preferentially utilised by microorganisms with the desired metabolic capabilities,
such as antibiotic production (Boza et al. 2019; Foster et al. 2017). This hypothesis
can be extended, since resources can also drive competition between strains. Therefore, hosts could also provide their microbiome with resources that ensure beneficial
microorganisms successfully outcompete other species (Archetti et al. 2011;
Scheuring and Yu 2012). There are several examples of this occurring in corals
which, along with their dinoflagellate symbionts, produce large quantities of the
compound dimethylsulfoniopropionate (DMSP) (Raina et al. 2013). It is thought that
bacteria that can degrade DMSP may have a nutritional advantage over
non-degraders and that this compound could therefore be important in structuring
the initial coral microbiome (Apprill et al. 2009; Raina et al. 2010). Interestingly, one
bacterial coloniser, called Pseudovibrio, can also use DMSP as a precursor to
produce antimicrobial compounds that inhibit the growth of coral pathogens,
suggesting that DMSP may also play a role in fuelling competitive exclusion and
host protection (Raina et al. 2016).
Finally, a host can also direct microbiome establishment by producing compounds or barriers that block the colonisation and survival of non- beneficial species,
whilst still enabling or promoting colonisation by beneficial species (Boza et al.
2019). Plants exude a variety of toxic molecules, called allelochemicals, which
inhibit a broad range of bacteria, fungi and invertebrates, as well as other plants
growing in close proximity (Neal et al. 2012; Hartmann et al. 2009; Bais et al. 2006).
Beneficial microbial species must be able to tolerate allelochemicals to colonise the
root microbiome of the host plant. The compound DIMBOA (2,4-dihydroxy-7methoxy-1,4-benzoxazin-3-one) is an antimicrobial allelochemical that is constitutively produced by maize seedlings and is toxic to many bacterial species (Neal et al.
2012). However, the plant-beneficial species, Pseudomonas putida, is able to
degrade DIMBOA and additionally upregulates the production of a broad-spectrum
antibiotic called phenazine in response to detecting the compound, allowing effective colonisation of the root microbiome and host protection against fungal pathogens (Neal et al. 2012).
23.4 Taking Inspiration from Defensive Microbiomes
As discussed, defensive microbiomes appear to be a widespread phenomenon in
nature and in several instances, such as in the leafcutter ant and beewolf digger wasp
systems, there is evidence to suggest that they have remained effective at
suppressing pathogens over millions of years. On the flip-side, humans have been
extensively using antimicrobials as medicine and in agriculture for around a century,
but we have seen a rapid rise in pathogenic resistance and a concurrent decrease in
the effectiveness of clinically available antibiotics. This contrast begs the question of
whether there is anything to be learnt from the protective mutualisms that have
evolved in nature between hosts and microbial species and if an understanding of
how protective microbiomes evolve could lead to new ways to combat infections.
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S. Worsley
such as antibiotic production (Boza et al. 2019; Foster et al. 2017). This hypothesis
can be extended, since resources can also drive competition between strains. Therefore, hosts could also provide their microbiome with resources that ensure beneficial
microorganisms successfully outcompete other species (Archetti et al. 2011;
Scheuring and Yu 2012). There are several examples of this occurring in corals
which, along with their dinoflagellate symbionts, produce large quantities of the
compound dimethylsulfoniopropionate (DMSP) (Raina et al. 2013). It is thought that
bacteria that can degrade DMSP may have a nutritional advantage over
non-degraders and that this compound could therefore be important in structuring
the initial coral microbiome (Apprill et al. 2009; Raina et al. 2010). Interestingly, one
bacterial coloniser, called Pseudovibrio, can also use DMSP as a precursor to
produce antimicrobial compounds that inhibit the growth of coral pathogens,
suggesting that DMSP may also play a role in fuelling competitive exclusion and
host protection (Raina et al. 2016).
Finally, a host can also direct microbiome establishment by producing compounds or barriers that block the colonisation and survival of non- beneficial species,
whilst still enabling or promoting colonisation by beneficial species (Boza et al.
2019). Plants exude a variety of toxic molecules, called allelochemicals, which
inhibit a broad range of bacteria, fungi and invertebrates, as well as other plants
growing in close proximity (Neal et al. 2012; Hartmann et al. 2009; Bais et al. 2006).
Beneficial microbial species must be able to tolerate allelochemicals to colonise the
root microbiome of the host plant. The compound DIMBOA (2,4-dihydroxy-7methoxy-1,4-benzoxazin-3-one) is an antimicrobial allelochemical that is constitutively produced by maize seedlings and is toxic to many bacterial species (Neal et al.
2012). However, the plant-beneficial species, Pseudomonas putida, is able to
degrade DIMBOA and additionally upregulates the production of a broad-spectrum
antibiotic called phenazine in response to detecting the compound, allowing effective colonisation of the root microbiome and host protection against fungal pathogens (Neal et al. 2012).
23.4 Taking Inspiration from Defensive Microbiomes
As discussed, defensive microbiomes appear to be a widespread phenomenon in
nature and in several instances, such as in the leafcutter ant and beewolf digger wasp
systems, there is evidence to suggest that they have remained effective at
suppressing pathogens over millions of years. On the flip-side, humans have been
extensively using antimicrobials as medicine and in agriculture for around a century,
but we have seen a rapid rise in pathogenic resistance and a concurrent decrease in
the effectiveness of clinically available antibiotics. This contrast begs the question of
whether there is anything to be learnt from the protective mutualisms that have
evolved in nature between hosts and microbial species and if an understanding of
how protective microbiomes evolve could lead to new ways to combat infections.
504
S. Worsley