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CURRENT RESEARCH

Biogeography of soil microbial communities:Andes

Despite their ubiquity, the biogeographical patterns exhibited by soil microorganisms have received little attention. While manstudies have examined microbial community structure at local scales, we do not adequately understand the extrinsic and intrinsic factors that regulate the structure of soil microbial communities across regional and continental scales. We have ongoing projects examining the spatial variability in soil archaeal, bacterial, and fungal communities across scales ranging from many thousands of kilometers to < 1 meter. We have also examined the biogeographical patterns exhibited by stream bacteria, soil ammonia-oxidizers, soil acidobacteria, and bacteria that inhabit leaf surfaces. Our current work employs a novel barcoded pyrosequencing technique that allows us to rapidly survey hundreds of microbial communities at an unprecedented level of detail.


Airborne microorganisms:

air samplingMicroorganisms are surprisingly abundant in the lower layers of the Earth's atmosphere with a wide diversity of microorganisms capable of being transported long distances in the atmosphere. The nature of these airborne microorganisms is likely to be highly relevant to human health (particularly with regards to allergies and asthma) and the health of agricultural crops. We are working on a series of projects examining the spatial and temporal variability in airborne microbial populations across North America. We are particularly interested in examining how land-use type influences the diversity and abundance of microorganisms found in the atmosphere. The MiASMA Project was started very recently and represents a 'citizen science' project attempting to construct the first continental-scale atlas of microbial diversity in the lower atmosphere with the goal of understanding the factors driving spatial and temporal variability in these airborne communities.

The human body as a microbial habitatvoc soil:

The human body harbors more microbial cells than human cells. Although our microbial symbionts help us acquire nutrients, resist pathogens, and educate our immune system, the fundamental ecology of the human microbiome is poorly understood. We have been collaborating with Rob Knight's group here at CU to explore the ecology of bacteria and archaea on and within the human body. Specifically, we have been examining variability in microbial communities across body habitats (e.g. skin, mouth, gut, etc.), between individuals, or within a given individual over time. Ongoing work includes: linking microbial production of volatile organic compounds in the mouth (a.k.a. 'bad breath') and bacterial community composition, detecting 'residues' of skin bacteria left on objects that we touch, and using metagenomic tools to determine how shifts in gut microbial communities may impact nutrition.

Linking microbial communities and processes in soil:

Pine forestThe role that soil microorganisms play in mediating global biogeochemical processes is a significant area of uncertainty in ecosystem ecology. One of the main reasons for this uncertainty is that we have a limited understanding of belowground microbial community structure and how this structure is linked to soil processes. Building upon established theory in soil microbial ecology and ecosystem ecology, we predict that the structure of belowground microbial communities will be a key driver of carbon dynamics in terrestrial ecosystems. We are combining molecular analyses of microbial communities (both metagenomic and small subunit rRNA surveys) with techniques to assess microbial carbon utilization to advance our conceptual and practical understanding of the fundamental linkages between soil microbial community structure and ecosystem-level carbon dynamics. Currently, we are exploring these linkages across soils that differ with respect to land-use, nitrogen fertilization rates, and plant species composition.


Microbial communities in the built environment:

leaves

Although we spend the majority of our lives indoors, we have a surprisingly limited understanding of the microbial diversity found inside our homes and offices. Surfaces inside and outside our homes likely harbor a diverse array of bacteria and fungi, but the composition of these communities, their spatial variability, and the sources of the microbes remain poorly understood. With funding from the Sloan Foundation's Indoor Environment Program, we have recently started a project exploring the microbial biogeography of the kitchen, producing a detailed map of microbial distributions throughout the entire kitchen and identifying possible linkages between the kitchen-associated microbes and those microbes associated with our bodies and the food we eat. We are currently expanding our sampling efforts, working with Rob Dunn's group to initiate a 'citizen science' program whereby volunteers from across the United States send us samples from selected locations in their homes so we can begin to assess how building characteristics, occupancy, usage, and location influence those microbes found inside and outside our homes. For more information on this 'Wildlife of Our Your Home" project, see here.


Volatile organic compound (VOC) production by soil microorganisms
voc soil:

The flux of VOCs from terrestrial sources to the atmosphere has an important impact on atmospheric chemistry at local, regional, and global scales. For this reason, many studies have focused on the production of VOCs by plants, assuming that plants are the largest terrestrial source of biogenic VOCs. Surprisingly, only a handful of studies have looked at the production of VOCs by soil microbes despite a number lines of evidence suggesting that, like plants, microbes may also be an important terrestrial source. We are currently examining soil VOC production across a wide range of soil and litter types with the goal of understanding how these VOCs may regulate soil microbial communities and processes. In addition, we are assessing VOC production during litter decomposition and the influence of N fertilization on the quantities and types of VOCs released.