the hologenome

Question 1

lichens

Answer 1

• fungal partner is the larger organism (unusual)
• transfer of sucrose from photobiont rapidly converted into mannitol, a fungus-specific sugar
• ~10% terrestrial environment dominated by lichens, usually extreme environments (tundra/desert)
• seen on branches if air is clean (most obvious in winter, not shaded by leaves, occupies niche
• latin name describes fungus
• photobiont lives inside thallus, algae or cyanobacteria

Question 2

lichen, soil-crust stabilisation

Answer 2

• desert soil crusts often dominated by lichens
• ‘Toyota-isation’, car tyre tracks remain for years until soil crust habitat recovers (0.01-90mm growth per year)

Question 3

lichens, mycobionts

Answer 3

• fungal partner
  -usually ascomycetes, ~20spp. basidiomycetes
• obligate mutualists
• 13,000 spp. lichenised, ~20% known fungi
• lichens are polyphyletic (convergent evolution)

Question 4

lichens, photobionts

Answer 4

• 25 genera chlorophyta (90%), 80% unicellular, 10% filamentous
• 15 genera cyanobacteria (10%), usually Nostoc or Scytonema species
• cyanobacteria can fix N2 (heterocysts)
• Treboxia spp. = most common chlorophyta, not often free living
• ‘trapped’ by fungi, most can also be free living

Question 5

lichen, variable photobionts

Answer 5

e.g. Sticta canariensis
has an algal and cyanobacteria photobiont in different parts of its thallus

Question 6

attachment of foliose lichens to surface

Answer 6

• rhizines
• can also secrete organic acids that weather the rock to obtain nutrients

Question 7

lichen morphology

Answer 7

crustose, foliose, leprose or fruticose

Question 8

lichen dispersal

Answer 8

• asci/ascospores = dispersal of fungal partner only
• diaspores, fragmentation propagules of thallus
• contain algal cells surrounded by fungus
• maintain the partnership
• come from soredia/isidia, thallus outgrowths

Question 9

lichen, thallus ultrastructure

Answer 9

• upper cortex, symbiont layer, medulla, lower cortex
• pores in upper cortex coated in hydrophobins allow CO2 in for photosynthesis
• algal cells protected by fungal cortex
• lower cortex acquires nutrients from substrate
• algal cells more ‘leaky’ within thallus (more sucrose transfer)
• nutrient transfer interface, haustorium pushes into algal cells (increased surface area)

Question 10

lichens, somatic incompatibility

Answer 10

• intra/interspecific competition for light and space
• avoid disease transmission
• genetically distinct individuals create zone lines, non-self recognition
• foliose lichens can overgrow crustose lichens

Question 11

lichens, air pollution

Answer 11

• inhabit exposed habitats so very sensitive to airborne pollutants
• sensitive to SO2 pollutants (acid rain), mostly been removed from air so some lichens are recolonising cities
• NOx gases (NO and NO2, mainly from car exhaust and agricultural fertilisers) affects competitive interactions, reducing fitness of N fixing cyanobacterial photobionts

Question 12

useful lichen indicators of airborne pollutants

Answer 12

• Lobaria (lungwort), rare, seen in West of Scotland and Ireland but not West Wales as it is sensitive to NOx, agricultural fertilisers
• Xanthoria, tolerant of NOx and high nitrates, often seen on landward sides of rooves and cliff faces (bird faeces)

Question 13

Mynnyd parus, copper mine in Anglesey

Answer 13

• Thomas Pennant (1773) noted fumes from smelting copper had killed surrounding lichen and mosses
• first evidence of industrial pollution

Question 14

the human microbiome

Answer 14

• can assess gut health through stool sample then NextGen sequencing, bacteria identified via 16S sequences
• different microbes occupy different parts of skin surface, can map skin

