20 A.H.C. van Bruggen, A.M. Semenov Applied Soil Ecology 15 2000 13–24
Fig. 4. Damping-off of tomato seedlings caused by Pythium ultimum and Pythium aphanidermatum naturally occurring in soil
collected 1 day before, 1 day after and 1, 2, 3, and 5 weeks af- ter incorporation of a vetchoats cover crop ‘Cover crop’ or the
same amount of vetchoats cover crop foliage ‘Fallow+debris’ into soil, or after leaving the soil unamended ‘Unamended’ no
soil collected 7 weeks after incorporation, compare with Figs. 1 and 2.
soil, the soil ecosystem is subjected to oligotrophi- cation, and the ratio of oligotrophic to copiotrophic
micro-organisms changes during microbial succession Grunwald, 1997; van Bruggen and Semenov, 1999.
It is therefore likely that a particular range of this ratio is associated with general disease suppression.
The actual range may depend on the pathogen and its position on the scale from R- to K-strategists. For
example, Pythium ultimum, a typical R-strategist, was not suppressed immediately after cover crop incor-
poration Fig. 4, but also not in highly decomposed peat, when the proportion of ‘putative’ oligotrophs
was high Boehm et al., 1997. Soil with organic mat- ter at an intermediate level of decomposition may be
most suppressive in this case. On the other hand, R. solani, a typical K-strategist, was suppressed at later
stages of decomposition of organic debris in soil and at higher ratios of oligo- to copiotrophic bacteria than
Pythium aphanidermatum Grunwald, 1997.
6. Indicators for disease suppression
Similar to the search for indicators of soil qual- ity or soil health, the search for indicators of dis-
ease suppression has not always been systematic. A variety of physical, chemical, and microbial charac-
teristics of soil has been tested for their relationship to root disease suppression Hoeper and Alabouvette,
1996; van Bruggen and Grunwald, 1996; Grunwald, 1997; Oyarzun et al., 1998, unfortunately with mixed
results. Numerous investigations have been conducted to
find individual microbial species that may be respon- sible for the suppressiveness of soils to a variety of
root diseases, with the ultimate aim to find suitable biocontrol agents. If there were individual organisms
responsible for disease suppression, these could then also function as indicators for soils suppressive to
that particular disease. However, this strategy has been successful only for a limited number of cases of
specific disease suppression, in particular, for take-all decline which is primarily caused by phloroglucinol
producing P. fluorescens strains Raaijmakers and Weller, 1998. Since the gene coding for the antibi-
otic has been identified, the presence of quantities of this gene in soil above a threshold level can be used
as indicator for suppressiveness of take-all Raaij- makers, personal communication. Another success
story is the somewhat less specific suppression of wilt-inducing formae speciales of Fusarium oxyspo-
rum by non-pathogenic strains of the same species Hoeper and Alabouvette, 1996; Larkin and Fravel,
1998. However, the genetic characteristics of the sup- pressive strains have not been identified yet. Several
well-known fungal antagonists can often be found in soils with general disease suppressiveness, for exam-
ple Trichoderma, Fusarium, Gliocladium, Penicillium and Acremonium spp. Castejon-Munoz and Oyarzun,
1995; Kurakov and Kostina, 1998. Similarly, cer- tain bacterial genera, such as Pseudomonas, Bacillus,
Burkholderia, and actinomycetes are often found in high populations in soils with general disease suppres-
siveness Workneh and van Bruggen, 1994; Larkin and Fravel, 1998. However, there is not always a
clear relationship between the effectiveness of strains as biocontrol agents and the suppressiveness of the
soil from which they are isolated Castejon-Munoz and Oyarzun, 1995. In fact, most investigations
aimed at finding individual species responsible for disease suppression have been unsuccessful.
Therefore, several investigators have tried to find other microbiological variables that could function
as indicators for general disease suppression. Flu- orescein diacetate FDA hydrolysis proved to be
a good indicator of suppressiveness to several root pathogens, including P. ultimum Boehm et al., 1997,
A.H.C. van Bruggen, A.M. Semenov Applied Soil Ecology 15 2000 13–24 21
Pyrenochaeta lycopersici Workneh et al., 1993; Workneh and van Bruggen, 1994, and Phytophthora
parasitica Workneh et al., 1993. However, FDA hy- drolysis was not a reliable predictor for damping-off
caused by R. solani and sometimes not even for Pythium damping-off Grunwald, 1997. In a study
on cover crop decomposition, high FDA hydrolysis activity coincided with high activity of P. aphanider-
matum Grunwald, 1997.
