Gene copy numbers of defense responses affect seedling survival
The result of partial linear regression analysis showed that at species
level the copy numbers in defense response to insect have a negative
effect on survival rates, and at community level (seedling stations) the
copy numbers of defense response to fungus, insect and virus showed a
negative effect on seedling survival. These results are inconsistent
with some previous studies that showed that resistance was enhanced as
gene copy number increased (Slabaugh et al. 2003, Bradeen et al. 2009).
However, low gene copy numbers of biotic resistance are also found in
some plant species (Lin et al. 2013, Xue et al. 2020), which may help
them to gain evolutionary advantages due to a trade-off effect between
cost on biotic resistance and growth performance. Although high copy
number of defense gene is expected to be advantageous for better
resistance against pathogens, the copy number is also limited to balance
biological cost including not only energy for transcription and
translation but also their toxic effect (Lin et al. 2013). Another
potential explanation is that the low gene copy number within the GO in
a local community may be due to the low presence of attacks from natural
enemies. This hypothesis was supported by a recent genomic research on
balsam poplar, which showed that a lower pathogenic pressure resulted in
a lower defense gene copy number (Prunier et al. 2019). In the
evolutionary process, plant-pathogen and plant-herbivore interactions
may influence gene gain-and-loss and gene copy number of plant species
(Liu 2014) and the copy number of defense related genes can act as an
indicator of the abundance of natural enemies (Zhai et al. 2011). In our
study, all tree seedlings within one community are exposed to the same
putative natural enemy pool, which means that a species with lower copy
number of defense genes may be less attacked by natural enemies and thus
has a higher survival rate.
Moreover, this result also indicated that tree seedlings seemed more
susceptible to gene copy numbers of defense response to insect rather
than to other natural enemies, suggesting that the pressure from insect
pests could be a key driver in structuring seeding community.
Conspecific NDD and neighborhood functional CNV
dissimilarity in defense affect seedling survival
A significant NDD effect from con-specific seedlings was detected in our
study, which agrees with the result of Wang et al. (2020) in the same
forest. The significant NDD in the subtropical forest infers a high
intra-specific competition because of the increased seedling density in
these years after an extreme winter storm (Wang et al. 2020).
Additionally, conspecific neighboring adults had no significant effect
on seedling survival, which can be explained by storm-induced decrease
in tree neighbor density (Man et al. 2011, Wang et al. 2020).
In theory, all the four lineages of natural enemies can mediate negative
density dependence (NDD) caused by Janzen–Connell mechanisms (Song et
al. 2021). Many studies so far have focused on fungal pathogens rather
than other natural enemy types and it is suggested that fungal pathogen
is the key diver of NDD (Bell et al. 2006, Liang et al. 2016, Song &
Corlett 2021). However, we didn’t detect significant effects of
functional CNV dissimilarity on defense to fungus in the present study.
There may be two potential reasons for this. Firstly, the transcriptome
extracted from the leaves cannot reflect the defense responses to
root-associated pathogens, which play a vital role in structuring plant
community (Chen et al. 2019, Tedersoo et al. 2020). Secondly, a
counteraction effect may occur since both fungal pathogens and
mutualistic endophytes exist simultaneously in seedlings (Chen et al.
2019).
Our results also show, for the first time, that pressure from bacterial
and viral pathogens may also be a key driver of NDD for seedlings in
subtropical forest. Functional CNV dissimilarity to adult neighbors in
defense response to bacterium showed a significant and positive effect
on seedling survival, which means that seedlings with distinct defense
response to bacterial pathogens from adult neighbors have higher
probability of survival as predicted by NDD. This pattern is similar to
the results of Zambrano et al. (2017) who also found that neighborhood
dissimilarity of several defense genes have positive effects on
individual survival. Our result suggests that the functional CNV
dissimilarity between plants species can well reflect the niche
differentiation in response to specialized bacteria. In other words,
species with similar defense responses to bacterium may have similar
bacterial pathogen profiles and thus seedlings may be killed by
bacterial pathogen accumulated by adult neighbors with similar defense
responses to bacterium. Moreover, since the defense response to
bacterium has significant phylogenetic signal, this result may also
explain conspecific and phylogeny related NDD. At last, this result is
reasonable because many bacterial pathogens can infect plant leaves and
are fatal to seedlings (Xin et al. 2018) and our transcriptomic data
from seedling leaves can well reflect the interation between seedlings
and phyllosphere bacteria.
The Functional CNV dissimilarity to adult neighbors in defense response
to virus also had a significant and positive influence on seedling
survival. In other words, seedlings growing near adult neighbor with
distinct defense response to virus survive more, similar to the NDD
pattern in defense response to bacterium. While viral pathogens infect
almost all plants in terrestrial ecosystems (Lefeuvre et al. 2019),
plant viruses also have high host specificity. For example, a study on
host range of 29 plant virus species indicated that 69% viruses were
restricted to a single plant family (García-Arenal & McDonald 2003).
Due to the high host-specificity of plant virus, the positive effect of
functional CNV dissimilarity in defense response to virus on seedling
survival is also reasonable.
Although the NDD mediated by insect herbivores have been well documented
in natural forests (Forrister et al. 2019) and manipulative experiment
using insecticide (Jia et al. 2020), the contributions of insect
herbivores to NDD are still debated (Bagchi et al. 2010, Gripenberg et
al. 2014, Song & Corlett 2021). In this study we detected an opposite
pattern that functional CNV dissimilarity to seedling neighbors in
defense response to insect had a negative effect on seedling survival
(Fig. 3), suggesting that seedling survival was higher when surrounded
by neighbor seedlings with similar defense response to insect. This
result is similar to previous studies showing that the survival of focal
species increases in the presence of functionally similar or
phylogenetic related neighbors, which could be explained by habitat
preference (Godoy et al. 2014, Lebrija-Trejos et al. 2014, Wang et al.
2020). However, it seems unlikely the case in this study, because we
found the neighbor seedlings rather than adults with similar anti-insect
responses have a significant positive effect on seedling survival, while
the habitat preference states that the habitats occupied by closely
related adult neighbors might provide suitable resources and enhance
seedling survival (Lebrija-Trejos et al. 2014). This indicates that
insect-mediated biotic filtering rather than habitat preference may be
involved in the mechanism underlying seedling dynamics that only
specific seedlings beyond the host range of local insects survive.
Another possible reason for this pattern is competitive exclusion driven
by competitive ability rather than niche differences (Cavender-Bares et
al. 2004, Mayfield & Levine 2010). During the competitive process,
species with high competitive ability can displace the others and result
in a clustering pattern (Mayfield & Levine 2010). We also found that
the gene copy number of defense response to insect is negatively
associated with seedling survival. This result, together with negative
effect of functional CNV dissimilarity of defense insect on neighbor
seedlings, suggests that the copy number of defense response to insect
can reflect competitive ability of plant species and result in
functional clustering of the seedling community. Taken together, it can
be concluded that the competitive exclusion mechanism caused by the
fitness difference of defense response to insect should be a key driver
of seeding communities.