1
Q
Operational vs biological definition of species
A
Biological: Individuals can mate and produce offspring (that can reproduce)
Operational: OTU vs. ASV; 16S >= 97% similar vs. any one of the inferred single DNA sequences recovered from a high-throughput analysis of marker genes
2
Q
Though bacterial communities are diverse, they are also________
A
Uneven
3
Q
How many microbial species on Earth?
A
10^11 - 10^12
4
Q
what conclusions can we draw about microbial diversity in different environments?
A
More diversity in soil
5
Q
What are environmental variables that shape microbial diversity?
A
Salinity, temperature, nutrients
6
Q
What are LDG gradients
A
Latitudinal diversity gradient: pattern of increasing species diversity from the poles to the equator
7
Q
What are some explanations of LDG gradients
A
Physiological tolerance, kinetic energy, productivity/resources, environmental stability hypothesis
8
Q
What are 2 major patterns in bacteria species composition?
A
Different bacteria found in soils, freshwater, oceans
A few bacteria are widely distributed (SAR11 in oceans and verrucomicrobia in soils)
9
Q
What is Shannon-Wiener
A
Diversity as a measure of entropy. Given uncertainty in outcome of sampling process, the more species there are in a sample, the closer their proportional abundances, and the more difficult to predict identity of the next species that will be sampled
10
Q
What is Simpson diversity
A
Represenets the probability that 2 entities sampled at random belong to same species
11
Q
How do we relate simpson, shannon wiener, and richeness
A
Hill numbers (D) = effective # of species = # of equally abundant species needed to give same S value
For every value of q, D = S
. q: Order of diversity vlass, which indicates sensitivity of the class to common and rare species
12
Q
What do q values of 0 1 and 2 mean for species diversity
A
0: Diversity insensitive to species (richness)
1: Shannon
2: inverse simpson
13
Q
What is species abundance distribution
A
Abundance of species vs. number of species.
14
Q
What is RAD (rank abundance distribution)
A
Species rank vs. abundance
15
Q
What is Rskew
A
Rarity. Skewness of frequency distribution. Higher Rskew = larger # of rare species
16
Q
What is Nmax
A
Dominance. Calculated using peblished estimates of total cell count numbers.
17
Q
What kinds of organisms do we find in each layer of a winogradsky column?
A
Top layer: aerobes
Middle: microaerophilic to anaerobic; sulfur fixing compounds (purple sulfur, green sulfur), iron oxidizing
Lowest layer: anaerobes, sulfate reducing, fermenters
18
Q
Why are microbial traits relevant
A
Natural selection operates on traits within species, traits govern organismal physiology and ecology, collective traits regulate ecosystem functioning, same trait can be studied over short time scales w/i population and across phylogeny
19
Q
What are microbial traits
A
Phenotypic characteristics
20
Q
What is phylogenetic conservatism of traits
A
The tendency of closely related species to share similar ecological traits, meaning they retain ancestral characteristics over time
21
Q
Given that depths of trait conservations differ, how do we measure traits
A
Linking phenotypic traits of isolates to their evolutionary relatedness,
quantifying presence/absence of genes (glycoside hydrolases for carbs) or modules (oxygenic photosynthesis) within genomes,
and looking at composition variation among sampled communities
22
Q
How does trait conservatism relate to biogeography
A
The depth of trait conservatism varies in respect to biogeography
23
Q
How do the idea of differentially conserved traits generally help to predict compositional variation?
A
The resolution at which microbiome composition varies among samples may give information about the phylogenetic conservation of the traits under selection
24
Q
What are some challenges in trait based approaches
A
- Trait conservation sensitive to the particular taxa present in a study. If a phylum is only represented by a handful of narrow lineages, then these lineages may not be representative of the phylum in other systems.
