4 Discussion
Two successive invasions of Dickeya potato pathogens occurred in
Europe: first D. dianthicola in the middle of the
20th century, this pathogen being now considered as
endemic, and second, D. solani at the beginning of the
21th century. Dickeya solani and D.
dianthicola cause similar symptoms on potato plants, so that they are
expected to compete for the same resources. Over ten years, our
epidemiologic surveys revealed a successful establishment of D.
solani together with a maintenance of D. dianthicola . Our
experiments contributed to explain such puzzling co-existence by
contrasted advantages in different parts of the plants and therefore
partially different ecological niches.
By comparing ecological traits of D. solani and D.
dianthicola , using multiple strains representative of the population
diversity, we indeed found contrasted behaviors in these species with
respect to aerial parts versus tubers of S. tuberosum . The
resident D. dianthicola more efficiently exploited host stems
after an inoculation of the wounded and unwounded roots than did the
invader D. solani, i.e., causing higher symptom incidence, and
exhibiting greater proliferation and relative fitness in competition
assays. In contrast, D. solani more efficiently initiated the
rotting process (especially at a low bacterial inoculum) and outcompetedD. dianthicola in tubers, with potential consequences on tubers
in the fields and during storage. Our experimental assays suggested that
tubers represent an entry route of the D. solani invader into the
potato agrosystems.
The capacity of D. solani to cause rooting at a lower bacterial
load than D. dianthicola is likely at least partly due to a
higher expression of the pel enzymes, especially PelE that acts
as an initiator of the plant cell wall degradation (Duprey et al.,
2016). By comparing the expression of some pel genes in emerging
lesions in potato stems and tubers, we observed a higher expression of
the virulence genes pelD and pelE in D. solanicompared to D. dianthicola. Remarkably, by comparing pelgenes in several Dickeya species, Duprey et al. (2016) showed
that D. solani evolved specific regulatory sequences that
contributes to a different expression level of the pelD andpelE genes compared to D. dianthicola . The pelAgene is truncated in D. dianthicola (Duprey et al., 2016; Raoul
des Essarts et al., 2019), but full-length and expressed in D.
solani (as shown in this study), reinforcing their virulence arsenal.
Other metabolic traits could also contribute to the fitness advantage ofD. solani for exploiting tubers: comparative transcriptomics
revealed a higher expression of the glyoxylate shunt in D. solanithan in D. dianthicola, a pathway that contributes to exploit
alternative carbon sources when sugar availability is low (Raoul des
Essarts et al., 2019).
Beside the tripartite interaction between potato plant host, D.
solani and D. dianthicola , additional environmental (soil and
climate) and biological factors (microbiota includingPectobacterium species, other hosts and non-host plants) may
facilitate or limit D. solani establishment (Charkowsky 2018;
Shyntum et al., 2019; Toth et al., 2011). We showed thatD. solani efficiently outcompeted D. dianthicola in
hyacinths, in line with the epidemiologic data supporting the bulb
plants as potential intermediate hosts with an important role in the
recurrent invasion of potato agrosystems (Chen, Zhang, & Chen, 2015;
Slawiak et al., 2009; van der Wolf et al., 2014). Prophylactics may
allow circumventing the propagation of D. solani from an
agrosystem to another. Competition and facilitation processes have been
well studied in pathogenic fungi (Al-Naimi, Garrett, & Bockus, 2005;
Abdullah et al., 2017; Gladieux et al., 2015; Zhan & McDonald, 2013).
Another factor that could reduce competition between the twoDickeya species is their natural low abundance in soils and
surface waters, as well as in tuber seeds that are subjected to
prophylactic diagnosis. A small population size belonging to a single
species could proliferate in a plant individual without any interactions
with another Dickeya or Pectobacterium pathogen species.
These effects linked to size population and dispersal are expected to
delay invasion. In line with this hypothesis, the observed slow increase
of the percentage of Dickeya -positive fields over one decade
(2004-2015) suggested that the Dickeya invasion was still
ongoing. Among the emerging literature on microbial invasion, theD. solani pathogen appears as a good example illustrating how
different ecological components (here, the plant host and a resident
pathogen) should be considered to understand the biological invasion by
a bacterial pathogen (Cadotte et al., 2018; Germain, Mayfield, &
Gilbert, 2018).
The genome sequencing data indicating low diversity in D. solanisuggest a bottleneck during introduction in Europe. The dispersal modes
(either horizontally via soil, surface water, insects and some
agricultural practices or vertically by asymptomatically contaminated
tuber seeds) could contribute to further bottlenecks in D. solani(Charkowsky 2018; Toth et al., 2011). Selection on some genes may also
have further reduced genetic diversity through selective sweeps across
the whole genomes as these bacteria are clonal. Allelic changes related
to quorum-sensing systems were already observed in different plant and
animal pathogens along the host-colonization process (Feltner et al.,
2016; Guidot et al., 2014; Tannières, Lang, Barnier, Shykoff, Faure,
2017), indicating that balancing selection contributed to maintain their
variability. Remarkably, we observed balanced frequencies of two alleles
in the VfmB protein involved in the Vfm-type quorum-sensing inDickeya bacteria. The chemical structure of the Vfm signal is not
known, but it has been involved in tuber rotting and upregulation of
some virulence genes including pectate lyases (pel genes),
proteases (prt genes) and cellulases (cel genes) (Nasser
et al., 2013; Potrykus et al., 2018). Using tuber assays, we observed a
slightly higher aggressiveness in VfmBSer strains
compared to VfmBPro strains. Using transcriptomics ofD. solani pathogens recovered from tuber symptoms, we confirmed
an enrichment of upregulated genes, including pel and prtgenes, in the VfmBSer strain Ds0432.1 compared to
VfmBPro strain IPO2222. Because of the role of the VfmB
protein in Vfm signaling is not completely elucidated, it was premature
to go deeper into the mechanistic characterization of the
VfmBSer and VfmBPro alleles. In a near
future, the reconstruction of allelic mutants and comparison with the
wild strain with otherwise the same genetic background should help
characterizing the role of VfmB in Vfm quorum-sensing and ecology ofD. solani .
In this work, we strongly suggested that the VfmBSerstrains were more aggressive than the VfmBPro strains in
potato tubers, but not more virulent in potato stem assays, and that the
VfmBSer strains were less competitive than the
VfmBPro strains in tuber and stem symptoms. Such an
environment-dependent advantage of VfmBser and
VfmBPro alleles in plant infection assays predicts
balancing selection in natural populations. The VfmBserallele could thus provide an advantage when competition is reduced at
the beginning of the establishment in potato agrosystems and under a
high dispersal condition. In contrast, VfmBser could be
outcompeted by VfmBPro when D. solani is already
established. Our epidemiologic data revealed up and down variation of
VfmBser relative abundance in field populations over the
past decade, in agreement with an increase of competition betweenD. solani VfmB alleles in the more recent sampling year. There is
a very low number of SNPs/InDels (<12) in the genomes beyond
those in Vfm, however, functional genetics will be required to fully
validate the causal role of the Vfm alleles.
In conclusion, this study using complementary approaches, multiple
strains representative of the population diversity and multiple
ecological conditions, brings novel insights allowing a better
understanding of the pattern and causes of the D. solani invasion
into potato production agrosystems, and the reasons whyD. dianthicola nevertheless persisted. More broadly, this study
contributes to our understanding the ecological determinants of pathogen
invasion and of the conditions for the maintenance of endemic
competitors.