Module One Flashcards
1
Q
what is the physiology of organisms?
A
Genomes
Proteins
Metabolism
Growth and reproduction
2
Q
what allows organisms to survive in an environment?
A
traits of the organism
3
Q
what do we need to understand in order to understand an organism?
A
physiology
ecology
evolution
4
Q
what do we need to know in order to understand the planet?
A
how microbes respond at a cellular level and how they respond to an environments
5
Q
how old is planet earth?
A
~4.5 billion years old
6
Q
how long have humans been around compared to the earth?
A
0.02%
7
Q
what was the first form of life on the planet?
A
microbes
8
Q
how long have microbes been on the earth compared to the earth’s life?
A
88% of its existence
for 50% of the time they were the only organism
9
Q
what created the first oxygen on earth?
A
microbes
10
Q
what was the environment of early earth?
A
anaerobic environment
11
Q
what are the major changes in the earth’s atmosphere linked to?
A
microbes
12
Q
what is the common ancestor of all life on earth?
A
LUCA
13
Q
what does LUCA stand for?
A
Last Universal Common Ancestor
14
Q
what can we learn from the fact that all life stems from one common ancestor?
A
by understanding one group of cells we can learn things about another group of cells because we are all related
15
Q
what is the similarity between all life domains?
A
all three domains of life have common biochemistry
they have shared architecture
common basic mechanisms of biochemistry
16
Q
what are the major components of cells?
A
membranes
nucleic acids (DNA/RNA)
proteins
17
Q
what are the basic components of life?
A
CHONSP
18
Q
what are the CHONSP elements?
A
Hydrogen Carbon Oxygen Nitrogen Sulfur Phosphorus
19
Q
what are the features of CHONSP elements?
A
all can form covalent bonds (stable)
-more than one link is possible (except in H)
20
Q
why is water so important for life?
A
chemical reactions occur in a solvent and water is the universal solvent
21
Q
what did the Miller-Urey Experiment show?
A
-Succeeded in creating many organic molecules, most essential amino acids, and most nucleic acid bases
22
Q
what was the conclusion of the Miller-Urey Experiment?
A
the organic building blocks of life are generated in the probable atmosphere of early earth
23
Q
what was the environment of early earth?
A
Anoxic
High Temp
High UV
Alternative energy forms, radiant, geothermal, electric-discharge
24
Q
what are the tendencies of early molecules?
A
aggregates
membrane-like interfaces
25
what are the types of self-assembled membranes?
coacervates
micelles
liposomes
26
What did the formation of early membranes allow?
formed a semi-permeable membrane that allows the formation of chemical gradients and allows the harvesting of energy from these gradients
forms different environments for reactions to occur
27
why is DNA the nucleic acid that the genome is most commonly stored in?
DNA is more stable
| -less reactive in the presence of oxygen
28
what is the prebiotic world (chemistry)?
Precursors -> Nucleotides -> Random RNAs -> Ribozymes
this is a very random and rare occurrence
29
what is the RNA world (biology)?
Precursors -> Nucleotides -> Ribosymes
Ribozymes become recombinases
Ribozymes form polymerases
Ribozymes facilitate Nucleotide synthesis
Ribozymes reduce reliance on precursors
30
where did the first organisms live?
at the bottom of the ocean in thermal vents
| Likely surviving on inorganic nutrients
31
what are the features of the first organism?
anaerobic
| Chemolithotrophic (FeS and H2S)
32
what was the likely metabolism of the first organism?
FeS + H2S --> FeS2 +H2
the resulting H2 could have been used to drive a primitive ATPase with S as a potential electron acceptor
33
what is the panspermia hypothesis?
Alternative explanations for life or life-forming compounds
Carbonaceous meteorites may have brought the prebiotic seeds of life to early earth
No evidence to date to convincingly support this idea
34
what has shaped the current planet earth?
major transformations in the microbial world
35
How do gradients cause speciation?
gradients cause different niches which create different habitat types that different species can evolve to enhance
36
what are four types of gradients that can be caused by bacteria?
oxygen gradient
nutrient gradient
pH gradient
chemical gradients
37
how is an oxygen gradient formed by microorganisms?
oxygen is consumed faster than the rate of diffusion
38
what speciation can an oxygen gradient cause?
aerobes
fermenters
anaerobes
39
what speciation can a nutrient gradient form?
Metabolically active cells
| Starving cells, dormant cells, VBNC cells, persisters, and dead cells
40
how does a nutrient gradient form?
the further away from the nutrient source, the fewer nutrients there are
41
how is a pH gradient formed by microorganisms?
microorganisms consuming and producing waste products
42
how do microbes create gradients?
as they grow
43
what do the gradients create?
gradients create a diversity of habitats
44
what is an example of experimental evidence that supports evolution?
