Community: A group of two or more different species occupying the same geographical area at the same time.
The primary focus of community ecology is the interaction of species and the consequences of these interactions.
Symbiosis: A close and prolonged association between two organisms of different species.
Each species in the symbiosis can be affected positively, negatively, or not at all.
Symbiosis is NOT the same as mutualism.
Types of Interactions Between Two Species
Competition: Species compete for resources.
Competition is always a lose/lose interaction because no one will get all the resources.
Predation/Parasitism: One organism kills and consumes another.
Provides energy to prolong life and promote the reproduction of the organism that does the killing.
Predation influences organisms at two ecological levels:
Individual: The prey organism has an abrupt decline in fitness, as measured by lifetime reproductive success, because it will never reproduce again.
Community: Predation reduces the number of individuals in the prey population. Adaptations to reduce predation in prey species significantly affect population.
Predation and resource availability drive changes in natural populations through:
Bottom-up control: Limiting resources determine population size.
Top-down control: Predation limits and determines population size.
Mutualism: Both species benefit from the interaction.
Trophic: Partners specialize in helping each other gain energy or nutrients.
Defensive: One partner receives food or shelter in return for defending the other partner against predators, parasites, or herbivores.
Dispersive: One partner disperses pollen or seeds while the other partner receives pollination or nutrition. Often plant/animal partnerships.
Commensalism: One species benefits from the interaction while the other is unaffected.
The type of species interaction between bacteriophages and bacteria is predation because they are viruses that infect and kill bacteria.
The interaction that occurs between bacteriophages and humans is mutualism because bacteriophages will infect pathogenic bacteria in the human gut, and the gut gives the bacteriophages a nice place to live.
Ecological Niche
Ecological niche: The combination of a species’ physical habitat and its ecological role in the habitat (role in the environment).
Fundamental niche: The range of conditions and resources within which individuals of a species can exist.
However, other species may compete for the same resources, and a species may be exposed to predators or pathogens in that niche.
Realized niche: The range of conditions and resources within which a population can persist in the presence of competition and predators.
Intraspecific competition: Competition within individuals of a single species.
Interspecific competition: Competition among different species.
Limiting resources include food, mates, and space.
Competition is always a lose/lose interaction because no one will get all the resources.
Competitive Exclusion
A Russian biologist named G.F. Gause demonstrated the principle of competitive exclusion.
Competitive exclusion: The idea that two species cannot occupy the same niche at the same time.
One will always be better and outcompete the other.
Ex. Red squirrels and grey squirrels are in competition because the grey squirrel can eat nuts and seeds that haven’t fully ripened because their digestion system can handle it, but red squirrel digestion systems can't, so the food source will always be depleted by the grey squirrels first because both prefer eating broadleaf nuts. This is why red squirrels live in pine forests, because they can find food there.
Red squirrels have been competitively excluded from their preferred habitat.
Grey squirrels also have an accelerator in the form of parapox virus and give it to red squirrels and kill them even though the virus doesn’t affect them itself. This is why they can’t coexist.
Cultured two different species of paramecium, P. aurelia, and P. caudatum, and fed them a constant amount of food every day.
When grown in separate containers, both thrived.
But when grown together, species competed for limited food available.
Because P. aurelia could gather food more quickly, P. aurelia survived and reproduced, while P. caudatum starved. Eventually, only P. aurelia remained in the culture.
When two finch species feed on the same sized seeds, you might have competitive exclusion.
If they feed on different sized seeds, they will probably be able to co-exist.
Resource partitioning promotes coexistence.
Resource partitioning: An evolutionary history in which competition for similar resources promoted the use of different niches by different groups and eventually diversification of species within a group.
Ex. when P. caudatum and diff species, P. bursaria were placed in competition both could coexist.
Each specialized in a different food source within the culture, bacteria near the surface, or yeast toward the bottom.
Niche Partitioning
In Robert MacArthur’s research, he concluded that birds behave in a way so they can be exposed to diff kinds of food.
They are partitioning a limiting resource––their supply of insects. This leads them to occupy diff niches.
Animals live in rainforests because there are so many ways to partition the resources.
