Ecological microbiology and the cycle of life

What are the underlying principles needed for life to form in microbiology?

The underlying principles needed for life to form include the presence of liquid water, essential elements like carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOPS), a suitable energy source, and a stable environment that allows biochemical reactions to occur.

How are biosignatures used to predict early life?

Biosignatures are indicators of life that can include specific molecules, isotopic ratios, or mineral forms that suggest biological processes. Scientists study these signatures in rocks or meteorites to identify possible evidence of past life, guiding the search for extraterrestrial life.

What are the key features of the metabolism and RNA world models to explain life today?

The metabolism model emphasizes the importance of chemical reactions providing energy to build cellular structures, whereas the RNA world model suggests that RNA molecules were primordial, capable of both storing genetic information and catalyzing reactions, serving as the foundation for early life.

What are the typical features of bacteria and outline the main similarities and differences between archaea and eukaryotes?

Typical features of bacteria include prokaryotic structure, lack of membrane-bound organelles, and a cell wall composed of peptidoglycan. Similarities between archaea and eukaryotes include the presence of RNA polymerase and similar ribosomal structures. Differences include cell structure (archaea have unique membrane lipids, while eukaryotes have a nucleus and membrane-bound organelles), and their environments (archaea are often extremophiles, thriving in extreme conditions).

What are the challenges in defining bacterial species?

Challenges in defining bacterial species include genetic diversity within species, horizontal gene transfer making it hard to classify based on genetic similarities, and morphological variations that can lead to misidentification.

Outline the general characteristics of the main bacterial phyla and cellular characteristics considered typical to bacteria

Bacterial phyla exhibit diverse metabolic pathways and cellular structures. Common characteristics include prokaryotic organization, the presence of peptidoglycan in the cell wall, ribosomal RNA similarity, and varied shapes (cocci, bacilli, spirilla). Major phyla include Firmicutes (Gram-positive), Proteobacteria (diverse metabolic potentials), and Actinobacteria (filamentous forms).

What are the three types of dna transfer in bacteria?

1. Bacterial transformation: donor cell releases antibiotic resistance gene to recipient cell

2. Bacterial transduction: phage infected donor releases phage to recipient cell

3. Bacterial conjugation: donor cell transfers plasmid directly to recipient cell

Differentiate informational genes from operational ones

• Informational genes are essential for normal cell processes and move by vertical transmission

• Operational genes have specific roles and move by horizontal transmission

What dictates cell shape?

Cytoskeleton

How much of ecoli is nucleic acid?

8%

What is the difference between a photoautotroph and a chemoheterotroph?

Photoautotrophs use sunlight as their energy source and convert CO2 into organic compounds through photosynthesis, while chemoheterotrophs obtain energy by consuming organic compounds from other organisms.

What is the importance of energy efficiency when using resources in environmental systems?

Energy efficiency is crucial in environmental systems as it maximizes resource utilization, minimizes waste, reduces greenhouse gas emissions, and supports sustainable practices that ensure the long-term viability of ecosystems.

What is the Gibbs free energy equation?

The Gibbs free energy equation is G = H - TS, where G is the Gibbs free energy, H is the enthalpy, T is the temperature in Kelvin, and S is the entropy. It is used to predict the spontaneity of reactions.

How do cells convert external resources into biochemical energy and use enzymes?

Cells convert external resources like glucose into biochemical energy (ATP) through cellular respiration, utilizing enzymes such as hexokinase to lower the activation energy of glucose phosphorylation.

what is a phototroph?

microbe that generates energy from light

what is a chemotroph?

What is a organotroph and lithotroph?

• a microbe that generates energy from chemical rearrangement of molecules

• Organotroph: chemotroph that uses organic molecules

• Lithotroph: chemotroph that uses inorganic molecules

what is an autotroph?

microbe that fixes CO2 for carbon

what is a heterotroph?

a microbe that uses external sources of carbon for biosynthesis

entrophy becomes… as temperature approaches zero

constant

what molecules are transported through membranes?

simple molecules

what is fermentation?

• breakdown of carbohydrates in ABSENCE of O2

• uses organic electron acceptor

why is oxygen bad for anerobes?

• O2 and FAD+ generates reactive oxygen species

• anerobic microbes cannot detoxify reactive oxygen species

• reactive oxygen species damage DNA, RNA, membranes

Why use fermentation rather than anerobic respiration?

• lower energy yield

• produces wide range of compounds

• is faster

why is a proton motive pump important?

creates a difference in pH and electrical chargeacross a membrane, driving ATP synthesis and enabling nutrient transport.

where does iron oxidation occur?

wetlands and acid mine drainage

what does oxidation of sulphur compounds lead to?

acidification (common in marine environments)

what causes corrosion of underwater steel bridge supports?

sulphur reducing bacteria

what is bacteriorhodopsin?

