Introduction
Bacterial symbiotic association with insect host is ubiquitous in
nature, which confers the host with traits to explore new ecological
niches (Sudakaran, Kost, & Kaltenpoth, 2017). Symbiotic bacteria
inhabit either intra- or extra-cellularly inside the insect, providing
hosts with vital benefits, including nutrition supply, pathogen
resistance, assistance in immunity development, among others (Engel &
Moran, 2013; McCutcheon, Boyd, & Dale, 2019). Mutualistic symbionts may
have various origins, including environmental bacteria or infective
parasites (Sachs, Skophammer, & Regus, 2011; Sachs, Skophammer, Bansal,
& Stajich, 2013). Despite of distinct evolutionary pathways, the
convergent transition to a mutualistic symbiotic lifestyle often
involves the loss of virulence factors, degeneration of superfluous
functions, and preservation or obtaining of traits beneficial to the
host (EWALD, 1987; McCutcheon & Moran, 2012). However, direct evidence
showing taxonomic turn-over in insect symbionts are scarce.
Alternatively, comparative genomic analysis of mutualistic symbionts
with the free-living lineages that are phylogenetically closely related
provides a feasible route to examine the evolutionary pattern and
adaptive mechanism accompanying the evolutionary transition to mutualism
(Boscaro et al., 2013; Zheng, Dietrich, & Brune, 2017).
The honeybees have simple but specific gut symbiotic bacteria from
genera of Gilliamella , Snodgrasella , Lactobacillusand Bifidobacterium (Martinson, Moy, & Moran, 2012). They
compose more than 95% of the whole gut community, and the association
with these five core bacteria can be dated back prior to the divergence
of corbiculate bees (i.e., honeybee, bumblebee, stingless bee, and
orchid bee) (Kwong et al., 2017). Although bee gut bacteria are not
intracellular inhabitant and maternally transferred, they are
inheritable among worker bees in the colony through social contacts
(Powell, Martinson, Urban-Mead, & Moran, 2014). Along with the
establishment of symbiotic association, these bacteria are subjected to
genome reduction and evolutionary adaptation (Kwong, Engel, Koch, &
Moran, 2014). This adaptive transition increases their fitness to the
bee gut niche, but also limits the capacity to thrive in other
environments (Ellegaard et al., 2019). As with other symbiotic microbes,
honeybee gut bacteria share ancestry with bacterial species carrying
varied lifestyles (Segers, Kešnerová, Kosoy, & Engel, 2017).
Subsequently, genomic changes are expected to be remarkably different
between the transitions from the common ancestry to gut symbionts and to
other lifestyles (Tamarit et al., 2015). Thus, the honeybee-gut bacteria
system provides a promising model to explore the genomic features
underlying lifestyle transition of free-living bacteria to mutualistic
gut symbionts.
Apibacter is a genus of bacteria that is prevalent in Apis
cerana , Apis dorsata and bumblebee species (genusBombus ), however, they are only sporadically reported inApis mellifera (Kwong et al., 2017; Kwong & Moran, 2016). Our
knowledge on Apibacter is primarily based on genome sequences of
only four strains till now (Kwong, Steele, & Moran, 2018). Phylogenetic
analysis showed that Apibacter spp. form a monophyletic lineage,
which is embedded in the Chryseobacterium clade (familyFlavobacteriaceae ) (Kwong & Moran, 2016). The members of theChryseobacterium clade show a variety of lifestyles, including
environmental free-living, opportunistic or obligate mammal and bird
pathogens (McBride, 2014), of which the genus Chryseobacterium is
the dominant member and consist of mostly environmental habitants. But
strains of Chryseobacterium gleum and Chryseobacterium
indologenes are common clinical isolates, which cause infections in
immunocompromised patients (Calderán et al., 2011). Type strains of
species from Elizabethkingia and Empedobacter are also
opportunistic human pathogens that infect urinary and respiratory tract,
causing sepsis, pneumonia and meningitis (Bhat, Priya, Krishnan, &
Kanungo, 2016; Gupta, Zaman, Mohan, & Taneja, 2017; Lau et al., 2015;
Zaman, Gupta, Kaur, Mohan, & Taneja, 2017). Isolates of generaBergeyella and Weeksella infect mammal respiratory tracts
and female genitourinary tract, respectively (Hugo, Bruun, & Jooste,
2006; Lin, Chen, & Liu, 2007; Slenker, Hess, Jungkind, & DeSimone,
2012). Members of Riemerella and Ornithobacterium are
important bird pathogens, causing infections to respiratory tract and
other organs (McBride, 2014). These bacteria can be transmitted
horizontally by aerosol or vertically between host generations. Type
species of genera Bergeyella , Weeksella, Riemerella andOrnithobacterium are considered non-free-living, showing a
preference to micro-aerophilic conditions, which is different from most
other strictly aerobic members of the Chryseobacterium clade
(Mavromatis et al., 2011; Van Empel & Hafez, 1999). The common features
of the Chryseobacterium clade include proteolytic activity,
carbohydrate utilization and multiple antibiotic resistance, causing
challenges to the treatment of infection. Protease and biofilm formation
are suggested to be important for their pathogenesis (McBride, 2014).
However, the genetic mechanisms underlying the pathogenicity remain
uncovered.
In this study, we isolated and sequenced the genomes of 14Apibacter strains from the Asian honeybee Apis cerana .
Molecular and physiology experiments were conducted to characterize its
colonization positions and specificity inside the bee gut. Comparative
genomic analyses of honeybee symbiotic Apibacter spp. with
phylogenetically related free-living and pathogenic strains from theFlavobacteriaceae family revealed key genomic changes ofApibacter underlying adaptation to mutualistic symbiotic
relationship with the honeybee.