Biology and Fertility of Soils

, Volume 46, Issue 3, pp 199–213 | Cite as

Volatile organic compounds (VOCs) in soils

Open Access
Review

Abstract

Soils may act as sources or sinks of volatile organic compounds (VOCs). Many of the formed VOCs are produced by microorganisms, and it would be a challenge to investigate soil microbial communities by studying their VOC profile. Such “volatilomics” would have the advantage of avoiding extraction steps that are often a limit in genomic or proteomic approaches. Abundant literature on microbially produced VOCs is available, and in particular novel detection methods allow additional insight. The aim of this paper was to give an overview on the current knowledge of microbial VOC emissions from soils.

Keywords

Volatile organic compounds (VOC) Volatilomics Communities 

Introduction

During the last decades, soil microbiology underwent major changes. Initial attempts to understand the functioning of nutrient turnover by isolating organisms were followed by the age of activity measurements (enzymes, respiration). Following the trends in ecology, in the 1970s, soil microbiologists started to emphasize nutrient pools (microbial biomass) and fluxes until methods became available that were able to address more specific components of the community (Insam 2001). Specific structural components, like ergosterol or muramic acid, as well as phospholipid fatty acids (PLFAs), were successfully used to shed light on the composition of microbial communities. Finally, genome-based approaches were used for fingerprinting the soil microbiota down to the population level, like PCR–denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis, single-stranded conformation polymorphism, T-RFLP, and several others. Today, approaches like pyrosequencing (Roesch et al. 2007) are targeting the metagenome. Soil genomics, soil proteomics, and soil metabolomics are not catchwords any more, but state of the art. However, even the most sophisticated analyses of genetic properties or compounds do have their own limitations, starting from obtaining representative samples (e.g., DNA extraction is usually based on samples of less than a gram) and quantitative extraction of the molecules from the soil matrix (Roose-Amsaleg et al. 2001; Caldwell 2005; Bakken and Frostegard 2006; Pietramellara et al. 2009).

Similar to PLFAs, ergosterol, DNA, and other biomarkers, microorganisms are also responsible for producing microbial volatile organic compounds (mVOCs) in high diversity and quantity (e.g., Linton and Wright 1993; Isidorov and Jdanova 2002; Wheatley 2002; Leff and Fierer 2008) and for different purposes. Volatile organic compounds are available to the analyzer without tedious sample pretreatment and extraction, and for this reason, the measurement may not present biases, and might be of virtue compared to measurement of PLFAs, DNA, and other microbial biomarkers. The VOCs are commonly measured to characterize fungi, especially molds but also bacteria. Specific VOCs can be used to indicate fungal, bacterial, and other food spoilage (Börjesson et al. 1990, 1992; Bjurman et al. 1997; Kershi et al. 1998; Gao and Martin 2002; Mayr et al. 2003a), to characterize odor contamination in composting processes (Smet et al. 1999), or to detect mold growth in buildings (Wilkins et al. 2000; Fischer and Dott 2003). Volatile organic compound analysis may represent a new emerging field, soil volatilomics.

In soils, VOCs are mainly produced by plants (Stotzky and Schenck 1976; Kesselmeier and Staudt 1999) and microorganisms (Stahl and Parkin 1976; Leff and Fierer 2008). Volatile organic compounds emitted by plant roots (and associated mycorrhiza) or seedlings were identified, and suggestions for their functions were proposed (Kesselmeier and Staudt 1999; Wenke et al. 2009). Interactions between plants and microbes mediated by VOCs as well as plant VOC production, measurement, and the influences of VOCs on plants have been discussed in several reviews (Stotzky and Schenck 1976; Linton and Wright 1993; Peñuelas and Llusià 2001; Cape 2003; Tholl et al. 2006) and are far beyond the scope of this review.

Due to their ubiquitous detectability and their information content, VOCs have been extensively studied aiming at different organisms, functions, and interactions since the last 90 (!) years (e.g., Brown 1922 cited in Linton and Wright 1993). The scope of this review is to summarize the state of the art and latest advances in soil microbial VOC research, in particular since the excellent review by Stotzky and Schenck (1976).

Effects of soil-related properties on VOC production and release

Effects of soil-related properties on mVOC production

Investigation of soil VOC production is sophisticated as soil includes an enormous variability in parameters that influence (mVOC) production. Besides differences in soil-specific community composition, mVOC production in soils is strongly depending on nutrient and oxygen availability and on the physiological state of the microorganisms. The availability of nutrients and oxygen itself is again depending on several environmental factors such as soil moisture, soil texture, or microbial activity (McNeal and Herbert 2009). The availability of oxygen is a basic parameter determining the types of VOCs produced as it allows highly effective respiration. Under aerobic conditions, energy is produced using almost any organic C source, which is then almost entirely evolved as CO2 and used for cell growth. Only small amounts are used for secondary metabolite production, some of them may also be VOCs.

Under micro-aerobic and anaerobic conditions, a larger fraction of C ends up as end products of (hetero- and) homofermentative processes (primary metabolic products). Thus, under anaerobic conditions, the diversity and amount of VOCs emitted is increased (Stotzky and Schenck 1976), as has been confirmed by Seewald et al. (2010).

