Tracy Teal - Academia.edu (original) (raw)

Papers by Tracy Teal

PLOS Biology, 2015

Extremely large datasets have become routine in biology. However, performing a computational anal... more Extremely large datasets have become routine in biology. However, performing a computational analysis of a large dataset can be overwhelming, especially for novices. Here, we present a step-by-step guide to computing workflows with the biologist end-user in mind. Starting from a foundation of sound data management practices, we make specific recommendations on how to approach and perform computational analyses of large datasets, with a view to enabling sound, reproducible biological research.

Microbiome, 2015

The intestinal microbiome represents a complex network of microbes that are important for human h... more The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health. 16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections (n = 200) and 75 healthy family members to identify differences in intestinal community composition. Stools from 13 patients were also examined post-infection to better understand how intestinal communities recover. Patient communities had lower species richness, evenness, and diversity versus uninfected communities, while principle coordinate analysis demonstrated close clustering of uninfected communities, but not the patient communities, irrespective of age, gender, and race. Differences in community composition between patients and family members were mostly...

Environmental Science & Technology, 2015

Ballast water is one of the most important vectors for the transport of non-native species to new... more Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.

International Journal of Digital Curation, 2015

Cold Spring Harbor protocols, 2010

An intrinsic artifact of 454-based pyrosequencing leads to artificial overrepresentation of >1... more An intrinsic artifact of 454-based pyrosequencing leads to artificial overrepresentation of >10% of the original DNA sequencing templates. This artificial amplification of sequences is unbiased with regard to position on the pyrosequencing plate or sequence identity, and it occurs in all currently available 454 technologies. The amplified sequences start at the same position and are identical (duplicates), or vary in length, or contain a sequencing discrepancy. If the abundance of any sequence in a data set is going to be enumerated, either for comparative community analysis, transcriptional analysis or other applications, it is important to remove these artificial replicates before analysis. A web-based tool that incorporates the clustering algorithm cd-hit was developed to identify and remove artificially replicated sequences in 454-based pyrosequencing data sets. This tool cannot be used for data sets that have an initial amplification step before the standard pyrosequencing p...

Lecture Notes in Computer Science, 1999

What permits some systems to evolve and adapt more effectively than others? Gell-Mann [3] has str... more What permits some systems to evolve and adapt more effectively than others? Gell-Mann [3] has stressed the importance of “compression” for adaptive complex systems. Information about the environment is not simply recorded as a look-up table, but is rather compressed ...

ABSTRACT We developed an information retrieval and extraction system that processes the full text... more ABSTRACT We developed an information retrieval and extraction system that processes the full text of biological papers. The system, called Textpresso, separates text into sentences, labels words and phrases according to an ontology (an organized lexicon), and allows queries to be performed on a database of labeled sentences. The current ontology comprises approximately one hundred categories of terms, such as “gene”, “regulation”, “human disease”, “brain area” etc., and also contains main Gene Ontology (GO) categories. Extraction of particular biological facts, such as gene-­gene interactions, or the curation of GO cellular components, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences. Search engine for four literatures, C. elegans, Drosophila, Arabidopsis and Neuroscience have been established by us, and thirteen systems for other literatures have been developed by other groups around the world. Currently, our four systems contain 112,000 papers with 40 million sentences, all systems worldwide contain 190,000 papers with approximately 65 million sentences. @InProceedings{mueller_et_al:DSP:2008:1516, author = {Hans-Michael Mueller and Arun Rangarajan and Tracy K. Teal and Kimberly van Auken and Juancarlos Chan and Paul W. Sternberg}, title = {Textpresso - an Information Retrieval and Extraction System for Biological Literature}, booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives}, year = {2008}, editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann}, number = {08131}, series = {Dagstuhl Seminar Proceedings}, ISSN = {1862-4405}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany}, address = {Dagstuhl, Germany}, URL = {http://drops.dagstuhl.de/opus/volltexte/2008/1516}, annote = {Keywords: Information retrieval, literature search engine, information extraction, automated literature curation, semantic search, ontology,} }

The ISME Journal, 2011

Agriculture has marked impacts on the production of carbon dioxide (CO 2 ) and consumption of met... more Agriculture has marked impacts on the production of carbon dioxide (CO 2 ) and consumption of methane (CH 4 ) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH 4 . To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH 4 -oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH 4 and CO 2 at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH 4 consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH 4 consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH 4 consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO 2 emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH 4 oxidation, as compared with processes driven by widely distributed metabolic processes, like CO 2 production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

The ISME Journal, 2009

Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential a... more Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts.