- Traits within and among taxa are often correlated (across taxa, if many traits are correlated, then one may be able to reduce the multidimensionality of microbial traits)
- Effect of gene-by-environment interactions (trait plasticity) and biotic interactions (such as microbe with microbe or host with microbe) is not considered in this approach
25
Differences between copiotrophs and oligotrophs
copio: Prefer high nutrients, Large cells,
Fast growers (rapid response to nutrient upshift), Cell reduction induced by starvation
Transporters diversification/specialization → PTS, translation/transcription/CRISPR
oligo: small : high surface area / volume ratio,
Slow growers, Constant slow growth also when nutrients are at minimum conc, transporter minimalization
26
What is the definition of a trait?
Physiological, morphological, behavioral characteristics of an organism (phenotypic characteristics)
27
How do we classify traits based on complexity
Simplest traits encoded by 1 gene locus (eg. ability to degrade P from organic compounds depends on production of alkaline phosphotase, which is coded by 1 gene)
Complex traits involve interactions of many parts of the genome (epistasis) --> eg. salnity preference
28
How do we classify traits based on how they are measured
Discrete traits: binary traits, categorical (ability to degrade compound, salinity preference)
Continuous traits: Returns a numerical value in a range (kinetic activity, measuring rates, salinity performance curve)
29
What are ways to classify traits?
Complexity, based on how they are measured, based on what is a potential or realized phenotype
30
How do we classify traits based on potenial vs realized phenotypes
Potential range > realized one: modified by interactions/environemtn
Potential: Presence/absence of gene: potential/discrete, codon usage bia, rrna operon copy number, lab measurements
Realized: in situ measurements, inferred from biogeographic distrubutions, correlations **(opt temp)
31
How does phylogenetic conservatism of traits mean for microbes?
Organism defined by collection of traits, but potential for HGT means traits can be unrelated to evolutionary history
But despite HGT, closely relaed taxa share more similar traits that expected if traits were distributed randmly across tree
32
In the context of prochlorococcus, how are trait conservatism and biogeography related
At deep phylo level, divided into low light vs. high light adapted. At next level, high light clade can be divided into high/low iron. High iron clade can be divided into temperature preference, and finest level, variation in nutrient acquisition traits.
ability of specific environmental variables to explain Prochlorococcus composition varies in agreement with the relevant traits. Light level explains variation across samples from the Pacific and Atlantic oceans when Prochlorococcus is grouped into broad taxa, whereas nutrient concentrations only explain
variation at the finest taxonomic levels.
33
How can differential trait conservation help to predict compositional variation
The resolution at which microbiome composition varies among samples may give
information about the phylogenetic conservation of the traits under selection
34
What are viruses?
Made of protein capsid and genomic material. Infects and requires cellular host for replication.
35
What is the Baltimore Classification
Classifies viruses vased on genetic material present in virion (DNA, RNA, +, -, ds, ss)
36
What are the main kinds of virus structural diversity?
Non-enveloped vs. enveloped
complex, icosahedral, and helical
37
What is viral ecology
Studies of relationship between host, virus, and environment
38
Most viruses of microbes are _______
Bacteriophages
39
What are the three major viral replication cycles? Define them
Lytic cycle --> viruses burst and kill
host cell
Lysogenic cycle --> viruses are
“dormant”, inherited vertically when
host divides
Chronic cycle --> viruses can exit cell
via extrusion or budding without killing
the host
40
What are virulent phages and what cycle do they undergo?
Strictly lytic cycle.
1. phage attaches and injects DNA
2. phage DNA circularizes and enters lytic cycle
3. New phage DNA and proteins synthesized and assembles into virions
4. Cell lyses and releases virions
41
What are temperate phages?
Phages that can undergo lytic or lysogenic cycles
42
Decribe the lysogenic cycle
1. Phage attaches to host cell and injects DNA
2. Phage DNa circularizes and enters lytic or lysogenic cyle
3. Phage DNA integrates within chromosome
4. Lysogenic bacteruaum reproduces nromally
5. Occasionally, prophage excises from bacterial chromosome and enters lytic cycle
43
What is a prophage
the dormant, integrated form of a bacteriophage
44
What is the chronic cycle?
a persistent, productive infection where new virus particles are released from a host bacterium without immediately killing it, unlike the lytic cycle. This cycle is characteristic of filamentous phages
45
What causes temperate phages to switch to lytic cycle
Environmental switch
46
What does it mean for phages to have a narrow host range?