Similarly, the substrate quality impacts the composition of VOCs produced (Stotzky and Schenck 1976). It is also important to note that even small variations in nutrient composition (e.g., nitrogen supply in form of KNO3 or (NH4)2SO4) may change considerably the type and the amount of the individual VOCs produced (Wheatley et al. 1996, 1997).

As the pH value of soils impacts the nutrient availability for microorganisms and their physiological state it may affect VOC production (Stotzky and Schenck 1976). Also, soil temperature plays an important role in VOC production (Asensio et al. 2007a).

Effects of soil-related properties on VOC release

Apart from environmental factors that affect microorganisms and therefore the microbial VOC production, numerous factors impact VOC retention in soils, among them temperature, pH, and moisture content (Brinton 1998). As the vapor pressures of the different VOCs are different and correspond with temperature (Schade and Custer 2004). The pH of soils determines the charge of any acidic or alkaline compound according to its isoelectric value, thus changing the evaporation pressure of these compounds. Assuming that most microbial VOCs are produced in the cell or are released from substrates that are digested by extracellular enzymes, these VOCs are produced in the liquid phase and are emitted only after the solution equilibrium is exceeded. The effect of water is not similar for all VOCs; in particular, polar compounds are more strongly retained than aromatic and aliphatic molecules (Ruiz et al. 1998). Asensio et al. (2007a) investigated VOC exchange rates and how they were influenced by soil moisture, temperature, and the presence of plant roots in a Mediterranean forest soil using proton transfer reaction–mass spectrometry (PTR-MS) and GC-MS. They found soil to be a sink rather than a source of VOCs. Furthermore, their results pointed out that increases in soil temperature and decreases of soil water availability might enhance soil VOC emissions.

Effects of VOC properties on VOC release

Besides the availability of water (or other solvents and sorbents, see Chapter 4.3), the vapor pressure and the water solubility of VOCs affect the retention properties of all VOCs, which are defined as “organic compounds having at 293.15 K (i.e., 20°C) a vapor pressure of 0.01 kPa or more, or having a corresponding volatility under particular conditions of use” (EC Directive 1999). This definition includes members of many different chemical groups, thus showing a high variability in vapor pressure and water solubility, both depending on the physiochemical properties of the habitat. This dependence on environmental factors and the property-related differences between VOCs lead to biases. This was confirmed by a study that aimed to elucidate the effects of soil drought on CO2 and VOC exchange rates where, with changing soil moisture and temperature, different VOCs were emitted in changing ratios (Asensio et al. 2007a, b).

Effects of adsorptive substances on VOC release

In soils, most important is the action of adsorbents like clay minerals or humic acids. Ruiz et al. (1998) investigated the adsorption of n-hexane, n-heptane, n-octane, toluene, xylene, ethylbenzene, methyl ethyl ketone, and of water vapor on sand, clay, and limestone. They found considerable differences among the adsorption levels of the three soil minerals. Polar compounds were more strongly adsorbed than aliphatic and aromatic compounds. Serrano and Gallego (2006) investigated the effect of clay minerals and Corg contents in acid and alkaline soils on the sorption of 25 VOCs. All compounds were adsorbed more strongly in alkaline than in acid soils. In alkaline soils, VOC sorption increased with Corg content, while it decreased in acid soils. In acid soil, clay mineral (bentonite) played an important role in the sorption of VOCs. According to Aochi and Farmer (2005), the sorption/desorption behavior of VOCs must be seen in the context of soil texture and particle architecture. In their study, it was the soil physical properties that impeded the flow of both liquid and vapor phase within the pore network rather than chemical adsorption.

Microorganisms and VOC production

Microorganisms produce VOCs for different reasons. As already described above, highest amounts of VOCs are produced as metabolic end products of anaerobic fermentation processes. Also, the extracellular degradation of complex organic molecules or xenobiotics may result in the formation of VOCs that are lost before they can be absorbed and further degraded. At least some VOCs emitted from decomposing organic materials like leaf litter (Isidorov and Jdanova 2002; Leff and Fierer 2008) or organic waste (Mayrhofer et al. 2006) may originate from losses of such “almost-degraded” metabolites. But also the loss of intermediate products of metabolism is discussed. For example, members of the CytophagaFlavobacteriumBacteroides group that use valine, and others that use isoleucine for ketone biosynthesis, emit different ketones that serve as fatty acid precursor substances. These volatile intermediate products may be lost without any purpose (Dickschat et al. 2005a). Similarly, it is possible that other intermediate products especially metabolites of low molecular weight (e.g., isopropanol, isoprene, furan, etc.) reach the cell surface and escape from cytoplasm by diffusion. Future research in this direction could shed light on unknown aspects of microbial metabolism. Volatile organic compounds that are produced on purpose such as signaling substances are even more interesting as they are produced with high species specificity (see Chapter “Action potential of VOCs”).