Single E.coli inoculated and grown in glucose-limited media in a chemostat environment.
the glucose limitation introduced competition and so evolution of the E.coli to metabolize different growth rates and uptake of glucose.
45
what is a chemostat?
liquid culture maintained at a steady nutrient state
46
what are the three ways to classify microorganisms?
Taxonomy
Function
Metabolism
47
what are the three classification systems of organisms?
Biological
Phenetic
Cladistic (phylogenetic)
48
what is the biological classification system?
grouped based on their ability to breed. If they can breed and produce offspring that can only reproduce then they are considered the same species
49
why does the biological classification system not work for microbes?
microbes are asexual and do not require a mate to reproduce
50
what is the phenetic classification system?
grouped based on overall physical similarity with no account of evolutionary history
51
what is the disadvantage of the phenetic classification system?
liable to make errors due to convergent evolution. Microbes are also very similar to each other physically.
52
what is the cladistic (phylogenetic) classification system?
grouping based on evolution from a shared ancestor (clade) as determined from a shared trait
Can be deduced by comparing their base or amino acid sequences
53
what are the issues with the cladistic (phylogenetic) classification system?
Liable to ignore useful descriptive traits by being too focused on one evolutionary trait or gene
54
how does the cladistic (phylogenetic) classification system work?
The more similar the genomes of two organisms the more closely related they are
55
what is a molecular clock?
A molecular clock is a gene whose DNA sequence can be used as a comparative temporal measure of evolutionary divergence
56
what is the most commonly used molecular clock?
16S ribosomal gene (encodes the RNA sequence for the small ribosomal subunit)
57
why is the 16S ribosomal gene a good molecular clock?
universally conserved
| Every living creature needs to make proteins
58
what are the properties of molecular clocks?
1. Found in all living organisms
2. Maintains its function amongst all organisms (has the same selection pressure in all organisms)
3. Highly conserved, with multiple hypervariable regions (allows an anchor but also allows observation of evolution)
4. Sufficient length (enough information)
59
what was the genealogical tree before pre-16s rRNA taxonomy?
1. increasing complexity further away from the root
| 2. Man at top of the pyramid
60
who proposed the three domains of life?
Carl Woese
61
what are the three domains of life?
Eubacteria
Eukaryotes
Archaebacteria
62
what is the Eocyte hypothesis (two domain hypothesis)?
Implies that the closest relative to eukaryotes is one, or all of the TACK Archaea
63
what are TACK Archaea?
TACK archaea and eukaryotes share genes not found in other archaea
64
what are some examples of microbial species?
```
Bacteria
Archaea
Fungi
Algae
Protozoa
Viruses
```
65
how many species of fungi are there?
>70,000 species described
| estimated ~6 million exist
66
what is an example of decomposer fungi?
saprophytic fungi
67
what do decomposer fungi do?
convert dead organic material into fungal biomass, carbon dioxide, and small molecules, such as organic acids.
68
what is absorptive nutrition?
describes a way of obtaining energy and nutrients in which digestive enzymes are secreted into a substrate, then smaller, easily assimilated molecules are absorbed through the cell membrane
69
what is an example of mutualist fungi?
Mycorrhizal fungi
70
what is the function of mycorrhizal fungi (mutualist)?
Colonize plant roots. In exchange for carbon from the plant, mycorrhizal fungi help solubilize phosphorus and bring soil nutrients (phosphorus, nitrogen, micronutrients, and perhaps water) to the plant.
71
what are the three groups of fungi?
Mutualist
decomposer
pathogens
72
what is the function of pathogenic fungi?
cause reduced production or death when they colonize roots and other organisms
73
what are some examples of root-pathogenic fungi?
Verticillium
Pythium
Rhizoctonia
74
what are some definitions of species?
Taxonomic rank
A group of organisms capable of interbreeding and producing fertile offspring of both genders
A separately evolving lineage that forms a single gene pool
75
what is the issue with speciation?
the long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species'
There is no one species definition
76
how are different organisms defined as species?
different phyla of organisms are defined as species in different ways
77
what is the definition of a prokaryotic species?
defined as "a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardized conditions
78
what is the definition of a bacterial species?
a genomically coherent group of organisms
79
why are there issues with defining a species?
evolution is a continuum and so species will always have other organisms that are almost identical but are defined as different species
80
what is the phenotypic consistency between two organisms that defines them as the same species?
70% of DNA-DNA binding and over 97% of 16s ribosomal RNA gene-sequence identity
81
what are the features of the prokaryotic species definition?
Arbitrary
anthropocentric
rooted in practical necessity
82
what are the historical definitions of a bacterial species?
