Common to animal gut environments, the degradation of plant and animal matter
is a different type of broad function where distinct metabolic pathways are required
to break down large polymers into small molecules that can be then consumed and
reused as secondary metabolites (Henson and Phalak 2017; Coyte and RakoffNahoum 2019). Microorganisms at each point in a degradation line contribute to
the overall degradation rate. If each of these contributions constitutes a specific
function, then degradation can be considered as a broad function that encompasses
all necessary metabolic pathways and results in the provision of nutrients to the host.
This differentiation between the broad function of degradation and specific functions
may be key to drawing generalities in diversity–function relationships.
The whole must be viewed as the combination of its individual parts. Here, I
define a broad function as the outcome of multiple specific functions, each utilizing
its own more narrowly delineated specific metabolic pathways. Many of these
specific functions are subject to more narrow phylogenetic constraints or energetically expensive reactions than broader functions (Delgado-Baquerizo et al. 2016).
Depending on how specific functions contribute to the whole, broad functions can be
represented either as parallel contributions from independent specific functions
(Fig. 17.3a) or occurring in series, where each contribution depends on the previous
one in a sequence (Fig. 17.3b). Broad functions in parallel include biomass accumulation, or competitive exclusion of pathogen invaders (Casadevall and Pirofski
2015; García-Bayona and Comstock 2018). Broad functions in series may include
degradation pathways where each microbe uses the products of the previous reaction
to fully break down complex polymers in an animal’s gut (Henson and Phalak 2017,
Coyte and Rakoff-Nahoum 2019).
Each specific function has its own relationship with diversity (gray squares and
dotted arrows in Fig. 17.3): some will have positive relationships, while some will be
asymptotic or negative (Fig. 17.2). However, how the shape of a specific diversity–
function relationship contributes to the broad function is currently unknown. Their
input likely depends on whether specific functions are independent or dependent
upon one another. For specific functions contributing in parallel (Fig. 17.3a), the
broader function will reflect the biodiversity–function relationship of the majority of
its specific functions. For specific functions contributing in series, however
(Fig. 17.3b), I would expect that even one specific function under negative selection
could dramatically impact the diversity–function relationship at the level of the
broad function. Unfortunately, none of these models of functional contributions
have been tested empirically yet.
Similar to the role of scale in defining patterns of diversity and function (Levin
1992; Bond and Chase 2002), distinguishing between broad and specific functions
may play a major role in defining diversity–function relationships. At the smallest
scale, perhaps a specific metabolic transformation can be linked to an enzyme, an
enzyme to a gene, and a gene to one or more genomes. For metabolic processes,
functional rates will likely depend on how many microbial species have a functional gene of interest, and how active those genes are. While this is fitting for
degradative functions, it is more difficult to assign a specific function for other
activities, such as microbes that protect their hosts from disease. In that latter case,
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
309
is a different type of broad function where distinct metabolic pathways are required
to break down large polymers into small molecules that can be then consumed and
reused as secondary metabolites (Henson and Phalak 2017; Coyte and RakoffNahoum 2019). Microorganisms at each point in a degradation line contribute to
the overall degradation rate. If each of these contributions constitutes a specific
function, then degradation can be considered as a broad function that encompasses
all necessary metabolic pathways and results in the provision of nutrients to the host.
This differentiation between the broad function of degradation and specific functions
may be key to drawing generalities in diversity–function relationships.
The whole must be viewed as the combination of its individual parts. Here, I
define a broad function as the outcome of multiple specific functions, each utilizing
its own more narrowly delineated specific metabolic pathways. Many of these
specific functions are subject to more narrow phylogenetic constraints or energetically expensive reactions than broader functions (Delgado-Baquerizo et al. 2016).
Depending on how specific functions contribute to the whole, broad functions can be
represented either as parallel contributions from independent specific functions
(Fig. 17.3a) or occurring in series, where each contribution depends on the previous
one in a sequence (Fig. 17.3b). Broad functions in parallel include biomass accumulation, or competitive exclusion of pathogen invaders (Casadevall and Pirofski
2015; García-Bayona and Comstock 2018). Broad functions in series may include
degradation pathways where each microbe uses the products of the previous reaction
to fully break down complex polymers in an animal’s gut (Henson and Phalak 2017,
Coyte and Rakoff-Nahoum 2019).
Each specific function has its own relationship with diversity (gray squares and
dotted arrows in Fig. 17.3): some will have positive relationships, while some will be
asymptotic or negative (Fig. 17.2). However, how the shape of a specific diversity–
function relationship contributes to the broad function is currently unknown. Their
input likely depends on whether specific functions are independent or dependent
upon one another. For specific functions contributing in parallel (Fig. 17.3a), the
broader function will reflect the biodiversity–function relationship of the majority of
its specific functions. For specific functions contributing in series, however
(Fig. 17.3b), I would expect that even one specific function under negative selection
could dramatically impact the diversity–function relationship at the level of the
broad function. Unfortunately, none of these models of functional contributions
have been tested empirically yet.
Similar to the role of scale in defining patterns of diversity and function (Levin
1992; Bond and Chase 2002), distinguishing between broad and specific functions
may play a major role in defining diversity–function relationships. At the smallest
scale, perhaps a specific metabolic transformation can be linked to an enzyme, an
enzyme to a gene, and a gene to one or more genomes. For metabolic processes,
functional rates will likely depend on how many microbial species have a functional gene of interest, and how active those genes are. While this is fitting for
degradative functions, it is more difficult to assign a specific function for other
activities, such as microbes that protect their hosts from disease. In that latter case,
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
309