Production of mVOCs by microorganisms isolated from soil or similar habitats

Many investigations concerning soil microorganisms were performed under controlled conditions to overcome differences in mVOC production linked to heterogeneity of soil samples, differences in microbial community, and variability of soil properties. Most of the culturable soil microorganisms produce VOCs (Linton and Wright 1993), and it is assumed that similar mVOCs are the main contributors to total soil VOC production (Stotzky and Schenck 1976). Some VOCs are characteristically produced by specific phylogenetic groups or species and can therefore be used for taxonomic purposes (Larsen and Frisvad 1995a, c; Fischer et al. 1999). In a study on degrading household waste, high numbers of Lactococcus lactis were found to be correlating to certain VOCs. Measurement of the VOC emission pattern from a pure culture of L. lactis confirmed the positive correlations for butyric acid, dimethylsulfide, isoprene, and butanone (Mayrhofer et al. 2006). The investigation of VOCs excreted from Pseudomonas spp., Serratia spp., and Enterobacter spp. elucidated species-specific differences in dimethyldisulfide, dimethyltrisulfide, and isoprene production (Schöller et al. 1997). Schöller et al. (2002) screened 26 Streptomyces species and found a production of 120 different VOCs, among them isoprene, acetone, butanol, methyl propanol, methyl butenol, methyl butanol, cyclopentanone, dimethyldisulfide, dimethyltrisulfide, phenylethanol, and geosmin. Studies that investigated the VOC production from different bacterial species and mixed microbial communities of soil are listed in Table 1.
Table 1

References of in vitro and in vivo VOC production from different bacterial and fungal species and of whole microbial communities living in soils or on organic materials

Source

Year

Organisms investigated

Habitat/cultivation media

VOCs found

Method applied

Bacteria

Alström

2001

Different Enterobacteriaceae, Alcaligenes sp., Stenotrophomonas spp., Pseudomonas spp.,

Rhizosphere isolates of Verticillium dahliae, cultivated on PDA

No VOC identified

Petri dish detection assay for herbicidal activity

Bunge et al.

2008

Escherichia coli, Shigella flexneri, Salmonella enterica, Candida tropicalis

Complex media

Diverse VOCs, several unidentified and some identified compounds of low molecular weight < 150 u

PTR-MS

Dickschat et al.

2005a

Cytophaga-Flavobacterium -acterioides Group

Maritime arctic strains cultured on agar

Diverse VOCs, mainly methyl ketones

CLSA, GC-MS

Duponnois and Kisa

2006

Pseudomonas monteilii HR13

Mycorrhizal bacterium, cultivated on minimal medium with different C-sources

No VOC identified

Petri dish detection assay for antifungal activity

Farag et al.

2006

Bacillus amyloliquefaciens IN937a, B. subtilis GB03, E. coli DH5alpha, Pseudomonas fluorescens 89B61

Rhizosphere

Diverse VOCs, 10 identified, 28 not characterized, branched chain alcohols

GC-MS, SPME

Fernando et al.

2005

Pseudomonas fluorescens, P. corrugata, P. chlororaphis, P. aurantiaca

Isolated from canola steem, soy bean plants, cultivated on Luria Bertani broth (LBB)

Fungistatic VOCs

GC-MS

Fiddaman and Rossall

1993

Bacillus subtilis

Several media (potato dextrose Agar, PDA)

No VOC identified

Petri dish detection assay for antifungal activity

Hinton and Hume

1995

Veillonella spp., Bacterioides fragilis

Cecal contents of adult chicken, cultivated on agar medium

No VOC identified

Petri dish detection assay for antibacterial activity

Höckelmann and Jüttner

2004

Benthic cyanobacteria (Calothrix, Plectonema)

Cyanobacterial medium (Jüttner et al., 1983)

Limonene, cyclohexanone, straight chain aldehydes

GC-MS

Kai et al.

2006

Stenotrophomonas maltophilia R3089, Serratia plymuthica HRO-C48, Stenotrophomonas rhizophila P69, Serratia odorifera 4Rx13, Pseudomonas trivialis 3Re2-7, S. plymuthica 3Re4-18, Bacillus subtilis B2g, Pseudomonas fluorescens L13-6-12, Burkholderia cepacia 1S18

Rhizosphere isolates, cultivated on NBII

Diverse unidentified VOCs

GC-MS

Kai et al.

2008

Stenotrophomonas rhizophila P69, review on several other VOC producing bacteria

Batch culture

Diverse VOCs

GC-MS

Kai et al.

2009

Bacillus subtilis B2g, Burkholderia cepacia 1S18, Pseudomonas fluorescens L13-6-12, Pseudomonas trivialis 3Re2-7, Serratia odorifera 4Rx13, S. plymuthica 3Re4-18, S. plymuthica HRO C48, Staphylococcus epidermidis 2P13-19, Stenotrophomonas maltophilia R3089, S. rhizophila P69

Nutrient broth agar plates

No VOC identified

Petri dish detection assay for antifungal activity

Liu et al.

2008

Bacillus subtilis G8

Soil isolate, cultivated on agarose plates

Diverse VOCs , alkyls, alcohols, esters, ketones, acid, amines, oximes, phenols and heterocyclic compounds

SPME GC-MS

Mackie and Wheatley

1999

Diverse bacteria

Soil isolate, cultivated on trpsone nutrient broth (TSB) and nutrient agar (NA)

No VOC identified

Petri dish detection assay for antifungal activity

Mayr et al.

2003a

Pseudomonas spp., Enterobacteriaceae, lactic bacteria, Enterococcus spp.

Air and vacuum packed meat (beef and pork)

Diverse VOCs, several unidentified and some identified compounds of low molecular weight <150 u

PTR-MS

Peladan et al.