```
growth characteristics (morphology, gram stain, growth medium)
Diseases caused
```
83
what are the issues with historical bacterial species definitions?
those that do not cause disease
| they are useful identifiers but have no ecological or evolutionary meaning
84
what does the DNA-DNA hybridization comparison show?
phenotypic and genotypic differences
85
what does DNA-DNA hybridization measure?
the degree of genetic similarity between complete genomes by measuring the amount of heat required to melt the hydrogen bonds between the base pairs that form the links between the two strands of the double helix of the duplex DNA
86
what is the benefit of DNA-DNA hybridization classification?
provided a standardized means for identifying and classifying prokaryotes that lack well-defined morphological or phenotypic characteristics
87
when does DNA-DNA hybridization show the same species?
>70% = SAME species
88
what are the issues with DNA-DNA hybridization (DDH)?
1. Unclear how it relates to whole-genome relatedness
2. It is time-consuming
3. Carried out properly by a few laboratories
4. Ill-suited for rapid identification
5. Only suited for pair-wise comparison
6. the Previous classification must be present
7. Unavailable for non-culturable organisms
89
how many prokaryotic cells are culturable?
only 1-2%
90
what is the comparison between 16s rRNA sequencing and DNA-DNA hybridization?
No organisms sharing <97% sequence similarity at 16S meet the DDH criteria of >70%
91
what are the limitations of 16s genome vs. DNA-DNA hybridization?
Many examples of organisms with >97% similarity at 16s with <70% DDH
The rule only works to confirm differences not similarities
92
what are the limitations of 16s rRNA gene comparison?
- lack resolution compared to DDH
- Cannot discriminate between highly related species... >97% similarity
- does not relate to metabolic capabilities
- relies on a single gene
- 16s rRNA can be too conserved (slow evolution)
93
what is ANI?
average nucleotide identity
-a new method of comparison
allows many genomes to be compared at the same time
94
what is the correlation between DDH and ANI?
70% DDH = 95% ANI
| Good correlation between DDH and ANI
95
what are the issues in DDH and ANI comparison?
1. We are simply updating the way we measure and compare differences
2. No biological definition/explanation for why we sue 95% ANI or 70% DDH
3. Biased classification system
96
16s genomes sequence vs. ANI?
>95% ANI = >98.5% 16s rRNA
| Good correlation between DDH, ANI and 16s
97
what is Multilocus Sequence typing (MLST)?
A method for the genotypic characterization of prokaryotes at the infraspecific level, using the allelic mismatches of a small number (usually 7) of housekeeping genes
98
what is the purpose of multilocus sequence typing (MLST)?
designed as a tool in molecular epidemiology and used for recognizing distinct strains with named species
99
what is Multilocus sequence analysis (MLSA)?
a method for the genotypic characterization of a more diverse group of prokaryotes (including entire genera) using the sequences of multiple protein-coding genes
100
what are ecotypes?
Populations that are genetically cohesive and ecologically distinct
101
what are the pros of MLSA?
- higher resolution
- uses multiple genes
- whereas 16 s rRNA gene analysis provides a genus classification, MLSA gives a species or lower
102
what are the cons of MLSA?
- genes must be single copy
- must all be present in all the organisms being analyzed
- what constitutes a species
103
what is metabolism?
the sum total of all chemical reactions that occur in a cell.
the balance between catabolic and anabolic reactions
104
what is a catabolic reaction?
energy-releasing metabolic reactions (breaking down bonds that store energy to release the energy)
105
what is an anabolic reaction?
energy-requiring metabolic reactions (building things from simpler products, this requires energy)
106
what is the issue with our knowledge of metabolism?
mosy knowledge of microbial metabolism is based on the study of laboratory cultures
107
what are nutrients?
supply of monomers (or precursors of) required by cells for growth
108
what are macronutrients?
nutrients required in large amounts, make up a large percentage of the cell
109
what are micronutrients?
nutrients required in trace amounts in the cell
110
why are CHONSPs important in the cell?
stable enough but not too stable to breakdown
111
how are micronutrients utilized in the cell?
- Many are cofactors or part of the catalytic site of enzymes
- Transition metals (can have more than one charge state) -> role in mediating redox reactions)
112
what is energy defined by?
units of kilojoules (kJ), a measure of heat energy
113
what is Gibbs free energy?
the energy released that is available to do work
114
what is the first law of thermodynamics?
energy can be changed from one form to another, but it cannot be created or destroyed. The total amount of energy and matter in the Universe remains constant, merely changing from one form to another
115
what is an exergonic reaction?
Release free energy
- cell respiration
- catabolism
116
what is an endergonic reaction?
