Interactions with Other Organisms

1.3.4.1 Interactions between Microorganisms

Characterised interactions between microbes in the phyllosphere have been

mostly limited to BCAs acting antagonistically to plant pathogens. They have a great

economic value, as described in Section 1.1.2.3. The Trichoderma genus includes

many species with biocontrol activity. However, they act through a large range of

overlapping modes of action including parasitism, antibiosis and competition (Table

1.4) (Azcon-Aguilar and Barea, 1996; Howell, 2003; Kiss, 2003; Leveau and

Preston, 2008).

Other microbes have been described as “helper” (Dewey et al., 1999; Newton and Toth, 1999). During the axenic isolation of Phaeosphaeria nodorum (formerly

Septoria nodorum), a few bacterial isolates were tightly associated with the fungus.

Co-inoculation of a bacterial isolate with fungal inoculum on detached leaves

resulted in an increase in symptom size on wheat leaf segments. By analogy with

Botrytis cinerea on tomato leaves (Commenil et al., 1998), the mechanism involved

was thought to be due to lipase activity from the helper bacteria, as P. nodorum does

not produce any (Dewey et al., 1999). Located at the interface between a lipophilic

substrate (e.g. epicuticular waxes) and a hydrophilic medium (e.g. a cell), lipases

cleave insoluble glycerides into water-soluble molecules (Jaeger et al., 1999).

Lipases of B. cinerea were thought to be an important pathogenic factor in the early

infection step on tomato leaves (Commenil et al., 1998), but this finding was recently

20

Modes of Action

Target / Effect Active compounds

Mycoparasitism

Pathogen hydrolytic enzymes Extracellular enzymes (proteolytic enzymes)

Impair cell wall rigidity/integrity Extracellular enzymes ( -1,3- glucanolytic system, chitinase)

Antibiosis

Impair cell wall rigidity/integrity Extracellular enzymes Hinder or kill Volatiles

Hinder or kill Antibiotics (gliotoxin, gliovirin, peptaibols, peptaibiotics)

Competition

Space in rhizosphere Nutrition: carbohydrate

Nutrition: micro-element Siderophore Spore germination stimulant

Plant Defences Induction

Plant cell wall reinforcement Callose deposition

Defence proteins Pathogenesis-related proteins (chitinase) Peroxidase

Anti-fungal compounds Terpenoids (gossypol and intermediates)

Adjunct Mechanisms

Increase root and shoot growth

Changes in nutritional status Micro-element uptake improved Strong interaction with the N-fixing Bradyrhizobium japonicum

Microbial aggregations can facilitate exchange of genetic information, known

as horizontal gene transfer (Davey and O'Toole, 2000). Three mechanisms are

involved: transformation, transduction and conjugation. The mobile genetic elements

of the latter two mechanisms include bacteriophages, transposons and plasmids. All

three are considered as major elements of bacterial and fungal evolution (van Elsas et

al., 2003; Richards et al., 2011). However, in situ validation in plants is still lacking.

Table 1.4: List of modes of action and targets or effects with their identified mechanisms involved in Trichoderma spp. biological control (Howell, 2003).

21 1.3.4.2 Interactions with the Host

As the microbes invade and modify the plant environment, the host can detect

them and trigger defensive responses as described in Section 1.1.3.1. Hence

microbes, pathogenic or not, have evolved mechanisms to avoid detection or alter

host recognition. For example, Gram-negative bacteria can directly inject effectors

into plant cells, using a secretion system referred to as the type III secretion system

(T3SS). Pectobacterium atrosepticum, causal agent of potato soft rot on tubers and

black leg on stems, possesses one T3SS participating in pathogenesis (Holeva et al.,

2004). In addition, many mutualistic Rhizobium species have a T3SS, which has been

shown to be essential in the interactions with the host for nodule formation (Marie et

al., 2001). This secretion system has also been hypothesised to be used to interact

with many other eukaryotic organisms (Preston, 2007). The T3SS also promotes

survival of a P. syringae strain on non-host tomato (Lee et al., 2012)

Many of the previously described mechanisms are dependent on the bacterial

cell density (Liu et al., 2008; Ortiz-Castro et al., 2011). This phenomenon known as

quorum sensing (QS) relies on the perception of signal molecules such as acyl-

homoserine lactone (AHL). The more bacteria are present, the more AHL

accumulate in the micro-environment. Once a particular threshold is reached,

expression of particular genes is triggered. Bacteria can possess multiple QS

machineries regulating each other in a complex network (Williams and Camara,

2009). The AHL signal molecules can also be recognised by other bacteria.

Salmonella enterica strains unable to produce their own AHL, showed an up-

regulation of AHL-dependent genes in vitro when in contact with AHL from

Pectobacterium carotovorum, but did not do so in planta (Noel et al., 2010).

22 dependent gene control by quorum quenching, i.e. by secreting enzymes degrading

AHLs (Dong et al., 2001). Plants can also alter microbial communication by

degrading these AHLs (Dong et al., 2001; Chevrot et al., 2006) or sensing them and

triggering plant defences (Schikora et al., 2011). Plant-microbe interactions are

clearly the result of complex and multi-level networks.

Beyond all the strategies developed by both plants and microbes to interact

with each other, many other factors will affect the outcome of the interaction. The

scope of interactions between plants and microorganisms is vast and flexible (Figure

1.6). The fungus Ramularia collo-cygni, causal agent of the ramularia leaf spot

(RLS) on barley, is believed to promote plant health during its growth and trigger

pathogenicity later in the season at the sexual stage (Newton et al., 2010a). The

ability of plants to mobilise their resources (Bolton, 2009), the environment (e.g.

temperature (Wang et al., 2009) and light (Kroupitski et al., 2009; Roden and Ingle,

2009) as well as the plant circadian clock (Roden and Ingle, 2009) affect

pathogenesis but potentially could influence all other leaf-associated microorganisms

23 Figure 1.6: Scope of plant-microbe interactions with its three extreme tropisms: mutualism, pathogenesis and parasitism characterised by a vertical pathogenic gradient from biotrophic to necrotrophic and a horizontal symbiotic gradient from mutualistic to parasitic. Examples of microbes with variable trophic relationship include Rhynchosporium commune (1) and Ramularia collo-cygni on barley (2a), Pectobacterium atrosepticum on Brassica and Solanum tuberosum (2b), Leptosphaeria maculans on Brassica napus (2c), arbuscular mycorrhizal symbioses (3) and Ceratobasidium cornigerum on Goodyera repens (4). Their interactions with plants are further detailed by Newton et al. (2010a).

1.4 SHIFTS IN MICROBIAL POPULATIONS