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Featured researches published by Elizabeth A. Dinsdale.


Nature | 2008

Functional metagenomic profiling of nine biomes

Elizabeth A. Dinsdale; Robert Edwards; Dana Hall; Florent E. Angly; Mya Breitbart; Mike Furlan; Christelle Desnues; Matthew Haynes; Linlin Li; Lauren D. McDaniel; Mary Ann Moran; Karen E. Nelson; Christina Nilsson; Robert Olson; John H. Paul; Beltran Rodriguez Brito; Yijun Ruan; Brandon K. Swan; Rick Stevens; David L. Valentine; Rebecca Vega Thurber; Linda Wegley; Bryan A. White; Forest Rohwer

Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.


PLOS ONE | 2008

Baselines and degradation of coral reefs in the Northern Line Islands.

Stuart A. Sandin; Jennifer E. Smith; Edward E. DeMartini; Elizabeth A. Dinsdale; Simon D. Donner; Alan M. Friedlander; Talina Konotchick; Machel Malay; James E. Maragos; David Obura; Olga Pantos; Gustav Paulay; Morgan Richie; Forest Rohwer; Robert E. Schroeder; Sheila M. Walsh; Jeremy B. C. Jackson; Nancy Knowlton; Enric Sala

Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.


Proceedings of the National Academy of Sciences of the United States of America | 2009

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Dionysios A. Antonopoulos; Margret E. Berg Miller; Melissa K. Wilson; Anthony C. Yannarell; Elizabeth A. Dinsdale; Robert E. Edwards; Edward D. Frank; Joanne B. Emerson; Pirjo Wacklin; Pedro M. Coutinho; Bernard Henrissat; Karen E. Nelson; Bryan A. White

The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).


Environmental Microbiology | 2009

Metagenomic analysis of stressed coral holobionts.

Rebecca Vega Thurber; Dana Willner-Hall; Beltran Rodriguez-Mueller; Christelle Desnues; Robert Edwards; Florent E. Angly; Elizabeth A. Dinsdale; Linda Wegley Kelly; Forest Rohwer

The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic samples were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.


PLOS ONE | 2008

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Elizabeth A. Dinsdale; Olga Pantos; Steven Smriga; Robert Edwards; Florence Angly; Linda Wegley; Mark Hatay; Dana Hall; Elysa Brown; Matthew Haynes; Lutz Krause; Enric Sala; Stuart A. Sandin; Rebecca Vega Thurber; Bette L. Willis; Farooq Azam; Nancy Knowlton; Forest Rohwer

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the worlds most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.


Nature | 1999

Patterns of recruitment and abundance of corals along the Great Barrier Reef

T. P. Hughes; Andrew Baird; Elizabeth A. Dinsdale; Natalie A. Moltschaniwskyj; Morgan S. Pratchett; Jason E. Tanner; Bette L. Willis

Different physical and biological processes prevail at different scales. As a consequence, small-scale experiments or local observations provide limited insights into regional or global phenomena. One solution is to incorporate spatial scale explicitly into the experimental and sampling design of field studies, to provide a broader, landscape view of ecology. Here we examine spatial patterns in corals on the Great Barrier Reef, across a spectrum of scales ranging from metres to more than 1,700 km. Our study is unusual because we explore large-scale patterns of a process (recruitment by juveniles) as well as patterns of adult abundance, revealing the relationship between the two. We show that coral-reef assemblages that are similar in terms of abundance may nonetheless show profound differences in dynamics and turnover, with major implications for their ecology, evolution and management.


Archive | 2004

Coral disease on the Great Barrier Reef

Bette L. Willis; Cathie A. Page; Elizabeth A. Dinsdale

Coral disease is one of the most recent in a series of threats that is challenging the resilience of coral reef communities and is of particular concern because it may interact with and augment the impacts of other commonly recognised threats to coral health (e.g. bleaching, over-exploitation of fish stocks, destructive fishing practices and coastal developments). Since the first report of coral disease by Antonius in 1973, the rate of discovery of new diseases has increased dramatically with more than 29 coral diseases now described (Green and Bruckner 2000, Weil, this Vol.). Although coral disease is emerging as one of the major causes of coral reef deterioration in the Caribbean (Hayes and Goreau 1998; Harvell et al. 2002; Weil et al. 2002), at present we know very little about the ecology or pathology of coral disease on Indo-Pacific reefs. The comparatively few reports of coral disease from Indo-Pacific reefs, despite the region encompassing more than 80% of reefs worldwide (Bryant et al. 1998) is in contrast to the high proportion (>65%) of records in the Global Disease Database from the Caribbean reef region, now widely considered to be a coral disease hotspot (Green and Bruckner 2000; Weil, this Vol.). Such comparisons suggest that either disease is genuinely more prevalent in the Caribbean or lack of studies in other reef regions is underestimating its distribution and abundance. Distinguishing between these two alternatives represents an important step in advancing global epizootiological studies.


The ISME Journal | 2010

Viral and microbial community dynamics in four aquatic environments.

Beltran Rodriguez-Brito; Linlin Li; Linda Wegley; Mike Furlan; Florent E. Angly; Mya Breitbart; John Buchanan; Christelle Desnues; Elizabeth A. Dinsdale; Robert Edwards; Ben Felts; Matthew Haynes; Hong Liu; David A. Lipson; Joseph M. Mahaffy; Anna Belen Martin-Cuadrado; Alex Mira; Jim Nulton; Lejla Pašić; Steve Rayhawk; Jennifer Rodriguez-Mueller; Francisco Rodriguez-Valera; Peter Salamon; Shailaja Srinagesh; Tron Frede Thingstad; Tuong Tran; Rebecca Vega Thurber; Dana Willner; Merry Youle; Forest Rohwer

The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral–microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to >1 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.


PLOS Computational Biology | 2009

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Florent E. Angly; Dana Willner; Alejandra Prieto-Davó; Robert Edwards; Robert Schmieder; Rebecca Vega-Thurber; Dionysios A. Antonopoulos; Katie L. Barott; Matthew T. Cottrell; Christelle Desnues; Elizabeth A. Dinsdale; Mike Furlan; Matthew Haynes; Matthew R. Henn; Yongfei Hu; David L. Kirchman; Tracey McDole; John D. McPherson; Folker Meyer; R. Michael Miller; Egbert Mundt; Robert K. Naviaux; Beltran Rodriguez-Mueller; Rick Stevens; Linda Wegley; Lixin Zhang; Baoli Zhu; Forest Rohwer

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.


PLOS ONE | 2008

Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

Ani Qu; Melissa K. Wilson; Bibiana F. Law; James R. Theoret; Lynn A. Joens; Michael E. Konkel; Florent E. Angly; Elizabeth A. Dinsdale; Robert Edwards; Karen E. Nelson; Bryan A. White

Background The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni. Methodology/Principal Findings Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families. Conclusion/Significance This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

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Robert Edwards

San Diego State University

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Forest Rohwer

San Diego State University

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Matthew Haynes

San Diego State University

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Fabiano L. Thompson

Federal University of Rio de Janeiro

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