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.
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.
ABSTRACT A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain Coronado(T) falls within the _Erythrobacteraceae_ family based on 16S rRNA phylogenetic analysis, but is both phylogenetically and physiologically distinct from existing genera in the family. A phylogenetic tree inferred from 16S rRNA gene sequences shows a highly supported clade containing Coronado(T), _Porphyrobacter_, _Erythromicrobium_, and _Erythrobacter_. While this strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family, the fatty acid profile of this strain is distinct. Coronado(T) contains predominatly C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other _Erythrobacteraceae_. This strain is catalase-positive and oxidase-negative, the latter of which is unusual for the other genera present in the same clade. Coronado(T) can grow from 4-28°C, at NaCl concentrations 0.1-1.5%, and at pH 6.0-8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain Coronado(T) represents a novel species in a new genus in the family _Erythrobacteraceae_ for which the name _Kirrobacter mercurialis_ gen. nov., sp. nov. is proposed; the type strain is Coronado(T) (=DSMZ 29971, =LMG 28700).
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 A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain CoronadoT falls within the _Erythrobacteraceae_ family and the genus _Porphyrobacter_ based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other _Porphyrobacter_, however CoronadoT contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other _Erythrobacteraceae_. This strain is catalase-positive and oxidase-negative, can grow from 4-28 °C, at NaCl concentrations 0.1-1.5%, and at pH 6.0-8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain CoronadoT represents a novel species in the _Porphyrobacter_ genus for which the name _Porphyrobacter mercurialis_ sp. nov. is proposed; the type strain is CoronadoT (=DSMZ 29971, =LMG 28700).
ABSTRACT Background: While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, much less has focused on the non-pathogenic microbes in these habitats. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on earth. Here we report results of sending 48 bacterial strains, collected from built environments on earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Results: Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on earth. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain that avoided contamination showed significantly different growth in space. _Bacillus safensis_ JPL-MERTA-8-2 grew 60% better in space than on earth. Conclusions: The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on _Bacillus safensis_ could lead to interesting insights on why this bacteria grew so much better in space.
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.