1984

Pseudomonas spp.

Certain culture medium

Volatile fatty acids

GLC

Ryu et al.

2003

Pseudomonas fluorescens 89B-61, Bacillus pumilus T4, B. pasteurii C-9, B. subtilis (diverse tribes), B. amyloliquefaciens IN937a, Serratia marescens 90-166, Enterobacter cloacae JM22

Rhizosphere isolates of Arabidopsis thaliana, cultivated on tryptic soy agar plates

No VOC identified

Effects on A. thaliana growth

Schöller et al.

1997

Gram-negative bacteria

Minimal salt AB medium (Clark and Maaloe, 1976)

Diverse VOCs, dimethyl disulphide

GC-FID, GC-MS

Schöller et al.

2002

Actinomycetes (26 Streptomyces spp.)

Yeast starch agar

Diverse VOCs (120 characterized), mainly terpenoides

GC-FID, GC-MS

Vergnais et al.

1998

Staphylococcus spp.

PYS medium (Lechner et al., 1988)

Diverse VOCs

SPME GC-MS

Vespermann et al.

2007

Stenotrophomonas spp., Serratia spp., Bacillus spp., Pseudomonas spp., Burkholderia cepacia, Staphylococcus epidermidis

 

No VOC identified

Effects on fungal and A. thaliana growth

Wilkins and Parkkalle

1996

Actinomycetes (7 isolates)

Medium (not described)

Diverse VOCs,

GC-MS

Zhang et al.

2007

Bacillus subtilis (strain GB03)

Rhizosphere

No VOC identified

Effects on A. thaliana growth and gene expression

Zou et al.

2007

328 soil bacteria: Alcaligenaceae, Bacillales, Micrococcaceae, Rhizobiaceae, Xanthomonadaceae

Soil bacterial isolates

Diverse VOCs

GC-MS

Fungi

Bjurman et al.

1997

Penicillium

Pine wood

1-octene-3-ol, 2-heptanone, 4-allylanisole, 3-methyl-1-butanol

GC-ITD (ion trap detector

Börjesson et al.

1990

Penicillium aurantiogriseum

Barley-, oat-, wheat meal-, malt extract-, Czapek- and Norkrans agar

Diverse VOCs, most dominantly alcohols of low molecular weight and sesquiterpenes

GC-MS

Börjesson et al.

1992

Penicillium brevicompactum, P. glabrum, P. roqueforti, Aspergillus flavus, A. vesicolor, A. candidus

Wheat and oat grains

Diverse VOCs

GC-MS

Börjesson et al.

1993

10 Penicillium spp., Aspergillus spp.

Oatmeal agar

Diverse VOCs, including geosmin

GC-MS

Christen et al.

2000

4 Rhizopus spp.

Cavassa bagasse, apple pomace, soyabean, amaranth grain and soil bean oil

Diverse VOCs

GC-FID, olfactory sensation (6 persons)

Demyttenaere et al.

2004

Fusarium spp.

MEA and PDA

Sesquiterpenes, mainly trichodiene

SPME/HSSE GC-MS

Dickschat et al.

2005b

Streptomyces GWS-BW-H5

North sea water, cultured on agar, liquid culture

Diverse VOCs

GC-MS

Ezra et al.

2004

Muscodor albus

Soil, grown on potato dextrose agar (PDA)

Diverse VOCs

GC-MS/PTR-MS

Fiedler et al.

2001

4 Aspergillus spp., 2 Trichoderma spp., 4 Penicillium spp., Fusarium solani, Mucor sp.

Pure cultures cultivated on, MEA, conifer wood, beech wood, YGC agar

Diverse VOCs (more than 150)

HS-SPME GC-MS

Fischer et al.

1999

Aspergillus candidus, A. fumigatus, A. vesicolor, Emericella nidulans, Paecilomyces variotii, Penicillium brevicompactum, P. crustosum, P. clavigerum, P. cyclopium, P. expansum, P. glabrum

Airborne fungi, cultivated on YES agar

Diverse VOCs

GC-MS

Fravel et al.

2002

Sclerotinia minor, S. sclerotium, S. rolfsii

Lettuce and bean isolates, cultivated on PDA

Diverse VOCs

SPME GC-MS

Gao and Martin

2002

Stachybotrys chartarum

Moist wood

Diverse VOCs

GC-MS

Hynes et al.

2007

Hypholoma fasciculare Resinicium bicolor

Wood decaying fungi, cultivated on malt broth

Diverse VOCs

HS-SPME GC-MS

Kershi et al.

1998

4 Eurotium spp., Penicillium sp., Wallemia sebi

Food spoilage fungi, grown as spore lawn surface cultures on milled wheat agar

No VOC identified

14 polymer sensors (EN)

Larsen and Frisvad

1995a

Penicillium

YES agar

Diverse VOCs

GC-FID/ GC-MS

Larsen and Frisvad

1995b

Penicillium vulpinum

Czapek agar

Mono- and sesquiterpenes

GC-MS

Larsen and Frisvad

1995c

47 Penicillium spp.

Czapec yeast autolysat (CYA), MEA and YES agar

Diverse VOCs (196 characterized, 70 identified)

GC-MS/GC-FTIR

Mattheis and Roberts

1992

Penicillium expansum

Czapek agar

Geosmin

GC-MS

Matysik et al.

