Kathryn M. Docherty

The earth microbiome project: Meeting report of the "1 st EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 th 2010

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6th 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.

Size-dependent antimicrobial effects of novel palladium nanoparticles.

Investigating the interactions between nanoscale materials and microorganisms is crucial to provide a comprehensive, proactive understanding of nanomaterial toxicity and explore the potential for novel applications. It is well known that nanomaterial behavior is governed by the size and composition of the particles, though the effects of small differences in size toward biological cells have not been well investigated. Palladium nanoparticles (Pd NPs) have gained significant interest as catalysts for important carbon-carbon and carbon-heteroatom reactions and are increasingly used in the chemical industry, however, few other applications of Pd NPs have been investigated. In the present study, we examined the antimicrobial capacity of Pd NPs, which provides both an indication of their usefulness as target antimicrobial compounds, as well as their potency as potential environmental pollutants. We synthesized Pd NPs of three different well-constrained sizes, 2.0±0.1 nm, 2.5±0.2 nm and 3.1±0.2 nm. We examined the inhibitory effects of the Pd NPs and Pd2+ ions toward gram negative Escherichia coli (E. coli) and gram positive Staphylococcus aureus (S. aureus) bacterial cultures throughout a 24 hour period. Inhibitory growth effects of six concentrations of Pd NPs and Pd2+ ions (2.5×10−4, 10−5, 10−6, 10−7, 10−8, and 10−9 M) were examined. Our results indicate that Pd NPs are generally much more inhibitory toward S. aureus than toward E. coli, though all sizes are toxic at ≥10−5 M to both organisms. We observed a significant difference in size-dependence of antimicrobial activity, which differed based on the microorganism tested. Our work shows that Pd NPs are highly antimicrobial, and that fine-scale (<1 nm) differences in size can alter antimicrobial activity.

NEON terrestrial field observations: designing continental‐scale, standardized sampling

Rapid changes in climate and land use and the resulting shifts in species distributions and ecosystem functions have motivated the development of the National Ecological Observatory Network (NEON). Integrating across spatial scales from ground sampling to remote sensing, NEON will provide data for users to address ecological responses to changes in climate, land use, and species invasion across the United States for at least 30 years. Although NEON remote sensing and tower sensor elements are relatively well known, the biological measurements are not. This manuscript describes NEON terrestrial sampling, which targets organisms across a range of generation and turnover times, and a hierarchy of measurable biological states. Measurements encompass species diversity, abundance, phenology, demography, infectious disease, ecohydrology, and biogeochemistry. The continental-scale sampling requires collection of comparable and calibrated data using transparent methods. Data will be publicly available in a variety of formats and suitable for integration with other long-term efforts. NEON will provide users with the data necessary to address large-scale questions, challenge current ecological paradigms, and forecast ecological change.

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes.

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.

Ionic liquid biodegradability depends on specific wastewater microbial consortia

Complete biodegradation of a newly-synthesized chemical in a wastewater treatment plant (WWTP) eliminates the potential for novel environmental pollutants. However, differences within- and between-WWTP microbial communities may alter expectations for biodegradation. WWTP communities can also serve as a source of unique consortia that, when enriched, can metabolize chemicals that tend to resist degradation, but are otherwise promising green alternatives. We tested the biodegradability of three ionic liquids (ILs): 1-octyl-3-methylpyridinium bromide (OMP), 1-butyl-3-methylpyridinium bromide (BMP) and 1-butyl-3-methylimidazolium chloride (BMIM). We performed tests using communities from two WWTPs at three time points. Site-specific and temporal variation both influenced community composition, which impacted the success of OMP biodegradability. Neither BMP nor BMIM degraded in any test, suggesting that these ILs are unlikely to be removed by traditional treatment. Following standard biodegradation assays, we enriched for three consortia that were capable of quickly degrading OMP, BMP and BMIM. Our results indicate WWTPs are not functionally redundant with regard to biodegradation of specific ionic liquids. However, consortia can be enriched to degrade chemicals that fail biodegradability assays. This information can be used to prepare pre-treatment procedures and prevent environmental release of novel pollutants.