Require free energy
- active transport
- cell movements
- anabolism
117
what is the function of ATP?
is released in the catabolic reaction and used to drive anabolic reactions
118
what is oxidation?
loss of electrons
119
what is reduction?
gain of electrons
120
what is the most energy-rich state?
the more negative the element the more energy that it has
121
what is the electron donor?
the substance oxidized in a redox reaction
122
what is the electron acceptor?
the substance is reduced in a redox reaction
123
how does a redox reaction occur?
occurs in two pairs (two half-reactions)
124
how are redox reactions used in biology?
we can tap into the flow of electrons from one compound to another
- energy can be stored in bonds, and used at a later time
- Or, be used immediately as an energy source
125
what are the most common macronutrients?
metals and most common transition metals
126
what are the two classes of electron carriers?
```
Prosthetic groups (attached to enzymes)
Coenzymes (diffusible) NAD+ , NADP
```
127
what is the most common energy currency?
ATP
128
how does ATP work as an energy source?
ATP bonds can be broken again later to release energy
129
what are the different types of energy sources?
Chemoorgnaotroph (organic molecules)
Chemolothotroph (inorganic molecules)
Phototroph (light)
130
what are the different carbon sources?
Autotroph (CO2)
| Heterotrophs (organic molecules)
131
what are the different electron sources?
Organotroph (organic molecules)
| Lithotrophs (inorganic molecules)
132
what is the most efficient terminal electron acceptor?
oxygen
133
what are the two functions of the citric acid cycle?
energy harvesting
| Carbon harvesting through creating intermediates
134
what are the features of anaerobic respiration?
the use of electron acceptors other than oxygen
- dependent on electron transport, generation of a proton motive force, and ATPase activity
- Less energy released compared to aerobic respiration
135
how many ATP molecules are released from full energy production aerobic respiration?
38
136
why is oxygen the best terminal electron acceptor?
while the other electron acceptors are good at capturing electrons, the electron transport chain is simpler with oxygen
137
what is involved in amino acid biosynthesis?
- Carbon skeletons come from intermediates of glycolysis or citric acid cycle
- Ammonia is incorporated by glutamine dehydrogenase or glutamine synthetase
- Amino group transferred by transaminase and synthase
138
what are the technological advances in microbiology?
Direct cell counts
Culturing
16s surveys
Metagenomics
139
how do microscopic and culture enumerations differ?
by orders of magnitude
140
reasons for culture number difference?
different nutritional requirements
Cells may be in a non-dividing state
Organisms may rely on other organisms (cannot grow alone- obligate)
141
what is selection bias?
most people will pick organisms that will stand out
142
what is enrichment bias?
each culture media selects for only a few organisms
| Microorganisms cultured in the lab are frequently only minor components of the microbial ecosystem
143
what are the reasons that some organisms are hard to culture?
- nutrients available in the lab culture are typically much higher than in nature (can be toxic to some cells)
- Narrow set of conditions
- selects for organisms that can grow alone
144
how do we minimize the effect of cellular competition in culture?
dilution of the inoculum
| Eliminate rapidly growing, but quantitively insignificant, weed species
145
what is the issue with PCR analysis of microbial communities?
need to have information about the genome of the microorganism to create a primer
Primers can also have a bias towards certain microorganisms
146
what are the results of PCR phylogenetic analyses?
several phylogenetically distinct prokaryotes are present
-rRNA sequences differ from those of all known laboratory cultures
Molecular methods conclude that less than 0.1% of bacteria have been cultured
147
what is the rare biosphere?
a concept describing the observation that a very large proportion of the taxa in microbial communities are extremely uncommon
massive diversity at low abundance
148
what did 16s genome analysis enable when compared to prior technology?
prior techniques lacked the resolution to detect rare biosphere
149
what is the genome?
- the entire complement of genetic information
| - includes genes, regulatory sequences, and noncoding DNA
150
what is genomics?
the discipline of mapping, sequencing, analyzing, and comparing genomes
151
what is bioinformatics?
the multidisciplinary field that combines biology, computer science, information engineering, mathematics, and statistics to analyze and interpret biological data
152
what defines the biology of a particular organism?
complement of genes, but genomes are also molded by an organism's lifestyle
153
what does bioinformatics explore?
gene functions
who carries what genes
where are these genes/organisms found
154
what is comparative genomics?
Many genes can be identified by sequence similarity to genes found in other organisms (comparative analysis)
Comparative analyses allow for predictions of metabolic pathways and transport systems
155
what are hypothetical proteins?
uncharacterized ORFs; proteins that likely exist but whose function is presently unknown
- likely encode nonessential genes
- in E.coli, many predicted to encode regulatory or redundant proteins
- considered to be biological 'dark matter'
156
what is the issue with metagenomics?
to separate the individual genomes
157
what is metagenomics?
the total sequence of DNA from a total sample of DNA (unbias)
158
what are the pros of metagenomics?
- detects as many genes as possible
- Yields picture of gene pool in environment
- can detect genes that are not amplified by current PCR primers
- Powerful tool for assessing the phylogenetic and metabolic diversity of an environment
159
what is total DNA extraction?