Typically only infect a subset of strains within a species, rarely infecting across
genera
* Environmental context also shapes “host range”
* Viruses may only be able to infect a certain host in certain environmental conditions
47
What is important for phage host range in nature?
Defense elements
48
How is bacterial evolution heavily shaped by viruses?
Defense evolution, virus-encoded novel functions (auxiliary genes, ie cholera), mechanisms of horizontal gene transfer
49
What are ways of studying viral eccology
Culturing (plaque assay), microscopy, sequencing
50
Pros and cons of culturing (viral ecology)
Pros: Cheap, low barrier, measure traits, rates of interests
Cons: Need to be able to culture hosts and virus, can easily distinguish between species
51
Pros and cons of microscopy (virus ecology)
Pros: Count environmental virus like particles without host
Cons: Requires specialized equipment, Can’t determine host, Can’t determine if active/infectious
52
Pros/cons of sequencing (virus ecology)
Pros: Determine genomic diversity
Rapidly getting easier and
cheaper
Lots of genomes already
available to explore
Cons: No 16S – community composition
requires metagenomics,
ss+ds/DNA + RNA
Hard to tell what actually is a virus
53
What do host-virus population dynamics look like?
Mirrors predator prey dynamics, a la red queen hypothesis
54
Under logistic growth, what happens to bacterial populations with virulent phage?
Depends on starting amounts of phage and bacteria, virulence of phage, but virulent phage population generall crashes after multiple rounds of infection
55
Which parts of bacterial growth correspond to which stages of lytic phage cycle?
Latent period: adsorption, rise period: genome replication and protein production, plateauephase: burst
56
What are factors that cause viral particles to decay
Disinfectants, UV, temperature, salinity
57
What drives lysis vs. lysogeny
* Host density (more hosts --> better to be lytic)
* Virus density (more free viruses around --> better to stay inside)
* Superinfection exclusion
* Host physiological state (high stress --> leave the sinking ship)
58
What is the relationship between prophage infection and thermal responses
High temperature often increases lytic replication in many prophage systems
59
High temperature growth mutants make _____ phage
Less
60
What is the effect of lysis on species abundance
Reduction in abundance
61
How can viruses maintain bacterial diversity?
Kill the winer hypothesis. Start with bacteria that share same limiting resource (but diff growth rates), give each strain one virus, leads to diversity
62
Which factors influence viral diversity
Microbial diversity, particle persistence, dispersal (high local, low global)
63
Why are viruses important in ecosystems
Most abundant biological entity on Earth: 10^31!
* Encode genes that alter ecosystem-relevant functions
* Example: photosynthesis
* Major source of microbial mortality across environments
64
What is the viral shunt and shuttle?
Shunt: Viruses infect and lyse (burst) microbial cells. The lysed cells release carbon and nutrients into the water as dissolved organic matter (DOM). Keeps carbon in upper oceans microbial loop.
Shuttle: Viruses also cause host cells to release substances that promote aggregation.
his includes sticky polymers, proteins, and DNA, which cause cellular debris and even whole infected cells to clump together. likely to be exported to deep sea, sequestering carbon from atmosphere.
65
What is the relationship between embryo and maternal/paternal genes?
The embryo develops from both maternal and paternal genetic material (true for 1% of genes)
66
*gut microbiome lecture (16)
67
What are mobile genetic elements?