Population Cycles in Predator-Prey System
The snowshoe hare is primary lynx food.
When hares are plentiful, lynx eat little and take two hares every three days.
As predation increases and starvation sets in, the population declines for the hare.
Lynx population will decline following hare population crash after a delay of one and two years.
When hare population declines, lynx continue to eat because it's easier to catch a starving hare.
When hares become scarce, the lynx population declines because a lack of fat reserves makes them less fit to live through starvation and cold temperatures.
Fertilizer and extra food indicate bottom-up regulation.
Biological Control
Example of successful biological control
Opuntia stricta was introduced to Australia around 1840 but became a pest.
Moth cactoblastis cactorum was introduced to infest prickly pear.
Less than a decade 1.5 billion tons of prickly pear were consumed by larvae.
Successful example of the introduction of new organism into Australia without generating secondary damage.
Successful Specificity:
The success of this example of biological control is due to the particular adaptation of cactus and moth.
The cactus spread because it uses CAM photosynthesis.
The cactus moth senses the depletion of CO2 near the surface of the plant through a specific sensor and lays eggs only on plants where this is the case.
Predator-prey interactions often rely on particular adaptations with each organism trying to gain an advantage.
Scientists have to be really careful when they introduce a species because they risk eating native organisms too if it goes wrong.
Predators have adaptations for exploiting prey.
The form and function of predators is related to their need to capture and eat prey.
Predators must actively pursue individual prey or consume a large amount of small prey. Predators must also be able to ingest and digest prey.
Prey have adaptations for avoiding and deterring predators.
Crypsis: Camouflage appearance and resting position to avoid detection.
Warning coloration: Produce noxious chemicals or obtain them from food. Advertise with bright colors and conspicuous patterns. Production and ability to withstand noxious chemicals requires a considerable amount of energy.
Defenses against Herbivory
Plants can't run or move so they produce special defenses.
They have adaptations to hide or look less appealing.
Have structural defenses like thorns or spines.
They can produce poisonous or distasteful chemicals.
Pandas have a long cecum.
Community Ecology 2
If species can split resources up, they can co-exist = resource partition
If species can’t split resources up, they can’t co-exist = competitive exclusion
Usually in situations there is only bottom up and top down regulation, but sometimes you can have both
Goals
Be able to predict the progression of species establishing during succession
Explain the processes determining succession of plant species
Be able to explain why it’s difficult to clearly define a healthy microbiome.
Be able to state factors that can affect a person’s microbiome.
Explain how a baby’s microbiome differs by their mode of delivery.
Explain the potential effects of antibiotics on the microbiome.
Notes
Succession: Change in community composition over time, often with a predictable pattern:
Community Composition: Identity of members of the community and their relative abundance
A combination of who is there and how common or rare they are.
Primary succession: Colonization of habitats devoid of life (volcanism, dune, barrier island formation, and glaciation)
Pioneer stage, very first plant species after primary succession (moss, weeds that don’t need too much nutrient or good soil)
Species are r-selected because they die fast but have lots of babies
Dryas stage, woody species are coming in because there is better soil to support them now
Alder stage, small fast-growing trees start growing
Spruce stage, longest place of exposition because now big trees can form
Late-stage species are k-selected because they live longer
These species also need more quantity and nutrient-dense soil to grow
Secondary succession: Habitats following a disturbance (biotic or abiotic), which leaves seeds, spores, etc. as well as soil intact
How do early successional species affect later species?
Facilitation: Species modify the environment and facilitate colonization by other species
Ex. The nitrogen-fixation by dryas and alders that allows spruces to become established in Glacier Bay
Inhibition:
Ex. Old field species such as goldenrod and thistle produce root exudates that inhibit the germination and growth of potential competitors
It is hard to maintain lawns because you are battling secondary succession every time you mow your lawn
Succession can take place over much smaller scales and shorter time intervals.
It can happen within our bodies
Ex. When you get your teeth cleaned you are setting them up later for succession
There is the potential for evolution during succession
The Human Microbiome
The human microbiome is the collection of microbes that live on and in us
Bacteria
Fungi
Viruses
Archaea
Microbes and human interactions can be:
Mutualistic
Commensal (benefit bacteria, but we are unaffected)
Parasitic (benefit bacteria and is bad for us)
Also, microbe-microbe interactions
How are microbiomes identified and analyzed?