- environmental single-gene surveys
| - Shotgun studies of all environmental genes
160
what is metagenomic DNA sequencing?
- identify common genes within a community
| - identify genome contents favored by current environmental conditions
161
what is the difference between 16s surveys and metagenomics?
16s is not metagenomics
| -a survey of a particular gene that uses PCR
162
what is the cascade of omics?
```
Genomics
Transcriptomics
Proteomics
Metabolomics
Glycomics; Lipidomics; Fluxomics
```
163
what is a transcriptome?
the entire complement of RNA produced under a given set of conditions
164
what can be learned from RNA experiments?
- an expression of specific groups of genes under different conditions
- an expression of genes with unknown function; can yield clues to possible roles
- comparison of gene content in closely related organsims
- identification of specific organisms
165
what is proteomics?
Genome-wide study of the structure, function, and regulation of an organism's proteins
166
what is metabolomics?
The complete set of metabolic intermediates and other small molecules produced in an organism
167
what effects the unknowns in a microbial community?
the more diverse the ecosystem, the more unknowns you will find
168
what is the new type of phototrophy?
Light-driven ion pumps of bacteria that assist in the generation of ATP in the absence of photosynthesis
-prototype in bacteriorhodopsin
169
where are proteorhodopsin found?
in every single body of water
170
what is the mechanism of proteorhodopsin energy generation?
several forms exist, each tuned to the absorption of different wavelengths of light
171
what are the variants of proteorhodopsin?
abundant in all GOS samples
a total of 2,674 putative proteorhodopsin genes were detected
variation in the residues responsible for light absorptive properties was strongly correlated with the origin of the sample
172
what are the stages from individual organisms to a biosphere?
```
Individual
Population
Community
Ecosystem
Biome
Biosphere
```
173
how was microbiology established?
by studying disease-causing organisms
174
how do most microorganisms live?
in communities of other microbes
175
what are the types of competition?
direct or indirect
176
what is the direct competition?
the competition that involves direct physical contact
177
what is interference competition?
direct; physical fighting over resources
178
what is the indirect competition?
use of resources or other things before another organism
179
what is the exploitative competition?
indirect, competition through consuming scarce resources
180
what are the patterns of competition via differential resource capture?
as one organism depletes its resources, its numbers decline and they lose its competitive advantage, and then the other organism that needs lower levels of nutrients can thrive
181
what is the pattern of competition exclusion via chemical aggression?
Production of an antibiotic that kills the other. One organism dies and the other lives
182
what is the effect of competition modulated by plant defense responses?
The plant will select for one organism to the detriment of another
183
what is the effect of niche specialization in space?
Competition is not always static
Two organisms that share the same niche but not at the same time
Community changing over space and time
184
what are the two ecological processes?
Stochastic
| deterministic
185
what is a stochastic ecological process?
processes occur at random. No set rules, so predictions are not possible. Outcomes will be impossible to determine
186
what is a deterministic ecological process?
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
187
how is initial colonisation deterministic?
most likely invaded by cells from nearby land masses
188
how is initial colonisation stochastic?
the species of organisms from the nearby landmass is random
189
what determines which organisms dominate an ecosystem?
determined by competition/cooperation outcomes
190
what happens to a new niche over time?
as time passes, and conditions change (due to the colonization of the organisms) it allows new niches to open up, allowing the replacement of species
191
what is ecological succession?
change in species composition observed upon a disturbance that opens up niches for colonization
192
what are the two types of ecological succession?
Primary and secondary
193
what is primary succession?
environments are colonized for the first time (e.g. after a volcanic eruption)
194
what is secondary succession?
occur in established systems when a disturbance (e.g. N deposition) reduces diversity leading to a renewed succession thanks to newly available resources or removal of competition
195
what is the driving force of microbial succession?
gradients
196
what are gradients?
can be metabolic side effects (fewer substrates, change in pH)
Or purposely generated metabolites (bacteriocins, antibiotics)
197
what is a disturbance?
processes/events which affect the species composition, structure, and function within an ecosystem
- disturbances can have both positive and negative effects
- can be drivers of change and increased diversity
- can also collapse a community
198
what are the two ways to respond to a disturbance?
resistance
| resilience
199
what is resistance?
Staying essentially unchanged despite the presence of disturbances
200
what is resilience?
Returning to the reference state (or dynamic) after a temporary disturbance
201
what are the stages of plant succession?
1. bare rock
2. mosses, grasses
3. grasses, perennials
4. woody pioneers
5. Fast-growing trees
6. climax forest
202
what is the 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
203
what are the features of r strategists?
- don't compete well
- need lots of resources
- major "skill" is high reproduction
- do not depend on others
- have extreme population fluctuations
204
what is an example of an r strategist?