Genetic parasites of bacteria that self replicate and move within or between genomes
68
What are examples of MGEs
Plasmids, phages, phage plasmids, transposons, etc
69
Plasmid details
‣ Reside in the cytoplasm (plasm-id)
‣ Auto-regulate their copy number
‣ Can carry “cargo” genes
‣ Often spread via cell-cell contact through
a conjugative pilus
‣ ‘Backbone’ carries genes for replication
and transfer
‣ Costs from gene expression, conjugation
70
What are the two main groups of plasmids that coexist in bacterial populations
‣ Small, mobilizable, high copy number plasmids
‣ Large, conjugative, low copy number plasmids
*hosts carry many compatible plasmid families simultaneously
71
How do bacteria have sex
Conjugation of fertility factor F
‣ Long flexible pili extend, attach, and retract
‣ The plasmid is replicated through rolling circle replication
‣ ssDNA passes through the pilus or the mating pore
‣ Leading strand contains defense and anti-SOS genes
72
What are the 3 primary modes of HGT in plasmids
Conjugation, transformation, transduction
73
How do plasmids drive bacterial antibiotic resistance?
by carrying genes that confer resistance to one or more antibiotics
74
What are transposable elements
Most fundamental units of mobile DNA. They translocate through cut-paste or copy-paste mechanisms
75
What are insertion sequences, and how are they relevant
small, mobile DNA segments that can move within a genome
promote rapid adaptation
76
What are phage plasmids
Reside in the cytoplasm
‣ Carry replication and partitioning genes
for reliable vertical transmission
‣ Carry lysis, capsid and tailfiber genes for
horizontal transmission
77
What are ICE
Interactive conjugative elements.
‣ Reside in the chromosome
‣ Carry integration genes for reliable
vertical transmission
‣ Carry excision, and type 4 secretion
system genes for horizontal transmission
78
What are the key characteristics that drive population dynamics of MGEs
Mobility (w/i or btwn genomes), genomic location, fitness effect, duplication (cut-past, copy-paste), transmission
79
What are phage satelites? What are mobilizable plasmids
Phage satellites: a phage that hijacks a phage
Mobilizable plasmids: a plasmid that hitches
a ride with a plasmid
80
How do phages exploit plasmids?
Phages can attach to the plasmid pilus
Increased phage susceptibility can be used to
eliminate a resistance plasmid from chickens
81
How do plasmids benefit from phages
Phages create more intermixing between
hosts and benefit plasmid transmission
82
What is symbiosis/mutualism, and what are three examples?
Associations between different species in persistent and close contact (1 definition says beneficial only, other definition say all interctions_
Termite-microbe: symbiotic microbes degrade and transfer ligno-cellulose of wood to usable organic compounds allow termites to live in wood
Ant tended fungal gardens:
Fungi help ants live on indigestible plant material. Ants farm fungi and bring them leaf pieces --> fungi (and nitrogen fixing bacteria) eat the leaf fragments, and get eaten by the ants
Rumen microbiome: microbes in ruminant gut help to digest otherwise indigestible compounds (eg. plant polymers)
83
What are the different forms of nitrogen (naturally occuring)
N2 (atmospheric), NO3-, NH3, NH2
84
Why should we care about Nitrogen?
1. Major component of cell
- often limiting resource for growth
2. Involved in redox reactions (can take on many oxidation states)
3. Many N compounds in microbial metabolism
85
What are the most and least oxidized forms of nitrogen, and what are their oxidation states?
Most: NO3- (+5)
Least: NH4+ (-3)
86
What are the (relevant) natural processes involved in the N cycle
Denitrification, nitrification, assimilation, ammonification
87
How have anthropogenic activites tampered with nitrogen cycle?
𝑁2𝑂 (nitrous oxide)
* potent green house gas and destroyer of O# layer
* concentration in atmosphere driven up by agricultural activities
𝑁2
* anthropogenic fixation via Haber-Bosch process to produce fertilizers
𝑁𝑂 (nitric oxide)
* major component of acid rains
* Introduced in atmosphere via wildfires and burning of fossil fuels
88
What is diazotrophy
Capacity to fix N2
89
Do eukaryotes fix nitrogen
No. None
90
Which kinds of bacteria/archaea fix nitrogen
Anaerobic heterotrophs, oxygenic phototrophs, anaerobic anoxygenic phototrophs, one species of aerobic anoxygenic phototroph
91
What is nitrogenase?