Groups of bacteria can be identified by next-gen sequencing
Allows for sequencing of entire communities at once
Communities can be analyzed for their component taxonomic groups or compared to other communities
Plots are in different areas where you sequence it
When you look at the graphs, you should be able to determine the most common phyla in the bar chart (dark orange)
For the graphs, the further away from each other they are, the more different they are from one another
Communities in and on our bodies
Microbes have been on Earth for 3 billion years
We evolved in the midst of microbes
We evolved organs to house microbes
Microbial communities are highly personalized
Each body site has its own microbial community
We are ecosystems made up of many microbial communities
You will get different communities from every part of your body
Many factors influence a person’s microbiome
The most studied factor is diet
Diet changes the microbiome composition, but microbiome composition can also affect host metabolic capabilities
Diets can influence microbial diversity
Fermented foods can increase microbial diversity
A high-fiber diet does not create diversity
What do the microbes in the gut microbiome do?
Ferment dietary fiber to feed other microbes
Supply the gut with energy
Make vitamins
Break down toxins
Protect against pathogens (by setting up camp bacteria normally would and by producing antigens that defend the host against them).
When does a person’s microbiome form?
At birth, a baby’s gut microbiome is similar to the mother’s vaginal microbiome
It forms a lot during the first few years as the baby ingests food
The microbiome from breastfed babies has similarities to its mother’s breast milk
Non-breastfed babies have a different microbiome
Babies’ microbiomes DIFFER by delivery mode
Babies born vaginally have a similar microbiome to the mom’s vagina
Babies born by C-section have a similar microbiome to the mom’s skin
A healthy microbiome is a rich microbiome
Decreased richness (decreased number of bacterial species and their genes) is associated with:
Diseased states and the consumption of a westernized diet
Marked obesity, insulin resistance, dyslipidemia, and inflammatory phenotypes
Increased richness is associated with:
Consumption of an agrarian diet, rich in fruits and vegetables and higher in fiber
Energy-restricted diets
Long-lived Chinese people have richer microbiomes than younger adults
We’re still trying to figure out how the richness of the microbiome directly affects health outcomes
Effects of Antibiotics on the Gut Microbiome
Antibiotic treatment alters the population structure and composition of the microbiome community
Changes to the community lead to:
A change in resource availability and species-species interaction
Opening niches available for pathogenic intrusion and leading to the loss of colonization resistance
Antibiotics also select for antibiotic-resistant community members, enriching the presence of resistance genes in the microbiome
Treatment with antibiotics promotes the transfer of genetic information among bacteria by increasing conjugation, phage transduction, and plasmid mobility, primarily through the activation of cellular stress responses
When you take antibiotics, you are killing the bad bacteria in your body, but that also kills the normal bacteria too
You now have a different composition of bacteria in your gut, and if the remaining ones communicate with each other, they will build a resistant tolerance to the antibiotic, so your treatment won’t work as well anymore, and other bacteria might be affected easier.
You have also created open spaces that bacteria you may not want to colonize them
Clostridium Difficile Infection
On a healthy gut microbiota, C. difficile is typically unable to colonize the gut in the presence of hundreds of strains of bacteria that are normally present
After broad-spectrum or long-term antibiotics disrupt the healthy community, C. diff spores from the environment (usually hospitals) are able to germinate and grow within the gut and produce potent toxins
Because C. diff can form spores that are not killed by most antibiotics, and the normal microbiota is diminished, the infection is often poorly responsive to standard antibiotics
To treat C. diff infections, you take fecal microbiota transplants
FMT has an overall success rate of 92%, with 89% of patients responding after a single treatment
The first to use FMT transplants for medicinal purposes were Ancient Chinese
Watered-down stool and called it yellow soup
Something that would not disqualify you from being a fecal sample donor is eating a veggie diet
Traveling the world would disqualify you because different parts of the world have different microbes, and we have already adapted to the ones in ours.