Pseudomonas
205
what are the features of K strategists?
- excel in competitive environments (low resources)
- efficient but slow growing
- stable population
- often require interaction with other organisms to survive
206
what are marine microbial blooms?
transient events that typically last for several weeks and are large enough to be visible from space
207
what is the community succession from diatom blooms?
once the diatoms die, their biomass provides nutrients for other bacteria
208
what are the factors that affect community succession?
competition
cooperation
disturbances
209
what is parasitism?
one member in the relationship is harmed and the other benefits
210
what is mutualism?
both species benefit
211
what is commensalism?
one species benefits and the other is neither harmed nor helped
212
what are social cheaters?
Individuals in a population that benefits from the cooperative behavior of other individuals without themselves contributing to cooperation
213
what is the function of protozoa?
dissolve the microbes and eat them
214
how do fungi gain energy?
by consuming organic material, dead or alive
215
what is the nutrient level of salt water?
nutrients are limited
216
what does limited nutrients cause?
competition
217
what selects for different microbial conditions in the ocean?
Physical and chemical conditions
| Diversification (gradients drive conditions for an organsim)
218
what is the general surface temperature of the ocean?
surface (~35 degrees)
| seasonal fluctualtions no more that 20 degrees
219
what is the general temperature. ofthe ocean belwo 100m?
0-5 degrees
220
what is the pH of the ocean?
8.3-8.5
221
how is the pH of of the ocean changing with cliamte change?
rising CO2 levels are causing ocean acidification , the pH is decreasing
222
why is oxygen important for microbial growth?
is a major electron acceptor for many microbes
223
where are the regions in the ocean with near 0 oxygen at the surface?
in the tropics and around coasts
224
why are the regions in the tropics low in surface oxygen?
the higher the temperature of the water the less oxygen that can be dissolved in it
225
why are coastal regions low in oxygen?
they are high in nutrients and so can support a lot of life and the oxygen gets used up quickly,
226
what changes with the depth of the ocean?
temperature
pressure
light
227
what determines an microbes survival?
the availability of energy
228
what are microbial energy sources?
chemical
| light
229
what wavelength of light penetrates furthest into the ocean?
blue light
230
what is the difference between the open ocean and coastal water light penetration?
light penetrates deeper into the open ocean
231
why does light not penetrate as far in coastal water?
more sediment in the water and so the light is more likely to scatter
232
where do photoautotrophs live in the ocean?
in the surface waters
233
what is the function of photoautotrophs in the ocean?
they capture light energy and then transfer this light energy to other organsims when they are eaten or through their waste products
234
how much of the marine energy is produced by phytoplankton?
>90%
235
how does phytoplankton provide energy to other organsims?
they act as a carbon source
236
how does light effect productivity of life?
as light diminishes with depth, so does productivity
237
what is the microbial carbon pump (MCP)?
the microbial transfer of organic carbon from labile (easily degradable) to refractory (recalcitrant or non-degradable) states
238
what is the life cycle of carbon stored by microorgansims?
microorganisms transfer energy from matter
They die and, make the nutrients available to other organisms
Most of the carbon is released into the water
Some are released into the air as carbon dioxide
239
what is the biological carbon pump?
The biological pump refers to the export of phytoplankton-derived POM from the surface oceans ro deeper depths via sinking
240
what is the function of the biological carbon pump?
energy transfer and carbon transfer from the surface to the depths of the ocean
241
how does the rate of microbial growth differ with ocean depth?
at the top microbes are fast-growing
| at the bottom, they are very slow growing
242
what are proteorhodopsins?
membrane-bound proteins that change physical shape when exposed to light
243
what is rhodopsin?
membrane-embedded protein that absorbs a photon, causing a physical change
244
what does the conformational change in rhodopsin cause?
A cause a proton, or halide ion, to be translocated from one side of the cell to the other
can also be sued to initiate a signal or cascade, or can be used to directly power several energy-requiring celluralrfunctions
245
how do rhodopsins differ?
they respond differently to different wavelengths of light
246
what are the features of proteorhodopsin?
isolated deep in the photic zone (75-100m) and is blue light absorbing
when isolated from closer to the surface the light absorbancy is different (green and/or blue)
247
how is light important for ocean microbial growth?
light-driven processes sustain and control the flow of external energy into the global ocean
248
what are the three different types of photosynthesis?
oxygenic photosynthesis (OP)
Anaerobic anoxygenic photosynthesis (AnAnP)
Aerobic anoxygenic photosynthesis (AAnP)
249
what is oxygenic photosynthesis?
classic photosynthesis
250
what is anaerobic anoxygenic photosynthesis?
hydrogen sulfide is instead of water
| does not produce oxygen
251
what is aerobic anoxygenic photosynthesis?