Question 15

human gut biome, examples of ‘good’ flora

Answer 15

• high floral diversity indicates good health
• Bifidobacteria help to regulate levels of other bacteria, modulates immune response, prevents tumours, produces vitamins
• E.coli, involved in vitamin K2 production (important in blood clotting)
• Lactobacilli, vitamins and nutrients, immunity, protection against carcinogens

Question 16

human gut biome, examples of ‘bad’ flora

Answer 16

• Campylobacter e.g. C.coli, disease through contaminated bacteria
• E. faecalis, post surgical infections
• C.diff

Question 17

main bacterial phyla of human gut

Answer 17

• Firmicutes, gram pos, endospores, e.g. Clostridium, Lactobacillus
• Bacteroidetes, gram neg, associated with a high fibre diet e.g. Prevotella
• Proteobacteria, gram neg, associated with a high sugar/poor diet e.g. E.coli, pseudomonas
• Actinobacteria, gram pos e.g. Propionibacteria

Question 18

what main bacterial gut phyla can indicate

Answer 18

• babies have largely proteobacteria as milk is a high sugar diet, bacteriodetes increase with solid food (higher fibre diet)
• proteobacteria is also associated with malnutrition and obesity (poor diet)
• more firmicutes as we age (changing immune system)

Question 19

faecal transplants, C.diff

Answer 19

• antibiotics damage gut microbiome, creating a vacuum that C.diff can colonise (associated with hospitals,
  longterm antibiotic usage and
  old age)
• C. diff leads to colitis (inflammation of large bowel
• faecal transplants have 94% success rate in treating C.diff (vancomycin ~30%)
• stomach acid is barrier to colonisation, faecal transplant through duodenum
• recipient community outnumbered by donor community after a few days

Question 20

network analysis

Answer 20

• analyse interactions between gut flora
• which bacteria can co occur and which are mutually exclusive
• healthy guts have more positive interactions

Question 21

how gut microbiomes influence BMI

Answer 21

• mice inoculated with bacteria from lean/obese human twins followed similar BMIs (‘infectobesity’)
• notobiotic mice used, raised steriley, no microbiome
• bacteria digest polysaccharides (anaerobic fermentation) to create different volatile fatty acids
• fatty acids can interact with hormones associated with hunger (GLP-1/3 etc.)
• obese mouse had less propionate and butyrate levels

Question 22

TMAO

Answer 22

• gut microbial metabolite that diffuses through gut wall into blood stream
• enhances platelet hyperreactivity and thrombosis risk
• from bacteria associated with a poor diet
• increases risk of strokes, heart attacks and heart failure

Question 23

yeast Debaromyces

Answer 23

• prevents intestinal wound healing by colonising damaged area and disrupting repair process
• antibiotics kill Akkermansia bacteria, aids wound healing by colonising damaged parts and releasing deoxylcolate
• creates vacuum, fungi proliferate
• associated with dysbiosis including crohns, colitis, IBS etc

Question 24

assortative mating, Drosophilia hologenome

Answer 24

• drosophilia raised on a particular food tend to mate with flies raised on the same food, molasses vs starch
• flies raised on starch had more Lactobacillus plantarium
• cuticular volatiles (smell created from gut bacteria) of flies causes assortative mating, first step to speciation
• effect abolished by antibiotics and reestablished by reinfecting flies with Lactobacillus (Koch’s postulus)

Question 25

hologenome theory of evolution

Answer 25

• coined by Jefferson 1994, studying corals and photosynthetic symbionts
• extension of symbiotic theory, survival and evolution of host linked with symbiont
• have to evolve in tandem to increase fitness
• mechanisms of stable vertical transmission are important

Question 26

vertical transmission of hologenome

Answer 26

e.g. diaspores in lichens, queen ants/termites carrying fungus, acquisition of gut microbes from parent in mammals
- reptiles don’t often give offspring microbiome (no live birth, breastfeeding) e.g. turtles
- coprophagy of parent’s faeces common e.g. iguanas, tortoises