Proceedings of the National Academy of Sciences, 2014

Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global p... more Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands-farmland suboptimal for food cropscould help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks-primarily annual grain crops-on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, and bird diversity than maize. Although biomass production was greater in maize, all other ecosystem services, including methane consumption, pest suppression, pollination, and conservation of grassland birds, were higher in perennial grasslands. Moreover, we found that the linkage between biodiversity and ecosystem services is dependent not only on the choice of bioenergy crop but also on its location relative to other habitats, with local landscape context as important as crop choice in determining provision of some services. Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services. energy policy | greenhouse gas mitigation I n agricultural landscapes, balancing the provisioning of food and energy with maintenance of biodiversity and ecosystem functions is a global challenge. To avoid impacts on food production, attention is increasingly being focused on the potential for marginal lands to support bioenergy production (1). Marginal lands, those suboptimal for food production, may consist of relatively small areas within generally productive landscapes or larger regions where conditions generally limit crop productivity. However, there is increasing recognition that these lands are already performing a variety of useful functions, and their conversion to bioenergy cropping could reduce these services. For example, in the north central United States, rising commodity prices are predicted to bring marginal croplands-including Conservation Reserve Program lands-into annual crop production with negative impacts on wildlife habitat and water quality (2, 3). With 2013 corn plantings at recent record highs (4) and new reports of grassland and wetland conversion to cropland (5, 6), this may be occurring already.

Neuroinformatics, 2008

Textpresso is a text-mining system for scientific literature. Its two major features are access t... more Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www. textpresso.org/neuroscience/.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2004

Artificial Life, 2000

For many adaptive complex systems information about the environment is not simply recorded in a l... more For many adaptive complex systems information about the environment is not simply recorded in a look-up table, but is rather encoded in a theory, schema, or model, which compresses information. The grammar of a language can be viewed as such a schema or theory. In a prior study [Teal et al., 1999] we proposed several conjectures about the learning and evolution of language that should follow from these observations: (C1) compression aids in generalization; (C2) compression occurs more easily in a "smooth," as opposed to a "rugged," problem space: and (C3) constraints from compression make it likely that natural languages evolve towards smooth string spaces. This previous work found general, if not complete support for these three conjectures. Here we build on that study to clarify the relationship between Minimum Description Length (MDL) and error in our model and examine evolution of certain languages in more detail. Our results suggest a fourth conjecture: that all else being equal, (C4) more complex languages change more rapidly during evolution.

Applied and Environmental Microbiology, 2006

Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the env... more Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. An alternative hypothesis is that within the growth-inactive domains of biofilms, significant populations of living cells persist and retain the capacity to dynamically regulate their metabolism. To test this, we employed unstable fluorescent reporters to measure growth activity and protein synthesis in vivo over the course of biofilm development and created a quantitative routine to compare domains of activity in independently grown biofilms. Here we report that Shewanella oneidensis biofilm structures reproducibly stratify with respect to growth activity and metabolism as a function of size. Within domains of growth-inactive cells, genes typically upregulated under anaerobic conditions are expressed well after growth has ceased. These findings reveal that, far from being dead, the majority of cells in mature S. oneidensis biofilms have actively turned-on metabolic programs appropriate to their local microenvironment and developmental stage.

Artificial Life, 2001

The Editors of Artificial Life would like to express their deep gratitude to the people listed be... more The Editors of Artificial Life would like to express their deep gratitude to the people listed below, who anonymously refereed papers for the journal during the preparation of this volume (Vol. 7). Their generosity, judicious judgment, and prompt response substantially helped us to publish a journal that both is timely and has exacting scientific standards. The responsibility for sustaining the quality and relevance of the journal largely rests in the hands of our reviewers. We as editors, and all of our readers, are deeply indebted to them. ...

