1 Introduction
Biological invasions represent major threats to biodiversity as invasive
species can replace native species. Evolutionary and ecological studies
are of major importance for understanding the patterns and causes of
biological invasions and plant and animal invasions have been
extensively studied since the 19th century (Burns,
Murphy, & Zheng, 2018; Cadotte, Campbell, Li, Sodhi, & Mandrak, 2018;
MacDougall, Gilbert, & Levine, 2009). Evolutionary and ecological
approaches aim at elucidating the dynamics of invasions as well as the
advantages of invaders that allow them to outcompete resident species
(Facon et al., 2006; Gladieux et al., 2015). Although microbial
invasions can represent important threats to ecosystems and human
societies, they have been much less studied than invasive plants and
animals (Gladieux et al., 2015; Kinnunen et al ., 2016; Litchman,
2010; Mallon, Elsas, & Salles, 2015; Perkins, Leger, & Nowak, 2011).
In this work, we used evolutionary and ecological approaches for
understanding the patterns and causes of the establishment of the
bacterial pathogen Dickeya solani in potato agrosystems and the
maintenance of the resident, related competitor D. dianthicola .
There are two major clades of potato bacterial pathogens in Europe,Pectobacterium and Dickeya, two sister genera among the
order of Enterobacterales (Gamma-proteobacteria). While somePectobacterium species had settled since before the 1970s in
potato agrosystems in Europe (Pérombelon, 2002), Dickeya species
invaded later, in two successive waves. Mostly isolated from ornamental
plants such as Dianthus, Dahlia and Begonia , D.
dianthicola has been reported in Europe as early as the 1950s.
Isolation of D. dianthicola from Solanum tuberosum dates
back to the 70’s (Toth et al., 2011; Parkinson et al., 2009). Nowadays,D. dianthicola is considered an endemic pathogen of potato plants
in Europe. It is present in all continents, including North-America,
where it was associated with disease outbreaks in potato farms in 2015
(Oulghazi et al., 2017; Patel, Baldwin, Patel, Kobayashi, & Wyenandt,
2019; Sarfraz et al., 2018; Toth et al. , 2011; Wright et al.,
2018).
Dickeya solani has emerged in potato production systems in Europe
much more recently, in the early 2000s (Toth et al., 2011; van der Wolf
et al., 2014). Aside from potatoes, D. solani has been isolated
from ornamental plants such as Hyacinthus , Iris andMuscari , but the primary host(s) of that species remain(s)
uncertain (Chen, Zhang, & Chen, 2015; Slawiak et al., 2009; van der
Wolf et al., 2014). Population genomics revealed little genetic
variation in D. solani , in agreement with a recent spread of this
species following a bottleneck during invasion (Golanowska et al., 2018;
Khayi et al., 2015). An analysis of 20 D. solani genomes
identified a non-synonymous single nucleotide polymorphism (SNP) in each
of the two fliC and fliN genes that are involved in
bacterial motility (Khayi et al., 2015). Horizontal gene transfer events
from D. dianthicola to D. solani have been documented,
adding or replacing genomic fragments (Khayi et al., 2015).
The D. solani invader, as well as the D. dianthicola andPectobacterium spp. residents, are necrotrophic pathogens causing
similar symptoms, resulting in blackleg disease on stems and soft-rot
disease of tubers (Charkowski 2018; Toth et al., 2011). All these
bacteria secrete plant cell-wall macerating enzymes (including the
pectate lyases) and proliferate by assimilating the plant cell remains,
including iron by producing the chrysobactin and achromobactin
siderophores. Pectate lyases, i.e., PelA, PelD and especially PelE, play
a key role in the initiation of the plant cell wall maceration. Using
pectin as a substrate, these enzymes release oligosaccharides that
elicit expression of other plant-cell wall macerating enzymes in a
positive feedback loop (Duprey, Nasser, Léonard, Brochier-Armanet, &
Reverchon, 2016). Noticeably, the pelA gene is truncated, hence
non-functional, in D. dianthicola (Duprey et al., 2016; Raoul des
Essarts et al., 2019). The secretion of these virulence factors is a
costly process that is tightly regulated, being induced by the
perception of chemicals that inform the pathogen on plant host
physiology (mainly plant sugars) and on the size of its own population
(quorum-sensing signals) (Leonard, Hommais, Nasser, & Reverchon, 2017).Dickeya pathogens synthetize and sense two types of
quorum-sensing signals, the N-acylhomoserine lactones and Vfm compounds,
which activate virulence gene expression when a threshold concentration
of signals (reflecting the number of cells in the environment) is
reached (Crépin et al., 2012; Nasser et al., 2013; Potrykus, Golanowska,
Hugouvieux-Cotte-Pattat, & Lojkowska, 2014; Potrykus, ,
Hugouvieux-Cotte-Pattat, & Lojkowska, 2018). By modulating the
synthesis of virulence factors, the quorum-sensing signals participate
in the transition from an oligotroph lifestyle in soils and surface
waters, where Dickeya and Pectobacterium bacteria are
rare, to a copiotroph lifestyle on a plant host, where they increase in
number by several orders of magnitude (Laurila et al., 2008; Potrykus et
al., 2016). Functional differences such as metabolic capacities have
been identified between D. solani and D. dianthicola by
comparative genomics, transcriptomics and biochemical approaches
(Bellieny-Rabelo et al., 2019; Raoul des Essarts et al., 2019), but
fitness differences within host plants remain only partially
investigated (Czajkowski et al., 2013; Czajkowski, de Boer, Velvis, &
van der Wolf, 2010; Raoul des Essarts et al., 2019; Shyntum et al.,
2019). Whether the potato host could be differentially exploited byD. dianthicola and D. solani and whether the two pathogens
stably coexist by using different ecological niches or compete directly
when exploiting this host remain unsolved questions, despite their
importance for understanding the D. solani invasion.
Here, we combined epidemiological records in potato fields, experimental
inoculations and population genomics to contribute to our understanding
of the patterns and ecological determinants of D. solaniinvasion. Epidemiological records over one decade in France allowed to
compare the relative abundances of the D. solani invader, theD. dianthicola resident and Pectobacterium spp .
Using experimental populations and plant assays in greenhouse, with a
diversity of strains and of ecological conditions, we then focused onD. solani and D. dianthicola to determine the ecological
traits that could facilitate or constrain D. solaniestablishment, including competition or ecological niche differences
between the two Dickeya species. Finally, we obtained the genomes
of 56 D. solani isolates that we analyzed together with 20
genomes previously published (Khayi et al., 2015), revealing novel
variations in D. solani population. We focused on the
quorum-sensing gene vfmB to investigate whether its variation,
which has not been studied so far, could be associated to invasion
traits in D. solani .