Analogous to the search for soil health indicators, the usefulness of general variables like microbial
biomass and activity as indicators for disease sup- pression is limited as they are strongly dependent on
the time of sampling in relation to significant events and the composition of the organic food base. There-
fore, various characteristics of the organic food base itself have been investigated as potential indicators
for root disease suppression. The carbon to nitrogen ratio is one of the most frequently tested characteris-
tics; indeed a moderately high C:N ratio was usually least conducive for root disease expression Papavizas
et al., 1968. Grunwald 1997 found that the total C and N content and C:N ratio of coarse organic debris
extracted from soil was most consistently associated with growth of P. aphanidermatum and Pythium root
rot in discriminant analyses with 20 variables. Several techniques for determining the biochemical compo-
sition of the organic food base, such as cross polar- ization magic angle spinning 13C nuclear magnetic
resonance CPMAS 13C-NMR Boehm et al., 1997, have been used to search for indicators associated
with certain stages of organic matter decomposition when disease suppression was observed. This research
established a direct relationship between the concen- tration of pre-colonized cellulose in the substrate and
disease suppression.
As mentioned above, the composition and diversity of microbial communities changes during decompo-
sition of active organic matter in soil. Indeed, a rela- tionship has sometimes been found between microbial
diversity and root disease suppression Nitta, 1991; Workneh and van Bruggen, 1994. Diversity of fun-
gal genera isolated from roots was higher in rotated than in monocropped fields, and in fields amended
with manure or crop residues than in unamended fields. Fungal diversity was negatively correlated with
incidence of brown stem rot of adzuki bean caused by Acremonium gregatum Nitta, 1991. In another
study, the diversity index of functional groups of actinomycetes from tomato rhizospheres was higher
in organically than in conventionally managed soil, and negatively correlated with corky root severity
caused by P. lycopersici Workneh and van Bruggen, 1994. However, in a study with peat mixes at differ-
ent stages of decomposition, the diversity of bacterial species isolated from cucumber root tips was not re-
lated to suppression of Pythium damping-off although a species composition effect was identified Boehm
et al., 1993. Copiotrophic taxa, including fluorescent Pseudomonas spp., predominated in peat mix sup-
pressive to P. ultimum a typical copiotrophic organ- ism whereas oligotrophs predominated in conducive
substrate.
The difficulties encountered in the search for re- liable indicators for disease suppression point at the
need for a more systematic approach. If we assume that disease suppressiveness is a measure of ecosys-
tem stability and health, it is logical to investigate the relationships between diversity, resilience to dis-
turbance or stress, and disease suppression. Similar to our approach to searching for indicators of soil health,
we propose to view disease suppression in relation to resistance and resilience in the face of a disturbance
or stress. Thus, we propose that changes in microbial community structure and the time required to return
to the initial state after application of various distur- bances or stresses could be characteristic for disease
suppressive soils compare Figs. 1 and 2 with Fig. 4. Alternatively, the amount of force needed to perma-
nently damage the microbial community could be an indicator of disease suppressiveness and soil health.
Several characteristics of the microbial community could be measured over time as pointed out in the sec-
tion on indicators for soil health: the copiotrophic to oligotrophic ratio van Bruggen and Semenov, 1999,
the index of microbial succession stage Zvyagintsev et al., 1984, metabolic profiles Bossio and Scow,
1995, PLFA analyses Bossio et al., 1998, or various DNA finger printing techniques after increase of soil
microbial DNA using PCR Liu et al., 1997. This ap- proach seems to be promising based on the results of
Boehm et al. 1997 who found a consistent associa- tion between bacterial composition as determined by
fatty acid analyses and growth in culture at different stages of decomposition of peat with suppression of
P. ultimum.
22 A.H.C. van Bruggen, A.M. Semenov Applied Soil Ecology 15 2000 13–24
7. Conclusion