Catalyzes the reduction of N2 to NH3
92
What is the equation for the reaction that nitrogenase catalyzes?
N2 + 8H+ + 8e- + 16ATP--> 2NH3 + H2 + 16ADP
93
What is the oxygen issue in nitrogen fixation and how do organisms combat it?
Nitrogenase enzyme irreversible damaged by O2.
1. Avoidance
Life in low-oxygen environments
2. Compartmentalization of the enzyme
* Heterocysts: Thick cell wall limits diffusion; heterocyst lacks PSII, vegetative cells feed sugars and organic acids to heterocyst in exchange for glutamate
* Vesicles containing the enzyme
3. Time separation of fixation and photosynthesis
4. Maintenance of high respiration rates to consume oxygen
5. Proteins that bind to nitrogenase
6. Compartmentalization of the whole cell
- Cell fix 𝑁% only when coated in polysaccharide-rich slime that minimizes 𝑂% diffusion
- Nodules
94
What are limitations of N2 fixation?
* Light for autotrophic diazotrophs
* Supply of organic material for heterotrophic diazotrophs (this would explain why heterotrophic bacteria don’t play a huge role in 𝑁% fixation in the ocean, while they do in soils supplied with organic C from higher plants)
* Concentration of ammonium and nitrate (if they are available fixation is not favored)
* Iron (especially in limiting fixation in open-ocean regions)
* Phosphorous (another hypothesis for why fixation in open-ocean regions is low; supported by observations of cyanobacterial blooms promoted by release in water bodies of P-rich contaminants)
* Mo (especially in highly weathered acid soils of the tropics)
* Temperature (in the ocean it would limit oxygen diffusion and solubility, explaining why Trichodesmium does not exhibit heterocysts)
95
What is NH4+ assimilation and regeneration
—> organic n
96
Between NH4+ and NO3-, which is a preferred N source and why
𝑁𝐻4+ preferred N source over 𝑁𝑂3-
because oxidation state (-3) is the same as AA and other cell stuff
97
Why is ammonium preferable to nitrate- as a carbon source (use ideas of rates, flux)
* uptake rates of ammonium faster than nitrate in soils and aquatic habitats
* uptake rates of nitrate exceed those of ammonium only when ammonium concentration very low
* fluxes through ammonium pool high even because of rapid production and uptake by microbes and, in soils, exchange with negatively charged soil constituents and clay
* Nitrate, which is more mobile because it is typically less fixed onto silicate clays and is highly soluble, is also lost to leaching. It can follow flow paths down into groundwater, or into streams that accumulate to
rivers that accumulate in water bodies. This is relevant for agriculture
98
What are the two pathways of N assimilation
1. For high ammonium concentrations (enzyme = glutamine DH)
glutamate + NH4 + ATP --> glutamine + ADP
2. For low ammonium concentrations (2 enzymes: glutamine synthetase and glutamate synthetase)
glutamine + a -oxoglutarate + NADPH --> 2 glutamate + NADP+
99
What is nitrogen regeneration?
Ammonification (N2 to NH4+)
- Proteins hydrolyzed into AA; AA deamination results in ammonium
* ammonium directly secreted as waste by many organisms, together with urea and uric acid (birds, some
reptiles and amphibians), all eventually degraded to ammonium
* In the absence of 𝑂% microbes use other electron acceptors
* Fermentation of AA and nucleotide bases yields ammonium
100
Which organisms perform nitrogen regeneration
mostly bacteria and fungi
101
What is Nitrgen nitrification
NH4+ to NO2- to NO3-
102
Mineralization of organic material yiels which form of nitrogen
NH4+
103
What is the most common inorganic form of fixed N
NO3- (nitrate)
104
Where does NO3- come from (N cycle)
Nitrification aka oxidation of ammonia to nitrite and nitrate
105
Transition from ammonium to ammonia is set by:
pH
106
Is nitrification aerobic or anaerobic:
Aerobic
107
Nitrifying bacteria and archaea are _____
chemolithotrophs
108
What are the two nitrification pathways
* one with two steps performed by two different groups of bacteria and archaea (discovered by Winogradsky)
* the other entails the complete nitrification by one organism
109
What is the first step of nitrification
NH3 oxidation
110
What controls/drives NH3 oxidation
* Energetic yield (low: AOA and AOB are not good competitors for ammonium)
* Ammonium concentration (low in most oxyc environments)
* Inhibition by lack of oxygen, even though AOA pathway require less 𝑂% than atmospheric levels
* Inhibition by light at high intensities
* pH (AOA favored by acid pH over AOB in soils)
111
What are AOA and AOB, and how are they relevant?