PLOS Biology, 2015

Extremely large datasets have become routine in biology. However, performing a computational anal... more Extremely large datasets have become routine in biology. However, performing a computational analysis of a large dataset can be overwhelming, especially for novices. Here, we present a step-by-step guide to computing workflows with the biologist end-user in mind. Starting from a foundation of sound data management practices, we make specific recommendations on how to approach and perform computational analyses of large datasets, with a view to enabling sound, reproducible biological research.

Microbiome, 2015

The intestinal microbiome represents a complex network of microbes that are important for human h... more The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health. 16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections (n = 200) and 75 healthy family members to identify differences in intestinal community composition. Stools from 13 patients were also examined post-infection to better understand how intestinal communities recover. Patient communities had lower species richness, evenness, and diversity versus uninfected communities, while principle coordinate analysis demonstrated close clustering of uninfected communities, but not the patient communities, irrespective of age, gender, and race. Differences in community composition between patients and family members were mostly...

Environmental Science & Technology, 2015

Ballast water is one of the most important vectors for the transport of non-native species to new... more Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.

International Journal of Digital Curation, 2015

Cold Spring Harbor protocols, 2010

An intrinsic artifact of 454-based pyrosequencing leads to artificial overrepresentation of >1... more An intrinsic artifact of 454-based pyrosequencing leads to artificial overrepresentation of >10% of the original DNA sequencing templates. This artificial amplification of sequences is unbiased with regard to position on the pyrosequencing plate or sequence identity, and it occurs in all currently available 454 technologies. The amplified sequences start at the same position and are identical (duplicates), or vary in length, or contain a sequencing discrepancy. If the abundance of any sequence in a data set is going to be enumerated, either for comparative community analysis, transcriptional analysis or other applications, it is important to remove these artificial replicates before analysis. A web-based tool that incorporates the clustering algorithm cd-hit was developed to identify and remove artificially replicated sequences in 454-based pyrosequencing data sets. This tool cannot be used for data sets that have an initial amplification step before the standard pyrosequencing p...

Lecture Notes in Computer Science, 1999

What permits some systems to evolve and adapt more effectively than others? Gell-Mann [3] has str... more What permits some systems to evolve and adapt more effectively than others? Gell-Mann [3] has stressed the importance of “compression” for adaptive complex systems. Information about the environment is not simply recorded as a look-up table, but is rather compressed ...

ABSTRACT We developed an information retrieval and extraction system that processes the full text... more ABSTRACT We developed an information retrieval and extraction system that processes the full text of biological papers. The system, called Textpresso, separates text into sentences, labels words and phrases according to an ontology (an organized lexicon), and allows queries to be performed on a database of labeled sentences. The current ontology comprises approximately one hundred categories of terms, such as “gene”, “regulation”, “human disease”, “brain area” etc., and also contains main Gene Ontology (GO) categories. Extraction of particular biological facts, such as gene-­gene interactions, or the curation of GO cellular components, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences. Search engine for four literatures, C. elegans, Drosophila, Arabidopsis and Neuroscience have been established by us, and thirteen systems for other literatures have been developed by other groups around the world. Currently, our four systems contain 112,000 papers with 40 million sentences, all systems worldwide contain 190,000 papers with approximately 65 million sentences. @InProceedings{mueller_et_al:DSP:2008:1516, author = {Hans-Michael Mueller and Arun Rangarajan and Tracy K. Teal and Kimberly van Auken and Juancarlos Chan and Paul W. Sternberg}, title = {Textpresso - an Information Retrieval and Extraction System for Biological Literature}, booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives}, year = {2008}, editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann}, number = {08131}, series = {Dagstuhl Seminar Proceedings}, ISSN = {1862-4405}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany}, address = {Dagstuhl, Germany}, URL = {http://drops.dagstuhl.de/opus/volltexte/2008/1516}, annote = {Keywords: Information retrieval, literature search engine, information extraction, automated literature curation, semantic search, ontology,} }

The ISME Journal, 2011

Agriculture has marked impacts on the production of carbon dioxide (CO 2 ) and consumption of met... more Agriculture has marked impacts on the production of carbon dioxide (CO 2 ) and consumption of methane (CH 4 ) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH 4 . To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH 4 -oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH 4 and CO 2 at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH 4 consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH 4 consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH 4 consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO 2 emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH 4 oxidation, as compared with processes driven by widely distributed metabolic processes, like CO 2 production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

The ISME Journal, 2009

Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential a... more Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts.

