MODULE 2 - Microbial Interactions and Biogeochemical Cycles Flashcards
how is a microbial community established?
competition (direct or indirect)
what is direct competition?
competition that involves physical contact e.g. secretions, colicin production by E. coli
what is indirect competition?
competing without actually interacting
what is interference competition?
direct: physical fighting over resources
what is exploitative competition?
indirect: competition through consuming scarce resources
what are the two main categories that processes are grouped into in ecology?
stochastic
deterministic
what does stochastic mean?
processes occur at random. Not set rules, so predictions are not possible. Outcome will be impossible to determine
what does deterministic mean?
processes follow a consistent set of rules. Implies that given some input and parameters, the output will always be the same. You can easily predict what will happen once you know the rules and the conditions in the ecosystem
how is it determined what organisms takes over a newly opened environment?
competition/cooperation outcomes
why/how does microbial community succession occur?
as time passes and conditions change new niches open allowing replacement of species
what are ecological successions?
changes in species composition observed upon a disturbance that opens up niches for colonisation
what two categories can ecological successions be grouped into?
primary succession
secondary succession
what is primary succession?
environments are colonised for the first time (so there is no competition)
what is secondary succession?
occur in established systems when a disturbance reduces diversity leading to a renewed succession thanks to newly available resources or removal of competition
how is species succession a directional process with reproducible and thus predictable outcomes?
species replacement is driven by adaptation to a narrow set of environmental conditions so that when conditions change an existing species will be outcompeted by a different species which are better adapted to the newly emerging conditions
what is the driving force for microbial community succession?
gradients
these could be metabolic side effects (e.g less substrates, change in pH) or purposely generated metabolites (e.g. bacteriocins, antibiotics)
how can disturbances trigger secondary successions?
they affect the species composition, structure and function within an ecosystem
they can have both positive and negative effects
they can be drivers of change and increase diversity by reducing competition
they can also collapse a community
how do microbial communities respond to disturbances?
resistance (ability of an ecosystem/community to not react to a disturbance) or resilience (the ability to bounce back after a disturbance)
however a disturbance that is large or frequent enough can overcome both of these and collapse the community
what is life history strategy?
the general survival strategy used by a microbe to ensure species viability. Dictates the conditions under which a microbe can not only survive, but thrive
what are R strategists?
fast growers
don’t compete well, need a lot of resources, fast reproduction, do not depend on others, have extreme population fluctuations
e.g. pseudomonas
what are K strategists?
slow growers
excel in competitive environments with low resources, efficient, stable population numbers
e.g. streptomycetes
what are the factors that can affect community succession?
competition
cooperation
disturbances
what is commensalism?
one species benefits and the other is neither harmed nor helped
what are social cheaters?
individuals in a population that benefit from the cooperative behaviour of other individuals without themselves contributing to cooperation
what are siderophores?
compounds which scavenge for iron and bring it back to the cell
give an example of symbiosis between insects and a microorganism
insects such as termites collect biomass and feed gardens of fungi, which they prune and select for specific phenotypes and eventually eat. We know these insects are ‘farming’ the fungi because it can’t survive without the termites feeding them. These colonies are not pure cultures
what evidence is there to suggest that the insects and microbes in symbiotic relationships evolved together?
strong co-evolutionary signals
outline the symbiotic relationship between ambrosia beetles and fungi
ambrosia beetles have specialised structures called mycangium which they use to transport fungi
they plants the fungi by inoculating wood and are dependent on it for survival, while the fungus depends on the beetle for survival
what is bioaccumulation?
the idea that in a small organisms you have certain amounts of trace nutrients but as bigger animals eat them they accumulate
ants have higher nitrogen content than fungi or leaves, where are they getting this nitrogen from?
bacteria which fix nitrogen from the atmosphere live in the fungal gardens
how did they prove that the ants were getting nitrogen from nitrogen fixing bacteria in fungal gardens?
by radio labelling nitrogen in a simulated colony it was shown that the ants are obtaining nitrogen from nitrogen fixing bacteria. The N content of the ant was always higher in N2 enriched samples
what did a phylogenetic tree of bacterial isolates from other symbiotic ants fungal gardens show?
each ant species has its own nitrogen fixer
what evidence is there to suggest that there are strong co-evolutionary links between the ant, the fungi AND the bacteria?
the bacteria produce antibiotics which kill off unnecessary microbes in the insect farms and this process is very conserved
outline the termite digestive system with emphasis on its symbiotic components
termite eats wood, a protist breaks it down to release sugars, a bacteria (TG1) breaks that down to acetic acid which is what feeds the termite
there are a whole community of other microbes supplies essential nutrients (N through nitrogen fixation) or removes waste (CO2/H2)
what is the host termites role in the symbiotic relationship?
increases wood surface area and extracts easy carbohydrates
what is the protists role in the symbiotic relationship with the termite and bacteria?
continue complex carbohydrates breakdown leading to fatty acid absorption by host
what do hindgut bacteria take over in higher termites?
the role of the flagellates in cellulose degradation
what is wolbachia?