AOB = ammonia oxidizing bacteria
- AOB oxidize more ammonia
AOA: ammonia oxidizing archaea
- abundant in aerobic environments (sometimes more than AOB)
in acid soils, AOA oxidize more ammonia. AOA outcompete AOB when ammonium concentrations low
112
What is the second step of ntirification
NO2 oxidation
113
What is denitrification
N2 --> N2O --> NO --> NO2-
anaerobic respiration used by microorganisms to oxidize organic material
113
What is DNRA
Dissimilatory nitrate reduction to ammonium.
* Carried out by bacteria and fungi
* 50% reduction in yield compared to denitrification
* DNRA hypothesized to be advantageous in organic-rich but nitrate-poor habitats because DNRA requires
less nitrate than denitrification to oxidize one mole of glucose
114
What is anammox
Anaerobic NH2 oxidation
115
How is nitrous oxide produced
By denitrifyers and nitrifying microbes
116
How is nitrous oxide produced and by who?
* Denitrifiers can produce the gas if nitrate concentrations are too low or if oxygen is too high. 𝑁2𝑂 production in anoxic environments fueled by denitrifiers.
* Ammonia oxidizing microbes (AOA and AOB) are the most important 𝑁2 𝑂 producers in aerated soils (both AOA and AOB) and oxic oceans (mostly AOB). 𝑁2𝑂 production increases when oxygen levels drop.
* Control over 𝑁2𝑂 production mostly by oxygen
117
How is nitrous oxide consumed and by who?
Nitrous oxide (𝑁2 𝑂) consumed when it is reduced
* by heterotrophic denitrifiers
* by recently discovered 𝑁2 𝑂-reducing organisms that are not denitrifiers (they use 𝑁2 𝑂 as electron
acceptor for the oxidation of organic matter and release 𝑁2)
118
Where is the largest biological pool of nitrogen
atmosphere
119
New nitrogen comes in through _____ and is lost through ________
fixation, denitrification
120
How does human activity accelerate N cycle
* Production of N
fertilizer
* Fossil fuel combustion
and agriculture which
causes N pollution to
the atmosphere
* N fixation from
agricultural crops
121
What are the various reservoirs of carbon (organic and inorganic)
CO2 --> atmosphere
DIC (dissolved inorganic carbon) --> HCO3 and CaCO3 on land and oceanic sediments
DOC (dissolved organic carbon) --> largest reservoir is in soil, less in oceans
122
Summary of light driven primary production based on photosynthesis:
CO2 + H2O + nutrients + light --> biomass + O2
123
General photosynthesis eqn
CO2 + H2O + light --> CH2O + O2
CH2O = organic material
124
What is the difference between the first and second parts of photosynthesis
1. Light reaction
Generates reducing power (NADPH), ATP, and O2
2. Dark reaction
Use electrons produced to reduce NADP+ to NADPH, make ADP, reduce CO2
125
What is light harvesting
Key part of photosynthesis. All oxygen producing organisms have chlorophyll a. Accessory pigments allow phototrophs to harvest wavelengths of lights. Pigments can be used to track abundance of photosynthetic microbes.
126
What is the main pathway for CO2 fixation in oxic environments
CBB (calvin benson bassham cycle)
127
What is the light dark bottle method
Way to measure primary production.