The role of environmental microorganisms in ecosystem responses to global change: current state of research and future outlooks

The effects of human activities have dramatically altered our natural environment. Greenhouse gas production, nutrient loading, land-use change and water consumption, to name a few, can dramatically affect ecosystem processes by changing the dynamics of global biogeochemical cycles. Currently, one of the most crucial scientific objectives is to gain an understanding of how drastically anthropogenic changes have altered our planet and what those changes mean for the future. In order to predict accurate scenarios of how global change will affect terrestrial ecosystems, the effects and controls over biogeochemical pools and fluxes, as incorporated into predictive global change models, must be carefully examined. This is not only necessary to guide scientific endeavor, but also to inform policymakers and to serve as a basis for advocacy of social change. By examining and understanding the dynamics of carbon, nitrogen, and other nutrient transformations scientists can take the pulse of an ecosystem and predict changes into the future. Many of these biogeochemical cycles are catalyzed by abundant and diverse microorganisms, the ‘‘gatekeepers’’ that populate every ecosphere. However, most global change models treat ‘‘microbes’’ as a single pool, responsible for a single rate of flux (ToddBrown et al. 2011; Treseder et al. 2011). Advances in microbial molecular techniques, and increasing integration between microbiological and ecological disciplines have provided overwhelming evidence that microbial communities are far more diverse than could ever have been imagined (e.g. Roesch et al. 2007; Fierer and Jackson 2006; Schloss and Handelsman 2006; Gans et al. 2005). With these insights comes a whole new body of evidence that microorganisms are not simple bags of enzymes, the abundance of which directly relate to the rate of a chemical reaction in the environment. On the contrary, we find that microorganisms are dynamic catalysts with a rich evolutionary history spread across all three domains of life. This life history shapes what metabolic capabilities microorganisms have, and how they respond to a diverse array of ecological constraints, including nutrient and dispersal limitation, competition, predation, cooperation and disturbance. Microorganisms themselves are affected by the global changes that occur, and shifts in microbial communities are inevitably linked, through the biogeochemical cycles they mediate, to the entire ecosystem. How K. M. Docherty (&) Department of Biological Sciences, Western Michigan University, 1903 West Michigan Ave, Kalamazoo, MI 49008, USA e-mail: kdochert8@gmail.com

The biogeography of putative microbial antibiotic production

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.

Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments

The widespread use of antibiotics in human and veterinary medicine to treat pathogenic bacteria has resulted in the rapid emergence of antibiotic-resistant bacteria (ARB). Wild animals may enable the spread of pathogenic and non-pathogenic ARB when they are exposed to reservoirs (e.g., contaminated soil, water, or crops) and carry ARB in and on their bodies to other environments. We tested for the presence of ARB in four songbird species in southwest Michigan across a gradient of land use. Our specific objectives were to: 1) quantify the prevalence of ARB found in the gut microbiome of birds; 2) identify the specific bacteria exhibiting resistance; 3) assess whether ARB prevalence and identity varied among bird species; and 4) assess whether anthropogenic land use influenced the prevalence and identity of ARB found on birds. We sampled birds across a land use gradient consisting of urban, agricultural, and natural land covers using a randomized, spatially-balanced sampling design and cultured bacteria from fecal samples in the presence of three different antibiotics (amoxicillin, tetracycline, and ciprofloxacin). Overall prevalence of ARB was high, with 88% of total birds carrying ARB resistant to one of three antibiotics that we tested. Resistance to amoxicillin was more common (83% of sampled birds) than resistance to tetracycline (15%) or ciprofloxacin (1%). Identified ARB were diverse, and included 135 isolates representing 5 bacterial phyla and 22 genera. There was no effect of land use on ARB prevalence, with 90% of sampled birds captured in rural sites and 85% of sampled birds in urban sites carrying ARB. We provide the first analysis of ARB prevalence across multiple bird species and land uses utilizing a spatially-balanced, randomized study design. Our results demonstrate that nearly all sampled birds carried at least some ARB, and that they may serve as important dispersal agents of ARB across large spatial scales.

Identification of metabolites produced during the complete biodegradation of 1-butyl-3-methylimidazolium chloride by an enriched activated sludge microbial community

Ionic liquids (ILs) are highly polar solvents with unique physicochemical properties that make them promising green alternatives to volatile organic solvents. Since ILs can be toxic to organisms, the development of methods to degrade ILs into harmless molecules prior to disposal is critical to enhancing their green properties. In this study, metabolites generated during the biodegradation of 1-butyl-3-methylimidazolium chloride (BMIMCl) by an enriched, activated sludge microbial community were investigated. Biodegradation of BMIM and the metabolic products released into the growth media were examined using 1H-NMR spectroscopy and mass spectrometry. To the best of our knowledge, this is the first reported complete primary catabolism of the biodegradation-resistant BMIMCl ionic liquid. The bacterial community responsible for degradation was analyzed using a 16S-rRNA amplicon approach. Although the community was diverse, Bacteroidetes was the predominant phylum. The study provides a greater insight into imidazolium-based IL biodegradability and a means to proactively prevent the ecotoxicity of the BMIM cation and its metabolites, by complete primary biodegradation of the cation and removal of most resulting metabolites, prior to release into aquatic waste streams.

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials

The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.