2009

3 Penicillium spp., 3 Aspergillus spp., Cladosporium cladosporoides

Dichloran glycerol agar

Diverse VOCs

GC-MS

Minerdi et al.

2008

Fusarium oxysporum strain MSA 35

Agar (as described in experimental procedures)

Diverse VOCs

GC-MS/ growth inhibition of bacterial cultures

Nilsson et al.

1996

5 Penicillium spp.

YES agar

Diverse VOCs (17 identified)

HS-SPME GC-MS

Pasanen et al.

1996

Fusarium sporotrichoides (Sherbakoff), Penicillium verrucosum (Dierckx)

Straw wheat and oat grains

Diverse VOCs (12 identified)

GC-MS

Spilvallo et al.

2007a

Truffle (3 Tuber spp.)

Fruiting bodies

Diverse VOCs

Effects on A. thaliana growth

Spilvallo et al.

2007b

Truffle (3 Tuber spp.)

Fruiting bodies

Diverse VOCs (119 identified)

HS-SBSE GC-MS

Strobel et al.

2001

Muscodor albus

Endophytic fungus of Cinnamonum zeylanicum, cultivated on PDA

Diverse VOCs (28 identified)

GC-MS/ detection of fungal (human and plant pathogens) and bacterial growth inhibition

Strobel et al.

2007

Muscodor albus E-6

Endophytic fungus of Guazuma ulmifolia, cultivated on PDA

Diverse VOCs

GC-MS

Sunesson et al.

1995

Fungi (5 species)

MEA and dichloran glycerol agar

Diverce VOCs (57 identified)

GC-MC

Wheatley et al.

1997

Trichoderma spp.

Wood decaying fungi, cultivated on MEA

Diverse VOCs (45 identified)

GC-MS

Zeringue et al.

1993

Aspergillus flavus (8 strains)

Cultivated on PDA

C15H24 compounds

GC-MS

Communities

Asensio et al.

2007a

Microbial community

Mediterranean soil

Diverse VOCs (31 identified)

PTR-MS/GC-MS

Asensio et al.

2007b

Microbial community

Mediterranean soil

Diverse VOCs (24 identified)

PTR-MS/GC-MS

Brinton

1998

Microbial community

Compost

Volatile organic acids

Total distillation, GC

Leff and Fierer

2008

Microbial community

Different soils and litter

Diverse VOCs (17 identified)

GC-MS

Mayrhofer et al.

2006

Microbial community

Organic waste

various VOCs

PTR-MS

McNeal and Herbert

2009

Microbial community

Hyperthermic, hypersaline soils

Diverse VOCs (72 identified)

GC-MS

Seewald et al.

2010

Microbial community

Temperate soil under different compost load

Diverse VOCs (7 tentatively identified)

PTR-MS/ PTR-TOF-MS

Serrano and Gallego

2006

Microbial community

Different Mediterranean soils

Diverse VOCs (25 identified)

GC-MS

Smet et al.

1999

Microbial community

Aerobic and anaerobic composting of biowaste

Diverse VOCs

GC-FID

Stahl and Parkin

1976

Actinobacteria, bacteria, fungi

Soil

Geosmin, 2methylisoborneol, other VOCs

 

Turan et al.

2007

Microbial community

Poultry litter compost

Diverse VOCs (25 identified and quantified)

Open path fourier transform infrared spectroscopy (FT-IR)

Wang and Wu

2008

Microbial community

Orange waste

Monoterpenes, isoprene, other VOCs

GC-MSD (mass selective detector)

Wheatley et al.

1996

Microbial community

Soil cropped to potatoes

Diverse VOCs (35 identified)

GC-MS

Reviews

Kesselmeier and Staudt

1999

Review on VOCs produced by plants

   

Linton and Wright

1993

Review on microbial VOCs

   

Schnürer et al.

1999

Review on VOCs from food spoiling fungi

   

Schulz and Dickschat

2007

Review on bacterial VOCs

   

Stotzky and Schenk

1976

Review on VOCs from microorganisms

   

Wheatley

2002

Review on VOC mediated bacterial and fungal interaction

   

Like bacteria, also fungi produce a multitude of volatiles, some of which are common to several phylogenetic groups, while others seem to be unique for certain species (Larsen and Frisvad 1995a; Schnürer et al. 1999). Therefore, monitoring fungal metabolites can be used to detect fungal infestation. Larsen and Frisvad (1995a) investigated the VOC production of 47 different taxa within the genus Penicillium under different cultivation conditions. In total, 196 different volatile metabolites were characterized, among them isomeric sesquiterpene hydrocarbons (C15H24), monoterpenes, alcohols, esters, ketones, alkenes, and a few aromatic compounds like geosmin and methyl isoborneol. More than half of the metabolites detected came from one species only, and nearly all taxa produced a unique profile of VOCs, demonstrating the potential of VOC profile analysis to be a useful tool in chemosystematics.