Oxygen decreases in the dark bottle due to respiration (R), but it increases in the light bottle if photosynthesis exceeds respiration. The change in 𝑂2 concentration in the light bottle gives us a measure of Net Primary
Production (NPP). Gross Primary Production then is:
GPP = NPP + R
Assumption: respiration is the same both in the light and the dark bottles
128
What is gross primary production
GPP = NPP + R
129
What is NCP
Net community production.
NCP = GPP - RA - RH = NPP – RH
where RA is respiration by autotrophs and R H is respiration by heterotrophs.
* NCP> 0 → system is a sink (ecosystem is taking more inorganic carbon (out of its environment (e.g., the atmosphere or surface water) and converting it into organic biomass than it is releasing back through respiration)
* NCP<0 → system is a source (total carbon released through community respiration exceeds the organic carbon produced by photosynthesis)
130
Why can low biomass systems have high primary production rates.
P = mu* B
P = production, mu = growth rate, B = biomass
Growth rates of microbial autotrophs are estimated to be 100`-1000 times faster than growth rates of plants. So,
although biomass per square meter is much less in aquatic ecosystems than on land, the difference is nearly canceled out by the much higher growth rates in freshwaters and the ocean.
131
Who fixes CO2
Diatoms, coccolithophorids, phaeocyctis, cyanobacteria
132
Of CO2 fixed each year, who returns it to the atmosphere?
Almost all heterotrophic microbes
133
Which organisms degrade organic matter (estimates)
Aquatic environments: heterotrophic microbes
Soil: 5-30% large organisms, 70-95% microbes
*of this, half depend on root associated microbes (fungi, bacteria)
134
Why do fungi and bacteria have the same ecological role but in different habitats?
* Bacteria win the competition in water because their small size makes them better competitors for dissolved
compounds
* In terrestrial habitats, the hyphae life form taken on by fungi allows them to cross dry gaps between moist microhabitats and to access organic material not available to water-bound bacteria
* Fungi can move nutrients along the hyphae to support degradation in organic C-rich but other nutrient-poor microhabitats
* In soils, niche separation: bacteria use labile organic compounds, fungi refractory material (ligno-cellulose)
135
What is the detritus food web?
Bacteria/fungi/protists living directly (or indirectly) on dead inorganic material)
136
What is detritus
Particles formed through,d eath of plants/animals/algae, grazing, fecal mayyer, viral lysis
137
Unlike the old view of carbon flow, only a small fraction of primary production is consumed by ___________
herbivores
138
What is the role of detritivores in food web?
* Important role in physical breakup of detritus and plant litter, which in turn
favors adhesion and degradation by bacteria
* Release of polysaccharides (e.g. earthworms) and other compounds prime
bacteria
* Affect oxygen penetration and soil chemistry
139
How do microbial heterotrophs interact with detritus?
* Responsible for most of the mineralization of organic C in detritus
* Contribute to stable SOM (C storage)
140
In addition to detritus, how does plant and algal organic material become available to microbes?
Through the extretion of dissolced organic matter
141
Describe the flow of the microbial loop
Primary production --> DOM -> bacteria --> grazers
142
Does all carbon remain within the microbial loop?
No, some is respired to CO2
143
What is horizontal gene transfer
Movement of genes from from one
organism to another, unrelated organism, in
contrast with the vertical passing of genes
from parent to offspring.
144
What are mechanisms of HGT
Transformation, conjugation, transduction
145
What is transformation (HGT)
DNA directly uptaken from environment
146
What is conjugation (HGT)
Exchange of DNA from one cell to another via a proteinaceous tube (pilus) connecting two cells
147
What is transduction (HGT)
Mediated by viruses (generalized or specialized). movement of genetic material between bacteria by phage
148
What are beneficial HGTs
Provide inittial selective advantage to recipient
149
What are neutral HGTs
Maintained by random genetic drift
150
What are parasitic HGTs
Do not provide initial selective advantage. Over time may adapt to have a beneficial function or be maintained via pathways to neutral complexity in recipient
151
What are consequences of HGT
Expansion/enhancement of metabolic pathways, metabolic innovation, niche expansion, dominance because of increased immunity to viral predation
152
What is genome streamlining
evolutionary process of reducing a genome to its essential genes
153
What are the main characteristics of organisms with streamlined genomes
stable core metabolism, small genomes, low ratio of noncoding to coding genes, low number of paralogs (not many duplicates), high population size
154
What is phage therapy
New approach to treating bacterial infections. Uses phages to target/kill bacteria, or to steer evolution away from antibiotic resistance.
