INTRODUCTION: Plant-associated microbial communities are critical to the health and evolutionary success of their hosts. Plant-associated microbes provide nutrients, break down environmental toxins and even play a role in protecting their hosts from disease (Zamioudis and Pieterse, 2011). Plants curate these communities for their advantage, encouraging beneficial microbes to colonize themselves and their immediate surroundings. In this way, they can shape otherwise inhospitable environments to their advantage and make welcoming ones even more fertile. Although these microbial interactions are well documented in terrestrial systems, few studies have focused on their role in marine systems. Seagrasses are the only known marine angiosperms that live fully submerged and have retained many of the physiological traits of land plants after their invasion of the marine environment (Wissler et al. 2011). For typical land plants, the marine environment poses significant challenges - it’s low in light and oxygen and high in toxins such as sulfides and salts. Yet despite these environmental challenges, seagrasses thrive in their marine homes and there is evidence to suggest that their microbial communities may play an important role in this success. For example, toxic sulfide levels in seagrass meadow sediment are controlled in part by the actions of sulfide-oxidizing bacteria associated with bivalves feeding off of the biomass and oxygen released from seagrass roots (van der Heide et al 2012). Seagrasses also play a fundamental ecological role in coastal communities (Wissler et al. 2011). Seagrass meadows anchor coastlines, provide refuges for tidal organisms, and help filter the water that flows through them. Perhaps most importantly, seagrass meadows contribute greatly to nutrient cycling and intertidal biogeochemistry. Among marine ecosystems, seagrass meadows have one of the highest levels of primary production both from the seagrass themselves, and from the microbial autotrophs that live in the water column (Williams et al. 2009). The seagrass propagate clonally producing dense underground networks of roots and rhizomes which microbes decompose to provide complex organic carbon, phosphates and bioavailable nitrogen to the meadow community (Larkum et al. 2007, Chapter 6). The meadows are also marine hot spots of nitrogen fixation (Welsh et. al. 2000) and intriguingly, nitrogen fixation in seagrass meadow sediments has been linked to the production of toxic sulfide (Larkum et al. 2007, Chapter 6) suggesting that there may be important trade-offs in the relationship between seagrasses and their nitrogen-fixing microbes. Despite much indirect evidence for the ecological importance of the microbial communities closely associated with seagrass, few studies have focused on the microbial communities as a whole and none, to our knowledge, have used culture-independent methods to extensively document these communities. To better explore these seagrass-microbe interactions we must first understand no only which microbes are intimately associated with seagrasses but also how that association changes on a micro-scale since microbial community composition may vary widely across very small distances. Thus, to begin answering these questions, we present a detailed survey of the micro-scale variation of the microbial communities associated _Zostera marina_ , a model seagrass endemic to the coastal regions of the northern hemisphere.
ABSTRACT Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: 1) the Average American (AMERICAN): focused on convenience foods, 2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at \(1.3 X 10^9\) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at \(6 X 10^6 \)and \(1.4 X 10^6\) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbial approaches beyond probiotics taken as supplements - _i.e._, ingested as foods - are important contributors to the composition, inter-individual variation, and function of our gut microbiota.
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
ABSTRACT Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration and colonization of the solar system come to fruition. Results: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for 1) the Wildlife of Our Homes project and 2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both Earth homes and data from the Human Microbiome Project. Conclusions: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1036-4294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.
ABSTRACT Background Submerged aquatic vegetation (SAV) are plants that are rooted in sediment and fully submerged most of the time, and have many adaptations for coping with varied salinity and osmotic conditions. We focus here on one aspect of SAV - their microbiome - which was studied in the Potomac River along a salinity gradient as the river empties into the Chesapeake Bay. The goal was to find a link between the microbial communities on different SAV species and the changing salinity across the river. Results One of the four successfully sampled sites was very different from the rest in terms of microbial community and water/sediment chemistry, clustering separately from the other sites on PCoA plots. _Methylotenera_, _Planctomyces_, _Rhodobacter_, and _Providencia_ are commonly found amongst most SAV species across all sites, and sulfur oxidizing bacteria were present in high relative abundance in the roots of _Potamogeton perfoliatus_ at one site. Conclusions Site location, which had distinct water and sediment chemistries, was a main driver of the microbial community structure. Host species of SAV and sample types (leaves or roots) also have different microbial communities. Due to the small sample size in this study, it is difficult to draw robust conclusions about the impact of salinity on microbial community structure. Therefore, future efforts will sample more thoroughly along the Potomac river, as well as along the length of the James River, which provides a nearby, parallel salinity gradient.
EDUCATION University of California, Davis - Ph.D. Microbiology (2012) Dissertation Title: Exploring Microbial Community Composition and Genome Evolution Using Environmental and Comparative Genomics ##University of Texas, Arlington - M.S. Quantitative Biology (2001) Thesis Title: Worldwide Phylogeny of the Damselfly Genus Ischnura Based on Mitochondrial Cytochrome Oxidase II and Cytochrome B Sequence Data ##University of New Orleans - B.S. Biology (1995)
MOTIVATION A single microbial community can be composed of many thousands of species, and the tools most commonly used (pie charts and stacked bar graphs) to visualize the relative abundances of species in communities are inadequate. The human brain is not adept at estimating the areas of wedges in a pie or rectangles in a bar, and if it were, the color palette and graph size required to faithfully represent the relative abundances of thousands of species of even a single community would be prohibitively large. There is a great need to develop more intuitive visualization tools, especially for comparing microbial community composition across a large number of samples. Fortunately, human evolution, via natural selection has engineered a solution to this problem. The human brain has a region, the fusiform face area, that is entirely devoted to facial recognition. This region of the brain allows us to process a very complex image in an instant, requiring minimal decomposition into component parts. Instead, faces are perceived holistically, as a gestalt. Faces are infinitely variable, and we can quickly pick up on even very subtle differences and similarities between them.