11. Host-Symbiont Relationships II - Community Ecology

Question 1

Structure of the lecture (i.e., different aspects of microbiome community ecology)

Answer 1

1. Population genetic processes
2. Host control of community assembly
3. Host specificity
4. Evolutionary processes and phylogenetics
5. Metacommunities

Question 2

What are the four main population genetic processes that shape microbiome community ecology?

1.1

Answer 2

1. Dispersal
2. Selection
3. Drift/Stochasticity
4. Diversification

Question 3

How does dispersal impact community ecology of microbiomes?

1.2

Answer 3

Movement of organisms across space, and between different organisms (i.e., via horizontal or vertical transmission)

Question 4

How does selection impact the community ecology of microbiomes?

1.3

Answer 4

Selection is driven by host factors, such as physiology and immunity. This determines the fundamental niche that is available to microbes, and will then be further driven by processes such as competition, mutualism and exploitation

Question 5

How can stochasticity/drift impact the community ecology of microbiomes?

1.4

Answer 5

Stochastic changes in the relative abundances of different taxa within a community throughout time. Leads to differences between species/within species

Question 6

How can diversification impact community ecology of microbiomes?

1.5

Answer 6

Generationof genetic variation via mutation, which can lead to the formation of new species over time. This may then affect ecology, and lead to evolutionary-ecological feedbacks

Question 7

How can hosts control microbiome assembly pre-colonisation?

2.1

Answer 7

Pre-colonisation control occurs when a host controls the dispersal of microbes. This occurs via many multi-functional effects.

E.g., coprophagy, foraging behaviours, egg-smearing, movement etc.,

Early colonising microbes can often benefit from priority effects, in which the order of colonisation matters

Question 8

How can hosts control microbes during colonisation?

2.2

Answer 8

Compartmentalisation. Means that hosts can…

1. Physically contain symbionts to prevent parasitism
2. Regulate symbiont reproduction (e.g., rhizobial reproduction is controlled by legume host)
3. Engage in partner choice (e.g., Beanbug and Burkholderia)

Question 9

How can hosts control microbiome assembly post-colonisation?

2.3

Answer 9

1. Control of microbial environment
2. Control of immunity (either using microbiome to protect against other pathogens, or facilitate beneficial microbes)
3. ‘Reward and sanction’ (e.g., in rhizobia-legume)

Question 10

How can hosts create specificity in microbiome?

3.1

Answer 10

Host selection leads to microbial specificity. This can be tested for using community ordination analysis, or by measuring intraspecific/interspecific community dissimilarity

Question 12

What is the consequence of high levels of host specificity?

3.1

Answer 12

Tight control leads to low diversity. and highly specific symbioses

e.g., Beanbug and Burkholderia symbionts. There is an ‘obstacle course’ for symbionts, that involves a narrow, mucus-filled passage, competition based selection, and specific crypts in the host

Question 13

What is phylosymbiosis?

4.1

Answer 13

Phylosymbiosis is an ecological pattern that can be used to show host relatedness. Microbial compisition is correlated with phylogenetic relatedness between hosts

Question 14

Give an example of phylosymbiosis

4.2

Answer 14

Vertebrate gut microbiomes and phylogeny. There is strong variation in microbiomes between different clades, suggesting microbial diversification based on phylogenetics

Question 15

How is phylosymbiosis related to population genetics?

4/3

Answer 15

Community ecology could underlie phylosymbiosis

1. Dispersal could lead to diversification based on location
2. Selection could be a result of host contol and genetic divergence
3. Stochasticity/drift can emerge as a result of divergence in allopatry
4. Co-diversification can occur when hosts/symbionts speciate together

Question 16

How can we model microbiomes using metacommunity models?

5.1

Answer 16

Microbes experinece the world as a landscape of suitable habitats (host) within an inhospitable matrix

Question 17

How can we use laboratory methods to measure between-species variation?

5.2

Answer 17

1. Common garden experiments (e.g., Nasonia and Mosquito)
2. Microbiome transfer experiments (e.g., zebra-fish and mouse community shift experiments)
3. Manipulation of candidate host genes (e.g., measurement of AMP protein genes)

Question 18

How can we use field studies to measure between-species variation?

5.3

Answer 18

1. Comparison of host phylogeny and geography (e.g., sampling gut microbiomes across different habitats, which was done by Knowles et al., 2019)
2. Comparative studies for co-divergene (e.g., measuring the fast-evolving gyrB gene in wild great apes)

Question 19

How can we use laboratory methods to measure within-species variation?

5.4

Answer 19

1. Manipulation of candidate genes (e.g., measuring adaptive immunity and T-/B- cells)
2. Altering host genotype (e.g., measuring the impacts of high fat/low fat diets on the human microbiome, and genes activated)

Question 20

How can we use field studies to measure within-species variation?

5.5

Answer 20

1. Statistical comparison of microbial composition (e.g., PCO analysis)
2. Network creation (e.g., measuring microbial dispersal processes in natural populations)

Question 21

What are 3 major caveats in understanding community ecology in microbial communities?

6.1

Answer 21

1. It is hard to separate the impacts of host and environment effects
2. Community ecology processes are highly dynamic, and likely to change throughout lifespan
3. Different composition/taxa will change functional outputs