genus of gram-negative bacteria which forms intracellular inherited infections in many invertebrates and extremely common. Lives in ovaries of bacteria, so closely that some of there genome can be transferred to host
how is wolbachia inherited and how does it disproportionately affect males?
its is passed from mother to offspring, disproportionately affecting males through four reproductive phenotypes
- feminization
- parthogenesis
- male killing
- cytoplasmic incompatibility
what is feminisation?
turns all males into females or pseudofemales
what is parthogenesis?
if it can’t get rid of males it will just live without out them through reproduction without male interaction
what is male killing?
wolbachia just kills infected males
what is cytoplasmic incompatibility?
wolbachia doesn’t infect hosts that are already infected with wolbachia or another parasite or a wolbachia of different strain. This stops any reproduction that doesn’t result in infection
how could wolbachia be used instead of insecticide?
cytoplasmic incompatibility means if infected male mates with female it dies
pathogen blocking means wolbachia doesn’t share its host with other parasites so can be used as a blocker for other diseases
life shortening so wolbachia will shorten the life of the organism transmitting disease
how does establishment of symbiosis require two-way communication in bob tail squid?
squid sorts between glowing and non-glowing vibrio fischeri
squid has cilia an appendages to increase water movement next to it (encouragement) and excretes mucus stimulated by bacterial peptidoglycan to attract vibrio
once flagellated vibrio get inside squid it exposes them to nitric oxide and hypohalous acid which make them lose flagella and closes up pores (discouragement) so they are trapped indefinitely
what selects for different microbial communities in the ocean?
food and resources
physical and chemical conditions
why is there high competition for macronutrients and micronutrients in the ocean?
cause they are only found in very trace amounts (especially nitrogen, phosphorous and iron)
why is there more of a gradient at the ocean surface than deep down?
because there is more temperature fluctuation meaning more selective pressure
what is the usual ocean temperature and pH?
surface usually plus/minus 35 degrees Celsius with seasonal fluctuations of 20 degrees Celsius
below 100m temperature 0-5 degrees Celsius
pH 8.3-8.5
what is the thermocline?
the decrease in temp as you move down the water column
where are regions of low oxygen concentrated in the ocean and why?
tropics and coastal areas
cause cold water holds more oxygen and warm water means more microbial growth of microbes which consume oxygen as terminal electron acceptor creating dead zones
what do microbes in the ocean survive on?
availability of energy (e.g. through light penetration)
how do microbes in the ocean capture light energy and distribute it to the rest of the ocean?
photoautotrophs in surface water capture light and energy and then distribute it up the food chain
90% of marine primary production (energy produced) is from phytoplankton
how do microbes in the ocean capture light energy and distribute it to the rest of the ocean?
photoautotrophs in surface water capture light and energy and then distribute it up the food chain
90% of marine primary production (energy produced) is from phytoplankton
why is productivity heterogenous over space in the ocean?
because phytoplankton are the energy source for marine ecosystems but aren’t evenly distributed
as light diminishes in the ocean due to depth, so does…
productivity
how is energy and carbon transferred across the ocean?
the microbial and biological carbon pump which emphasises the microbial transformation of organic carbon from labile (easily degradable) to refractory (non-degradable) states
what does dissolved organic carbon from the microbial carbon pump serve as?
an additional reservoir of sequestered carbon in the ocean
what does the biological carbon pump do?
transfers carbon from surface waters to deeper waters through exportation of phytoplankton-derived particulate organic matter from surface waters to deeper depths via sinking
what are rhodopsins?
membrane embedded proteins which absorb a photon causing a physical change
each type of rhodopsin links this change to a specific outcome
the conformational change involves a proton or a halide ion to be translocated to the other side of the cell. It can also initiate a signal cascade or can be used to power energy-requiring cellular functions
what are proteorhodopsins?
proteins which have a pigment which allow them to harvest light
what is an example of different rhodopsin variants being adapted to different light regimes in order to optimise energy yields?
proteorhodopsin isolated from deep water are blue (deepest penetrating light) absorbing well proteorhodopsins from shallower waters include green absorption
what do light driven processes control and sustain?
he flow of external energy into the global ocean
what are the three modes of photosynthesis?
oxygenic photosynthesis
anaerobic oxygenic photosynthesis
aerobic anoxygenic photosynthesis
what are the two other light driven processes in the ocean other than photosynthesis?
rhodopsin based
phytochrome based
what can we learn from the responses of different organisms to light?
differing growth curves shows how some organisms have improved growth in presence of light which is an advantage and other organisms grow less without light but still grow indicating they are not completely dependent on light
all of this indicates that oceanic microorganisms survive by specialising. This involves coordinating gene expression between different organisms e.g. transcription of proteorhodopsin genes is synchronised with day and night cycles
what can pulses of organic carbon from prochlorococcus influence?
synchrony of oceanic microorganisms
why do chlorophyl levels change throughout the year in surface water but not deep water?
changes in chlorophyl levels is linked to changes in productivity i.e. phytoplankton blooms