wide variety of sources
| organisms often have a very flexible metabolism
252
what are the other two light-driven processes?
rhodopsin-based
| phytochrome-based
253
what do rhodopsin-based and phytochrome-based processes require?
carbon to be produced by other organisms
254
how does transcription of proteorhodopsin and photosynthesis genes differ?
transcription is tightly synchronized to the day/night cycle
255
what is the role of Prochlorococcus?
further establishes synchrony of microbes by pulses of organic carbon
256
what are the subtropical front zone (STFZ) and MOTS?
the transition zone between multiple water sources
257
what is linked to MOTS transections?
changes in physiochemical, nutrient, and biological parameters
258
how are microbial communities trales of space/time?
using 16s sequencing
259
what drives microbial seasonality?
phytoplankton blooms in surface waters
260
what changes in the water seasonally?
Chl levels change throughout the year in surface waters
| This change is linked to changes in productivity, even in deep water
261
what is a living bioreactor?
the symbiotic rumen microbiome
262
what is New Zealand's milk production annually?
3% of the world's milk
| 16 billion liters/year
263
how much of NZs meat production is exported?
>82%
264
why are the numbers of animals in the world increasing?
step rise in the number of animals due to the increasing population of humans and an increase in the demand for food
265
what makes an animal a ruminant?
they have a rumen
266
what are the features of a rumen?
has multiple chambers
| harbors microbes that feed the animal
267
how does a rumen create a mutualistic environment?
the microbes in the rumen feed the animal
| the animal feed the microbes in the rumen
268
what is the interaction between a ruminant and microbes?
the microbes and the ruminant have a symbiotic relationship
269
what are the four chambers of the rumen?
Rumen
Reticulum
Omasum
Abomasum
270
what is the rumen (chamber one)?
this is where food is churned in a rotary motion and fermentation takes place (9-12 hours)
271
what is the reticulum (chamber two)?
used for regurgitation of food "chewing the cud" to increase the surface area for microbial attack
272
what is the omasum (chamber three)?
acts as a filtering device to regulate the type of digest that enters the Abomasum
273
what is the abomasum (chamber four)?
true acidic stomach. Secretes gastric juices (e.g. mucus, pepsin, and HCl). Protein is denatured. Site of bacterial protein assimilation by the animal
274
what are the important features of the rumen?
large size
High constant temperature
Anaerobic environment
275
why is a large rumen important?
important for retention of food for microbial attach
276
why is a high constant rumen temperature important?
39 degrees
6.5 pH
carefully controlled habitat
277
why is an anaerobic rumen important?
supports microorganisms in "symbiotic association". Considerable capacity to digest cellulose.
Anaerobic fermentation
278
why are the microbes in the rumen so important to the animal?
because the animal does not have the enzymes required to breakdown cellulose but the microbes do
this means that the cow can get energy from cellulose, only if the microbes are present
without them, it would die
279
why is the animal so important to the microbes in the rumen?
the animals provide the microbes with their food source on a high scale level through masticated feed (grass)
280
how is energy from the microbes "paid" to the animal?
in the form of volatile fatty acids (VTFs)
281
what are the types of microbes that provide energy to the ruminant?
homoacetogens
282
what are the microbes that convert wasted energy into methane?
methanogens
283
what are the cellulose-degrading microbes in the rumen?
Fibrobacter succinogenes
| Ruminococcus albus
284
what are the starch degraders in the rumen?
Bacteroides ruminocola
| Streptococcus bovis
285
what are the lactate degraders in the rumen?
Megasphaera elsdenii
286
what are the methanogens in the rumen?
Methanobrevibacter ruminantium
287
what can shape the composition of microbes in a rumen?
species
| diet
288
what is most rumens comprised of microbially?
Prokaryotes (cellulose, starch, lactate degraders, and methanogens)
Protozoa
Fungi
289
what are the key products created by the microbes that benefit the cow?
Acetic acid
Propionic acid
Butyruc acid
290
what are the microbial processes that occur in the rumen?
Hydrolysis (cellulolysis, amylolysis)
| Fermentation
291
what are the microbial waste products of rumen microbes?
CO2
CH4
H2O
292
what is the final carbon and energy source of the cow procided by the microbes in the rumen?
Volatile fatty aicds (VFA)
293
what else are the microbes in the rumen used for?
once they pass into the small bowl of the ruminant they provide ~90% of the requirements of amino acids and vitamins
294
what is syntrophy/cross-feeding?
metabolic interaction between dependent microbial partners
| Also called obligately mutualistic metabolism
295
what is an example of syntrophy?
inter-species hydrogen transfer
production of H2 by one organisms and H2 consumption by another
296
what happens in the rumen without methanogens?
glucose undergoes glycolysis through bacterial metabolism and hydrogen is produced as a by-product
the build-up of hydrogen inhibits fermentation
297
which part of fermentation does the build-up of H2 inhibit?
the oxidation of NADH and H+
298
what is the role of methanogens in the rumen?