Proceedings of the National Academy of Sciences, 2014

Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global p... more Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands-farmland suboptimal for food cropscould help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks-primarily annual grain crops-on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, and bird diversity than maize. Although biomass production was greater in maize, all other ecosystem services, including methane consumption, pest suppression, pollination, and conservation of grassland birds, were higher in perennial grasslands. Moreover, we found that the linkage between biodiversity and ecosystem services is dependent not only on the choice of bioenergy crop but also on its location relative to other habitats, with local landscape context as important as crop choice in determining provision of some services. Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services. energy policy | greenhouse gas mitigation I n agricultural landscapes, balancing the provisioning of food and energy with maintenance of biodiversity and ecosystem functions is a global challenge. To avoid impacts on food production, attention is increasingly being focused on the potential for marginal lands to support bioenergy production (1). Marginal lands, those suboptimal for food production, may consist of relatively small areas within generally productive landscapes or larger regions where conditions generally limit crop productivity. However, there is increasing recognition that these lands are already performing a variety of useful functions, and their conversion to bioenergy cropping could reduce these services. For example, in the north central United States, rising commodity prices are predicted to bring marginal croplands-including Conservation Reserve Program lands-into annual crop production with negative impacts on wildlife habitat and water quality (2, 3). With 2013 corn plantings at recent record highs (4) and new reports of grassland and wetland conversion to cropland (5, 6), this may be occurring already.

Neuroinformatics, 2008

Textpresso is a text-mining system for scientific literature. Its two major features are access t... more Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www. textpresso.org/neuroscience/.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2004

Artificial Life, 2000

For many adaptive complex systems information about the environment is not simply recorded in a l... more For many adaptive complex systems information about the environment is not simply recorded in a look-up table, but is rather encoded in a theory, schema, or model, which compresses information. The grammar of a language can be viewed as such a schema or theory. In a prior study [Teal et al., 1999] we proposed several conjectures about the learning and evolution of language that should follow from these observations: (C1) compression aids in generalization; (C2) compression occurs more easily in a "smooth," as opposed to a "rugged," problem space: and (C3) constraints from compression make it likely that natural languages evolve towards smooth string spaces. This previous work found general, if not complete support for these three conjectures. Here we build on that study to clarify the relationship between Minimum Description Length (MDL) and error in our model and examine evolution of certain languages in more detail. Our results suggest a fourth conjecture: that all else being equal, (C4) more complex languages change more rapidly during evolution.

Applied and Environmental Microbiology, 2006

Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the env... more Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. An alternative hypothesis is that within the growth-inactive domains of biofilms, significant populations of living cells persist and retain the capacity to dynamically regulate their metabolism. To test this, we employed unstable fluorescent reporters to measure growth activity and protein synthesis in vivo over the course of biofilm development and created a quantitative routine to compare domains of activity in independently grown biofilms. Here we report that Shewanella oneidensis biofilm structures reproducibly stratify with respect to growth activity and metabolism as a function of size. Within domains of growth-inactive cells, genes typically upregulated under anaerobic conditions are expressed well after growth has ceased. These findings reveal that, far from being dead, the majority of cells in mature S. oneidensis biofilms have actively turned-on metabolic programs appropriate to their local microenvironment and developmental stage.

Artificial Life, 2001

The Editors of Artificial Life would like to express their deep gratitude to the people listed be... more The Editors of Artificial Life would like to express their deep gratitude to the people listed below, who anonymously refereed papers for the journal during the preparation of this volume (Vol. 7). Their generosity, judicious judgment, and prompt response substantially helped us to publish a journal that both is timely and has exacting scientific standards. The responsibility for sustaining the quality and relevance of the journal largely rests in the hands of our reviewers. We as editors, and all of our readers, are deeply indebted to them. ...