155
What kinds of phages do we want for therapy?
virulent
156
Which traits do we want to maximize in phages for therapy>
No virulence factor (dont carry genes that make bacteria virulent), no transduction, strictly virulent
157
How do we steer bacterial evolution towards better clinical outcomes?
If bacteria are antibiotic resistant and phage susceptible, we can use phages to steer evolution towards antibiotic susceptibility (and phage resistance)
158
How does diversity affect phage therapy.
Infections are often phenotypically diverse, which poses a problem for phage therapy
159
How do we measure phage susceptibility
EOP (efficiency of plating). Put phage stock on substrate (bacteria) lawn, and on a focal strain lawn. Divide colonies/plaques formed by focal lawn over substrate lawn.
160
Which "hidden" organ contains 150-fold more genes than our inherited genomes
Gut microbiome!
161
What is unique about the gut microbiome
Acquired from the environment, not human genes, enormous interpersonal variation, gene gain/loss during our lifetime (and even from one dat to next)
162
What is maltodextrin, and what breaks it down?
A simple sugar. Duodenal enzymes break it down.
163
Why is milk unusual?
It evolved to be a food, cant be broken down by human enzymes; gut microbiome helps break it down
164
Human milk oligosaccharides select _____?
Our gut bacteria
165
What is 16S rRNA
a ribosomal RNA molecule found in the small subunit of prokaryotic ribosomes that is essential for protein synthesis. Its highly conserved regions, combined with variable regions, make it a crucial tool for bacterial and archaeal identification and phylogenetic analysis
166
Why do we us 16S
Ribosomal subunit present in all bavcteria
Conserved regions
Variable regions
167
What is alpha diversiy?
Diversity within a community (richness and evenness)
168
What is beta diversity?
Between commmunities
169
What is UniFrac
a phylogenetic distance metric used to compare biological communities, particularly microbial ones, by incorporating information about the evolutionary relationships between organisms
170
How do we make trees relating microbial samples to one another?
Quantify alpha and beta diversity, perform unifrac, label species by community, label branches by community, count unique branch lengths, make trees of two communities at a time, distance matrix and clustering
171
What are the strengths of 16S?
Culture independent, highly scalable, does not rely on gene annotations
172
What are the weaknesses of 16S?
Gives us what species are present (no behavioral/traits etc.), low resolution (species/strains can appear same), only detects bacteria, relative abundance
173
What is shotgun metagenomics?
Complete community DNA randomly fragmented and sequenced, limited assembly, cluster like sequences and annotate against referemce genomes, provides information about gene content and strain diversity
174
How does metagenomic data allow strain specific analyses?
* Reads mapped to reference genomes
* SNPs that show similar relative abundance indicate strains
* Why could strain-level resolution
be important?
175
What is a challenge of gut microbiome studies?
Causation and correlation
176
What are gnotobiotic mice
animals with a known microbial composition
177
Gnotobiotic mice can be used to:
Separate host and microbial variation
178
How do you create germ free mice
C section and cross fostering, embryo transfer
179
How do we conduct microbiome experiments with mice?
Transplant into WT germ free recipients
180
How is the gut an "outside surface"
Must contain hundreds of trillions of diverse microbes
* An open system: constant challenges from pathogens in food and water
181
What are basic mechanisms of maintaining gut homeostasis
* Limiting epithelial cell contact
* Modulated immune response
182
microbial ecology
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