Cooperative Institute for Research in Environmental Sciences

A winning proposal for the Innovative Research Program, 2006:

VOC production by soil microorganisms: linking microbial ecology and atmospheric chemistry

Investigators: Noah Fierer, Russ Monson

Objectives. The goal of this study is to characterize the types and quantities of volatile organic carbon compounds (VOCs) produced by soil microorganisms. We will determine if microbial VOC (mVOC) production is a potentially important source of atmospheric VOCs and if VOC analysis holds promise as a tool for the rapid assessment of soil microbial community composition.

Background and Importance. The flux of VOCs from terrestrial sources to the atmosphere has an important impact on atmospheric chemistry at local, regional, and global scales (Monson & Holland 2001). 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 know that bacterial and fungal isolates grown in the laboratory can produce large quantities of VOCs and a diverse array of individual compounds, including: alcohols, aldehydes, amines, methylated halogens, terpenoids, and volatile fatty acids (Fall 1999). We also know that soil microbes are the dominant decomposers in terrestrial systems, converting organic C substrates to volatile forms of carbon. While CO2 is assumed to be the major product of microbial decomposition in aerobic soils, appreciable amounts of VOCs may also be released from soil during decomposition. Even if mVOC production is a small fraction of microbial CO2 production, mVOC production may represent a major pathway by which carbon is moved from terrestrial to atmospheric pools. At this point, the paucity of relevant data means that we can only speculate on the magnitude of mVOC production from soil.

In addition to the likely biogeochemical importance of soil mVOC production, we expect that VOC analyses will provide a unique method for the assessment of microbial community structure. Although factors other than microbial community composition are likely to influence the VOC "fingerprint" of a given soil, we expect a strong correlation between microbial community composition and VOC production. We know that the production of certain VOCs is associated with specific microbial groups in soil and we know that mVOC production can mediate microbial interactions in soil with some mVOCs acting as "infochemicals" capable of stimulating or inhibiting the growth of specific microbial populations. Since the composition of soil microbial communities has an important influence on ecosystem dynamics, a rapid technique for assessing broad differences in microbial communities would be very valuable. Soil VOC analysis holds promise as an alternative to the expensive and time consuming methods currently used to assess microbial community structure.

Why is this important? VOC production by soil microbes is likely to have an important influence on terrestrial carbon dynamics, atmospheric chemistry, and soil ecology.

What makes this innovative? We are proposing that mVOC production may be more important than previously recognized. As the first study to comprehensively examine mVOC production in soil, this work may open up a new field of scientific inquiry. Furthermore, if we can show that VOC analysis provides insight into soil microbial community structure, this work may lead to the development of new methodological approaches to study complex microbial communities.

How might this be interdisciplinary? The proposed project is a collaboration between a microbial ecologist (Fierer) and an ecosystem ecologist (Monson), using analytical techniques developed by atmospheric chemists. We expect that our findings will be of interest to researchers in a wide range of disciplines, including: atmospheric chemistry, ecosystem ecology, microbiology, and soil science.

Research Plan. We will collect organic and mineral soils from a range of sites across the United States. We will focus on sites within the NSF-funded Long-Term Ecological Research network so that follow-up studies will be possible and NSF funds can accessed. The goal is to collect a diverse array of soil types (30-50 soils) so we can examine correlations between mVOC production and soil/site characteristics. After an equilibration period, root-free soils will be incubated in gas-tight containers for 24-48 h with headspace samples analyzed for VOCs using proton-transfer-reaction mass spectrometry (PTR-MS). Headspace samples will also be analyzed for CO2 concentrations with an infrared gas analyzer so we can compare net CO2 and net VOC production rates. We will collect relevant site information and measure basic soil physico-chemical characteristics for each soil. In addition, we will use the quantitative PCR approach described in Fierer et al. (2005) to quantify the abundances of bacterial and fungal groups in each soil sample. By analyzing a relatively large number of samples we can determine if VOC "fingerprints" (the types and quantities of VOCs released) are unique to each soil type and we can assess relationships between specific soil characteristics and mVOC production. We will use multivariate statistical methods (non-metric multi-dimensional scaling and ANOSIM procedures, Fierer and Jackson 2006) to look for correlations between VOC fingerprints and soil/site characteristics.

Once the cross-site study has established linkages between microbial VOC production and soil/site characteristics we will test our hypothesis that VOC production is strongly correlated with microbial community composition. By simply screening the collected soils, we cannot distinguish the effects of microbial community composition from other factors (soil organic carbon characteristics, texture, nutrient status) that may also influence mVOC production. To determine the strength of the relationship between community composition and mVOC fingerprints, we will experimentally manipulate the microbial communities in five soils that have distinct VOC fingerprints by autoclaving each soil and re-introducing microbes with five different soil inocula, one from each of the five soil types. After an equilibration period, VOC production will be measured using the techniques described above. If VOC fingerprints correspond to microbial community composition, we should observe a strong effect of inoculum on VOC fingerprints from a given soil type. If VOC production is unrelated to microbial community composition, but is instead driven by intrinsic abiotic soil properties, we will see no apparent inoculum effect. The linkages between microbial community composition and VOC fingerprints will be further examined by adding known organic substrates (e.g. cellulose, proteins, sugars) to each of the five soils and measuring VOC production over time. If substrate characteristics are less important than community composition in controlling mVOC production, soils receiving the same substrate should yield distinct VOC fingerprints.

Expected outcome and impact. This work is just the first step towards understanding microbial VOC production and its consequences. This work will allow us to parameterize the relative importance of soil VOC production and assess how VOC production varies across a wide range of soil types. We expect that the proposed work will yield valuable data sets than can be leveraged to obtain extramural funding in the future. If we find that microbial VOC production is an important source of VOCs, more detailed experiments and field studies will follow. If we find that VOC analysis can be used to infer microbial community composition, this work may to lead to the development of new methods for rapidly assessing soil biological characteristics.

References

Fall, R. 1999. Reactive hydrocarbons and photochemical air pollution. In: Reactive Hydrocarbons in the Atmosphere, ed. C. N. Hewitt, pp. 41–96. Academic Press, San Diego, CA.

Fierer, N., J. Jackson, R. Vilgalys, and R. Jackson. 2005. The assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71:4117-4120.

Fierer, N. and R. Jackson. 2006. The diversity and biogeography of soil bacterial communities. PNAS 103:626-631. Monson, R.K. and E.A. Holland. 2001. Biospheric trace gas fluxes and their control over atmospheric chemistry. Ann Rev Ecol and Syst 32: 547-576.