Microbial VOCs from complex samples

Only a few studies tried to characterize total VOC production of a complex habitat like soil. The effects of drought on interannual and seasonal soil VOC and CO2 exchange rates were studied finding that responses of individual monoterpenes and other VOCs were different depending on the compound (Asensio et al. 2007a, b). However, in that study, no microorganisms were identified, and therefore, VOCs produced could not be related to any species. In another study on the VOC production of 40 root-free soil and litter samples, 100 different VOCs could be detected, 70 of which were identified by GC-MS. Furfural and similar furan compounds were found to be produced in highest amounts. The presence of propanoic and butanoic acids was attributed to microbial fermentation. No specific microorganisms could, however, be related to any VOC produced (Leff and Fierer 2008). The effects of composts, mineral fertilizer, and combinations thereof on VOC production have been studied together with determination of microbial community structure by DGGE. Aerobic and anaerobic soil VOC emission was determined after glucose amendment using PTR-MS. Sewage sludge composts and mineral fertilization showed distinct effects on VOC production as well as on microbial community composition. VOC patterns were found to be able to discriminate among soil treatments, but specific tracer VOCs could not be identified (Seewald et al. 2010).

In future studies, combining characterization of microbial community structure by culturing and molecular biological methods with VOC measurements could help to elucidate the origin of different VOCs.

Action potential of VOC

Interactions between bacteria, fungi, and plants mediated through VOCs

Living organisms use VOCs as signaling substances to synchronize certain actions such as sporulation mediated by geosmin (Schöller et al. 2002) within an organism or a population or to impact other organisms living in the environment (Stahl and Parkin 1976). Thereby, VOCs can act on different physiological processes, e.g., inhibition of laccase activity of certain fungi by bacterial VOCs (Mackie and Wheatley 1999), or alteration of processes like nitrification (Wheatley et al. 1996; Ward et al. 1997; Paavolainen et al. 1998; Bending and Lincoln 2000) or nitrogen mineralization (Bremner and McCarty 1996; Smolander et al. 2006). Antagonistic interactions between different species are recognized by growth inhibition (Wheatley et al. 1997; Bending and Lincoln 1999; Wheatley 2002; Bruce et al. 2003; Chuankun et al. 2004; Fernando et al. 2005; Kai et al. 2006). The effects of some VOCs may be perceptible over long distance, such as the antagonistic VOC-mediated action of Fusarium oxisporum strain MSA 35 against other Fusarium wild types (Minerdi et al. 2008).

Microbial volatile organic compounds as promoters and inhibitors of microbial and plant growth

The VOCs produced by bacteria and by some fungi can impact other individuals (Stotzky and Schenck 1976; Wheatley 2002; Farag et al. 2006); VOCs emitted from Bacillus subtilis GB03, Bacillus amyloliquefaciens IN937a, and Enterobacter cloacae JM22 promoted the growth of Arabidopsis thaliana (Ryu et al. 2003; Zhang et al. 2007).

Besides these positive interactions, there are many inhibitions mediated by VOCs. A great variety of antibacterial VOCs are produced from plants (Dorman and Deans 2000), preventing them from direct bacterial attack and thus contributing to soil disease suppressiveness. Also, antifungal VOCs are contributing to soil disease suppressiveness (Fuchs et al. 2004) and are therefore investigated with great interest. A multitude of antifungal VOCs are emitted by bacteria (Mackie and Wheatley 1999; Wheatley 2002; Bruce et al. 2003; Chuankun et al. 2004; Kai et al. 2006; Zou et al. 2007; Liu et al. 2008). The repression of phytopathogens in soils through VOCs emitted by microorganisms (or even transgenic plants) may be a future alternative to conventional bactericides and fungicides and may help to reduce the health risk for consumers and farmers. Examples for fungistatic VOCs are 1-octen-3-ol, mono- and sesquiterpenes, nonanal acid, trimethylamine, and dimethyldisulfide which are produced by actinobacteria and bacteria of the genera Bacillus and Pseudomonas (Wilkins and Parkkalle 1996; Schöller et al. 1997; Chitarra et al. 2004). The VOC production from bacteria isolated from canola and soybean plants inhibits sclerotia and ascospore germination and mycelial growth of Sclerotinia sclerotiorum under laboratory as well as under field conditions. Benzothiazole, cyclohexanol, n-decanal, dimethyltrisulfide, 2-ethyl 1-hexanol, and nonanal were found to completely inhibit mycelial growth or sclerotia formation (Fernando et al. 2005).

On the other hand, some plants are negatively affected by VOCs emerging from soil; e.g., truffle (Tuber melanosporum) volatiles are able to inhibit the growth of A. thaliana, inducing an oxidative burst in A. thaliana leaf parenchyma tissue (Spilvallo et al. 2007a).

Degradation of VOCs

Microbial degradation of VOCs

Since in soils anaerobic and aerobic microhabitats coexist, end products of anaerobic metabolism serve as nutrients for aerobic microorganisms that finally produce CO2 and water (Owen et al. 2007). Many anaerobic microorganisms are able to degrade VOCs like formic or acetic acid (Krzycki and Zeikus 1984; Guyot and Brauman 1986). This metabolic pathway is well known from syntrophic methanogenic archaea. In methanogenic environments, saturated fatty acids, unsaturated fatty acids, alcohols, and hydrocarbons are degraded by the action of syntrophic communities. These syntrophic communities consist of an acetogenic and a methanogenic partner who cannot grow alone on a certain organic compound, but when present together, they can (Stams and Plugge 2009). The degradation of a syntrophic substrate is thermodynamically unfavorable if the product concentrations are at standard conditions (1 M concentration or 105 Pa for gases). The function of methanogens is to consume such products to lower their pressure (10−4–10−5 atm) to improve thermodynamic conditions. The diffusion distances for metabolite transfer should be minimal to ensure physical proximity of the syntrophic organisms (Stams and Plugge 2009). In their natural habitat, syntrophic propionate-degrading bacteria such as Syntrophobacter fumaroxidans form microcolonies with methanogens (Harmsen et al. 1998).

