Meta-omics Analysis of Microbia Carbon Cycling Responses to Altered Rainfall Inputs in Native Prairie Soils

Introduction

Soils process and store large amounts of C; however, there is considerable uncertainty about the details that influence microbial partitioning of C into soil pools and what influential forces control the fraction of the C input that is stabilized. It is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts physiologically or in composition to changes in soil moisture brought about by shifts in precipitation.

Background

Prairie soils (Mollisols) cover ~25% of the US and store a disproportionate amount of C (~33%). Mollisols reach their greatest extent in the Great Plains, with greater C stores in prairie soils from more humid (Udolls) compared to drier (Ustolls) climates.

The Konza Prairie in Kansas is a native tallgrass prairie reserve. It is poised at the interface between Udolls and Ustolls, and therefore a good location to examine changes related to altered precipitation.  Furthermore, the Konza Prairie has a set of rainfall manipulation plots (RaMPs) that were established more than a decade ago. The RaMPs is a well replicated experiment consisting of two treatments: (1) ambient precipitation and (2) extended precipitation interval. The extended precipitation interval consists of storing rainfall and reapplying it at an interval 50% longer than that between natural rainfall events.

Approach

We will employ a systems biology approach, considering the complex soil microbial community as a functioning system and use state-of-the-art pyrosequencing, metagenomics, meta-transcriptomic, and metaproteomic techniques.

These omics tools will be refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments are designed to specifically identify microbial community members and processes that are instrumental to C cycling in prairie soils and impacted by climate change events, such as altered precipitation.

Objectives

Our goal is to harness the power of multiple omics tools to understand the functioning of whole-soil microbial communities and their role in C cycling. Towards this end, we will pursue three specific objectives:

Objective 1
Further develop and optimize a combination of omics approaches to study how environmental factors affect microbially-mediated C cycling processes.

A metagenome of the Konza soil has been generated (300 Gb) and is in the process of annotation
An incubation experiment using Konza prairie soil has been done to test metatranscriptome and metaproteome methods. Initial results show differential responses in the transcription of selected genes and production of microbial proteins.

Objective 2
Determine the impacts of long-term changes in precipitation timing on microbial C cycling using the RaMPs experiment.

 

Two field campaigns are planned for summer 2011. The first when plant growth is optimal and the second after plant senescence. We will sample soils prior to a major rainfall event (when soils are relatively dry), shortly after wet-up, and at one more time as the soils begin to dry. In addition to omics measurements, several soil enzymes involved in C cycling and soil respiration will be measured.

Objective 3
Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes.

We will test if there is a temporal lag between peak transcriptional activity and peak biomass/protein production.
Five bacterial species characteristic of the dominant taxa in the Konza soil will be evaluated to determine if they display different strategies to cope with modified wet/dry cycles. Model 13C-labeled substrates will be used to trace the fate of C during wet/dry cycles.

Research team (left to right): Maude David, Susannah Tringe, Stephanie Yarwood, Chuck Rice, David Myrold, Janet Jansson, Peter Bottomley, Nathan VerBerkmoes, and Lydia Zeglin. Missing from photo: Ari Jumpponen and Bob Hettich.

Acknowledgements

This research is sponsored by the DOE-BER, Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program, under Contract No. DE-SC0004953, and is a collaboration between Oregon State University, Kansas State University, Lawrence Berkeley National Laboratory, and Oak Ridge National Laboratory.

Publications

This project has produced the following publications:

Myrold, D.D., L.H. Zeglin, and J.K Jansson. 2014. The potential of metagenomic, and other omic, approaches for understanding soil microbial processes. Soil Sci. Soc. Am. J. 78:3-10. (doi:10.2136/sssaj2013.07.0287dgs)

Zeglin, L.H., P.J. Bottomley, A. Jumpponen, C.W. Rice, M. Arango, A. Lindsley, A. McGowan, P. Mfompeb, and D.D. Myrold. 2013. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales. Ecology 94:2334-2345. (doi: org/10.1890/12-2018.1)