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Alexandra Alexiev

and 1 more

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.
Aquarium.final.figure2

Holly Bik

and 15 more

In recent years, microbial ecology studies have increasingly focused on the "Built Environment", characterizing community assemblages across indoor habitats such as classrooms, homes, and hospitals. Human activity and manipulation of indoor spaces can impact both the microbial taxa present and changes in communities over time. In this study, we sought to characterize the spatial and temporal patterns of microbes in two saltwater aquariums at UC Davis; the goal of this project was to provide a substantial research experience for undergraduate students while examining the microbiology of the built environment. Aquariums are a common feature of homes and buildings, yet little is known about how environmental perturbations (water changes, addition of living rocks) can impact the succession of microbial communities. We monitored microbial succession as two "coral pond" aquaria were being established. Water and sediment samples were collected over a 3-month period from November 2012 to January 2013, in parallel with water chemistry data at each timepoint. Samples were subjected to DNA extraction and environmental amplification of the 16S rRNA gene, followed by sequencing on the Illumina MiSeq platform. High-throughput sequence data was processed and analyzed using the QIIME pipeline. Our results showed similar patterns of microbial community succession in both saltwater aquariums, in regard to the profiles of abundant taxa and the timing of successional changes. Furthermore, we observed a significant difference in microbial assemblages in sediment versus water samples, indicating strong heterogeneity and partitioning of microbial habitats within aquariums.
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Jenna M. Lang

and 2 more

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.