The removal of VOCs from airstreams, where VOCs often are contaminants, is a direct application of VOC degradation. Contaminated air is cleaned by microbes thriving in the biofilters and mineralizing VOCs (Malhautier et al. 2005). Volatile organic compounds are inaccessible to microorganisms as long as they stay in the gas phase. So the process of degradation has to start with the solubilization of contaminants in the liquid phase or after their adsorption to humic acid or clay mineral surfaces (polar and apolar interactions). The bioconversion of VOC pollutants to metabolic end- and intermediate products (VOCs), biomass, or carbon dioxide and water remains the second step. Malhautier et al. (2005) define working biofilters as a complex and structured ecosystem. Considering this, soils are perfect natural biofilters as they provide a multitude of species and microbial consortia (capable of different organic compound-degrading pathways), environmental conditions (from anaerobic to aerobic), and a variety of different VOC adsorbents (water, humic acids, clay minerals).

Physical–chemical degradation of VOCs

Little is known about abiotic VOC degradation processes in soils even though they seem to play an important role (Willson and Jones 1996). This lack of knowledge may be due to the inability to sterilize soils without directly impacting soil VOCs. Anyway, Atkinson and Arey (2003) give a very detailed overview on physical–chemical degradation of VOCs in the atmosphere where photolysis and spontaneous reactions with OH radicals (under the presence of light), NO3 radicals (under the absence of light), O3 (under the presence of light), and Cl atoms (at coastlines) are the main processes responsible for abiotic VOC degradation. Considering the fact that light can only reach habitats located in the soil surface (Woolley and Stoller 1977; Ciani et al. 2005), photolysis and other light-driven reactions (with OH radicals and O3) only occur in a thin surface zone (Konstantinou et al. 2001). In this zone, OH radicals and O3 are produced by microorganisms or they diffuse from the atmosphere. As reactions with Cl atoms play a role in VOC degradation in air of coastal regions, it is likely that this process also works in soils that contain free Cl atoms. The degradation of VOC through NO3 radicals seems to be a rather plausible way of VOC degradation in soils. Nitrate is formed in soils under aerobic conditions (nitrification) and undergoes homolysis (formation of NO3 radicals) if exposed to light, whereas the reaction between VOCs and NO3 radicals does not need light (Konstantinou et al. 2001). Similarly, other powerful oxidants that are formed by microorganisms, like hydrogen peroxide, could also react with VOCs. Nevertheless, these free radicals and oxidants could react with substances other than VOCs (like humic acids or phospholipids) more often as the concentrations of VOCs are comparatively low. This again shows the interdependence of soil organic matter and clay contents with VOC emissions.

Techniques for measuring VOCs

A new tool: PTR-MS

Volatile compounds derive from biotic or abiotic sources, and depending on their chemical constitution, organic VOCs can be differentiated from inorganic compounds that are volatile, such as CO2 or N2. For VOC detection and quantification, different technologies are available. Among the newest technologies to detect VOCs is the PTR-MS which is a very sensitive technique (pptv level) that allows online VOC measurements (Hansel et al. 1995; Lindinger et al. 1998) and that may be combined with time-of-flight (TOF) for higher mass resolution and other methods like gas chromatography. The PTR-MS technique has so far been used for the detection of mVOCs in food quality control (Mayr et al. 2003a, b), organic waste decomposition (Mayrhofer et al. 2006), various soils (Schade and Custer 2004; Asensio et al. 2007a, b; Seewald 2008; Seewald et al. 2010), and for several other habitats (e.g., Kreuzwieser et al. 2002; Karl et al. 2003; Grabmer et al. 2004; Beauchamp et al. 2005). The main benefit of PTR-MS is its high sensitivity that allows online measurement of any air or gas sample.

The PTR-MS was used for investigating interannual and interseasonal influences on the VOC efflux rates of a Mediterranean holm oak forest, finding that soil is rather a VOC sink than a source (Asensio et al. 2007a) and that soil temperature and moisture strongly influence the VOC detection rate (Asensio et al. 2007b). Proton transfer reaction mass spectrometry was also used to identify the VOCs produced by Muscodor albus, a fungus producing antibacterial compounds in soils (Ezra et al. 2004) and to detect VOC emissions from an agricultural soil in northern Germany (Schade and Custer 2004).

