There are >250,000 species of flowering plants, comprising 90 Here, we present a 16S rDNA PCR survey of microbes associated with seagrass roots (rhizosphere) and leaves (phyllosphere.) This was conducted in conjunction with a mesocosm common garden experiment, in which 7 genotypes of the seagrass Zostera marina were subjected to a month-long period of warming. Previous work has shown that these 7 genotypes differ significantly with respect to shoot production, biomass, and nutrient uptake rates. During the experiment, all plant genotypes responded positively to the increased temperature, but differed in their ability to tolerate the shift back to ambient. There were no significant differences in microbial community composition between the Z. marina genotypes, despite differential plant genotype performance during the experiment. However, specific microbial taxa were correlated with plant traits and responded to the warming treatment. For example, the relative abundance of Marinomonas on leaves was greater in plants subjected to warming. This genus has the odd ability to grow on DMSP as a sole carbon source. DMSP is an anti-stress compound produced by some seagrass species; increased abundance of Marimonas on these leaves could be indicative of plant stress. The most abundant rhizosphere taxa are involved in sulfur oxidation and nitrogen fixation, and thus are prime candidates for seagrass symbionts. We’ll discuss ongoing efforts to cultivate these taxa for future experimental work. The 60 plant species currently residing in the sea are the result of three independent invasions. In these three lineages (all called seagrasses, though they do not form a clade,) convergent evolution has led to similar morphological and physiological adaptations to the marine environment. Have the microbial communities associated with seagrass roots and leaves undergone a similar convergence? What role do the root- and leaf-associated microbial communities play in seagrass adaptation to the marine environment? The Seagrass Microbiome Project (http://seagrassmicrobiome.org/) is endeavoring to answer these fundamental questions about seagrass-microbe interactions. Here, we present the results of a 16S rDNA PCR survey of microbes associated with seagrass roots (rhizosphere) and leaves (phylosphere.) This survey was conducted in conjunction with a mesocosm common garden experiment, in which 7 genotypes of the seagrass _Zostera marina_ were subjected to a month-long period of warming. During the experiment, all plant genotypes responded to the increased temperature, but differed in their ability to tolerate the shift back to ambient temperature. We show that there is a significant shift in the phyllosphere microbial community during the course of the 3 month experiment, but not in the rhizosphere community. The effect of time was greater than the treatment effect, and there were no significant differences in microbial community composition between the different _Z. marina_ genotypes, despite marked differences in plant genotype performance throughout the experiment.
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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 very 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 samples swabbed from surfaces onboard the ISS. This sampling is a component of Project MERCCURI - a collaborative effort of the "microbiology of the Built Environment network" (microBEnet) project, Science Cheerleaders, NanoRacks, Space Florida, and Scistarter.com. 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. Methodology/Principal Findings 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 rRNA 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 the Earth homes and the Human Microbiome Project. Conclusions/Significance 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 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 very 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. This sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 samples swabbed from surfaces onboard the International Space Station. This sampling is a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS) - a collaborative effort of the "microbiology of the Built Environment network" (microBE.net) project, Science Cheerleaders, NanoRacks, Space Florida, and Scistarter.com. 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 International Space Station. 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 rRNA 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 the Earth homes and 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 International Space Station was more similar to home surfaces than to the human microbiome samples. The International Space Station surfaces are species-rich with 1036-4294 operational taxonomic units per sample. There was no discernible biogeography of microbes on the 15 surfaces, although this may be a reflection of the small sample size we were able to obtain.
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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.