Methanogens take CO2 and H2 and convert it into CH4 (methane) which is then released via respiration
H2 no longer builds up and fermentation can proceed
299
what is an example of a microbe in the rumen that produces H2?
Ruminococcus albus
300
what are the features of methanogens?
rumen methanogens are hydrogenotrophic (hydrogen eaters)
301
How are methanogens beneficial to the ruminant?
they keep the partial pressure of H2 low and therefore fermentations are directed towards the formation of organisms acids (ACETATE) used by the animal
302
how can the level of methanogens be measured?
methanogens are autofluorescent
303
what is the benefit of syntrophic relationships?
They allow reactions that are not energetically feasible for one of the microbes acting alone to be possible
304
what is IHT?
interspecies hydrogen transfer
305
what is interspecies hydrogen transfer?
refers to the syntrophic process by which one organism transfers hydrogen to another
306
what are the benefits of interspecies hydrogen transfer?
- keeps fermentation directed towards short chain volatile fatty acids like ACETATE
- without it H2 accumulates and inhibits fermentation leading to animal malnutrition
307
what is an example of a short-chain volatile fatty acid?
ACETATE
308
what are the main events that caused an increase in carbon emissions?
1. Mechanization, water power, steam power
| 2. Mass production, assembly line, electricity
309
how can we try and reduce agriculture's impact on methane production?
identify inhibitors to control the growth of methanogens
310
what is soil made from?
minerals (inorganic nutrients)
Air (O2 and other gases)
water
organic material (live and dead biomass)
311
what are the components of soil?
pore space (40-60%)
- air (20-30%)
- water (20-30%)
Soil solids (~50%)
- Mineral (45%)
- Organic (5%)
312
what is igneous rock?
rocks formed when magma (molten rock) from the interior of the earth cools and solidifies
313
what is metamorphic rock?
the heat and pressure of the earth's interior transform igneous rock and sedimentary rocks into metamorphic rocks
314
what is sedimentary rock?
atmospheric agents erode and transport igneous rock to the seabed, where they are compressed and merged with others into sedimentary rock
315
what is weathering?
the means by which soil, rocks, and minerals are changed by physical, chemical, and biological processes
316
what factors can influence the development of specific soil?
1. Parent material
2. climate
3. living organisms
4. Topography
5. time
317
what are the types of rocks that can result from weathering?
```
clay
silt
sand
granule
pebble
cobble
boulder
```
318
what are the stages of transition from soil to rock?
```
residual soil
fully weathered
strongly weathered
weak weathered
slightly weathered
intact rock
```
319
how do microbes affect the formation of soil?
introduction of microbes starts the enable the rock to sustain life
weeds add carbon which provides a direct source of energy and activity
the organic layer is directly proportional to the amount of biomass
320
what are the features of desert soil?
Aridisol forms in deserts. Rainfall is so low that no O-horizon forms and soluble minerals accumulate in the B-horizon
321
what are the features of temperate soil?
Alfisol forms in temperate climates. An O-horizon forms and less-soluble materials accumulate in the B-horizon
322
what are the features of tropical soils?
Oxisol forms in tropical climates where percolating rainwater leaches all soluble minerals, leaving only iron- and aluminum-rich residues
323
what are the factors that affect soil development?
1. Climate: rainfall and vegetation
2. slope
3. substrate
4. pH (most observed)
324
what are the six categories for soil classification?
```
order
suborder
great group
subgroup
family
series
```
325
What is soil taxonomy based on?
morphogenetic soil classification system using diagnostic horizons and features to infer pathways of soil genesis and formation
326
what are some of the features/components of soil?
```
Silt/clay particles
microbes
POM
pore space
virus
fungi
organic matter binder and pore space
mycorrhizal fungal hyphae
plant root
```
327
what are the six functions of soil?
- the extraction of raw materials and water
- physically supporting buildings and other man-made structures
- the production of biomass
- filtration, buffering, storage, and chemical/biochemical transformations
- the preservation of biodiversity or potentially useful genetic material
- the preservation of geogenic and cultural heritage
328
what factors can affect the nitrogen transforming pathways?
- pH
- Moisture
- Carbon availability
- genetic potential
- other microbe related factors
329
what is involved in nitrogen-fixing?
many organisms and many different genes
330
what can pH act to regulate?
Emissions
Denitrification
Community composition
pH has a direct and indirect effect
331
what is the effect of urine patches?
create a unique environment, with new rules
| pH control on emissions abolished
332
what are the effects of urea?
urea induces
- a decrease in community diversity
- a shift in community composition