Gas chromatography and mass spectrometry

A multitude of papers dealing with the microbial production of VOCs have been published so far. However, the number of VOCs is huge, and in any single publication, only a limited number of VOCs belonging to a few chemical groups can be considered. Most of the published papers describe the identification of VOCs, mainly polycyclic hydrocarbons or fatty acids, by head space or thermal desorption gas chromatography through different columns in combination with a detection by MS, flame ionization detector, flame photometric detector, infrared analyzer or photo ionization detector (Chung 2006). Soil microbial VOCs determined by GC-MS have been discussed in many publications (Mackie and Wheatley 1999; Schade and Custer 2004; Chuankun et al. 2004; Leff and Fierer 2008). Gas chromatography columns are selective for different chemical groups of VOCs and therefore incapable of total VOC estimation. Nevertheless, GC-MS is a valid and still the most common tool for VOC detection and identification. The combination of GC-MS with PTR-MS would not only allow estimating total VOC production but also their identification. To get a higher mass resolution (two orders of magnitude), these methods can be expanded with TOF mass spectrometry to PTR-TOF-MS. Another difference between PTR-TOF-MS and PTR-MS is that with the TOF mass filter, the different velocities of the ions, due to the differences in their mass (with a mass resolution of mm = 5,000), can be determined at once, whereas with PTR-MS, mass abundances are measured sequentially.

Other methods

Besides mass spectrometric approaches, other methods were also applied to detect VOCs. Among them are microresp tubes detecting single volatile compounds (Kaufmann et al. 2005) and metal oxide-based olfactory sensors, so-called electronic noses (Rajamäki et al. 2005; Bastos and Magan 2007; Bruins et al. 2009) or nanoparticle-structured sensing array materials (Han et al. 2005).

Uses in environmental ecology and future potential applications

Tracing organisms

The steady improvement of gas GC-MS methods, electronic noses, TOF-MS, PTR-MS, and other techniques and the use of VOC fingerprints open novel perspectives in microbial ecology. Already now, volatile organic compounds are used to detect microbial contamination of air (Wilkins et al. 2000), drinking water (Wood et al. 1985, 2001), food (Schnürer et al. 1999; Mayr et al. 2003b; Kershi et al. 1998; Gao and Martin 2002; Börjesson et al. 1990, 1992), and medicine (Bruins et al. 2009). Several researchers focus on specific VOCs produced by specific organisms or study the effects of VOCs on organisms (Wilkins and Parkkalle 1996; Schöller et al. 1997, 2002; Ezra et al. 2004). Related to soils, the target is to be able to trace certain microorganisms by measuring specific VOCs or VOC patterns or to be able to infer how a soil has been treated, e.g., if and which type of compost or fertilizer had been applied (Seewald et al. 2010).

Volatile organic compound fingerprinting as a new, rapid tool in microbial ecology

Volatile organic compounds are produced in a high diversity in soils, some of them reflecting physiological properties or the presence of certain species. In different soils or under varying environmental conditions, the amounts and the type of VOCs produced may differ because of differences in community composition or nutrient availability (Wheatley et al. 1997). Determination of total VOC production or at least of a certain fraction results in VOC emission patterns or VOC fingerprints. Such VOC fingerprints may be used for different purposes, and in the future, they could give us information about the state of the soil. McNeal and Herbert (2009) also claim that VOCs are potential indicators for microbial community shifts and community composition in saline coastal upland areas, seasonal wetland, and grassland habitats within the Laguna Atascosa National Wildlife Refuge. They observed significant differences among several environmental factors (different organic substrate amendments, water availability, and soil texture) by GC-MS identification of 72 VOC metabolites and were able to show a correlation between VOC patterns and community-level physiological profiles and fatty acid methyl ester patterns, claiming the suitability of soil VOCs as indicators of soil microbial community structure over large spatiotemporal dynamics and environmental perturbations. Bastos (2007) was able to differentiate among soils and soil treatments employing an electronic nose, suggesting that such non-specific sensor arrays for headspace monitoring provide a rapid and noninvasive method for characterizing soil microbial activity, as influenced by environmental factors and nutrient inputs. In an extensive study, Leff and Fierer (2008) investigated 40 root-free soil and litter samples from different ecosystems and found that VOC production rates were correlated with microbial biomass and CO2 production levels, and it was suggested that VOCs may impact belowground ecology and should therefore be identified and investigated.

Conclusion

Volatile organic compounds from soils have been intensively investigated in the 1980s. The excellent review of Stotzky and Schenck (1976) summarizes the knowledge of that time which has not evolved very much until a few years ago. With newly available tools that even allow online monitoring, soil volatilomics are anticipated to have a bright future. The increasing knowledge on VOC emission patterns from specific organisms of different habitats and under different conditions, together with modern bioinformatics, may in the future allow monitoring the community structure, physiological state, and activity of any microbial community without the need of extraction or cultivation procedures. To achieve this, more studies aiming at the characterization of microorganisms by analyzing their VOC emissions will be necessary. Also, the investigation of the VOC output of microbial communities (from complex habitats such as soils) has to be strengthened to evolve VOC fingerprinting. Additionally, isolation of species from communities investigated and characterization of their VOC emissions under different conditions should be performed.

Even though VOCs from microorganisms are investigated since nearly one century, application of VOC analysis in microbial ecology still is in its infancy.

Notes

Acknowledgments

We thank Hans van Veen and Paolo Nannipieri for the invitation to write this review. The FWF grant P189580 supported our work in this field.

Open Access

This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

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© The Author(s) 2010

Authors and Affiliations

  1. 1.Universitat InnsbruckInnsbruckAustria

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