.", "isbn": "9780122268007", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "2000", "pages": "332-338" }, { "id": "authors:vgfvv-j4756", "collection": "authors", "collection_id": "vgfvv-j4756", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130506-152623748", "type": "book_section", "title": "Genetic approaches to study of biofilms", "book_title": "Biofilms", "author": [ { "family_name": "O'Toole", "given_name": "George A.", "clpid": "O'Toole-G-A" }, { "family_name": "Pratt", "given_name": "Leslie A.", "clpid": "Pratt-L-A" }, { "family_name": "Watnick", "given_name": "Paula I.", "clpid": "Watnick-P-I" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Weaver", "given_name": "Valerie B.", "clpid": "Weaver-V-B" }, { "family_name": "Kolter", "given_name": "Roberto", "clpid": "Kolter-R" } ], "contributor": [ { "family_name": "Doyle", "given_name": "Ronald J.", "clpid": "Doyle-R-J" } ], "abstract": "Interest in the study of microbial biofilms has increased greatly in recent\nyears due in large part to the profound impact biofilms have in clinical,\nindustrial, and natural settings. Traditionally, the study of biofilms has\nbeen approached from an ecological or engineering perspective, using a\ncombination of classical microbiology and advanced microscopy. We and\nothers have begun to use genetic approaches to understand the development\nof these complex communities. To begin we must answer the question:\nWhat is a biofilm? This definition, by necessity, may be quite broad because\nit is clear that many organisms can attach to a variety of surfaces under\ndiverse environmental conditions. Therefore, in the context of this article\nwe will operationally define a biofilm as bacteria that are attached to a\nsurface in sufficient numbers to be detected macroscopically.", "doi": "10.1016/S0076-6879(99)10008-9", "isbn": "9780121822118", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1999", "pages": "91-109" } ]