• a protein that captures light energy to drive proton pumps

• absorbs green wavelengths, reflects blue and red

what is cyanobacteria?

Photosynthetic bacteria that release oxygen and fix nitrogen, playing a crucial role in aquatic ecosystems.

what is Asgard archaea?

• widely distributed in extreme environments

• similar proteins to eukaryotes

what is crenarchaeota?

• widest diversity of growth temperatures

• associated with plants and animals

where are methanogens found?

• wetlands

• marine sediments

• polar permafrost

• sewage treatment

• landfill

• animals

where does methanogenesis occur?

in archaea eryarchaeotes

what are some adaptations psychrophiles have?

• increased membrane fluidity

• cryoprotectant compounds

• low temperature enzyme optima

what are adaptations thermophiles have?

• saturated membrane lipids

• stable proteins

• supercoiled DNA

• heat shock proteins

what are some adaptations halophiles have?

• maintain high intracellular potassium conc

• cell envelopes contain pseudopeptidoglycan

• acidic proteins

Define:

• protist

• protozoan

• amoeba

• protist: single celled clonal eukaryotes (algae)

• protozoan: single celled heterotrophs (not algae)

• amoeba: single celled protozoans without defined cellular shape

how much do algae account for carbon fixation?

45% all

describe the fungal kingdom

• diverged from common ancestor with animals 800-900 mya

• over 140000 species

• heterotrophic

what is chemotaxis and what are the 2 ways of this in bacteria?

• Chemotaxis: cell movement along gradient to find where to pioneer

• Random walk- 1 flagellum spins in opposite direction to the others

• Biased random walk- swim staggered to an attractant

what factors affect biofilm formation?

• nutrient availability

• surface

• pH

• temperature

• oxygen

• co-colonisation

what is quorum sensing?

secretion of small molecules within a bacterial population that cause coordinated behaviour when a threshold (quorum) is reached

what is an example of quorum sensing?

mutualistic interaction between Hawaiian bobtail squid and bioluminescent Aliivibrio fischeri bacteria

what are actinomycetes?

A group of gram-positive bacteria known for their role in soil ecology and antibiotic production. They produce earthy smell after rain

what are streptomyces?

A genus of actinomycetes known for their prolific antibiotic production and soil-dwelling capabilities.

what is the proposed role of antibiotics in nature?

• High concentrations: used as a killing antibiotic

• Low concentrations: used as a signalling molecule

what is the main food of caribou?

Cladina lichens

what are mycobionts and photobionts?

mycobiont: the fungal partner in a lichen relationship

photobiont: the photosynthetic partner, usually algae or cyanobacteria.

what are the biotic components to environmental cycles?

• photosynthesis

• respiration

• environmental mediation

• elemental fixation for biomass

what are the abiotic components to environmental cycles?

• volcanic activity

• fires

• rock weathering

• gas absorption by oceans

what do you measure functional ecology by?

genetic diversity and functional diversity

what is microbial activity affected by?

• light

• pH

• temperature

• nutrients

• toxic compounds

• water availability

• redox potential

• interactions

Define:

• sources

• sinks

• reservoir

• sources- part of the biosphere that stores a lot of a particular element

• sinks- part of the biosphere that can receive a particular element

• reservoir- major parts of biosphere containing a lot of a particular element

what are the common principles of primary producers?

• absorb energy from outside ecosystem

• minerals assimilated into biomass

what are the three horizons of soil?

1. surface horizon

2. subsoil

3. substratum

what do small mineral particles do in soil?

provide structure and absob oxygen, water and nutrients

what is an oxygen minimum zone in oceans?

A layer in the ocean where oxygen saturation is very low, typically found at depths of 200 to 1,000 meters from the decomposition of organic matter and limited mixing of water.

how does pollution affect marine microbes?

• fertilizers provide algae with limiting nutrients

• blooms die and sewage directly feeds heterotrophs

• reduced oxygen so animal life isnt sustained

How much anthropogenic CO2 is absorbed by oceans and what affecr does it have on pH?

• 30%

• pH is currently 8, expected to be 7.8 by 2100

what are the effects of ocean acidification?

coral bleaching disrupts mollusc larvae shell and coral formation. Also affects animal physiology

describe the problems with climate change and methane in oceans

• oceans produce 85-300 Tg methane per year from deep sea habitats

• warming releases methane as well as extraction companies

• ocean methane will kill us all

• methane hydrates are oxidised by microbial mats so it can be prevented

how do microbes oxidise methane under aerobic conditions?

They remove the methyl group to get Phosphorus

what is saprotrophy?

microbesbreaking down dead and decaying matter for nutrients. Is a form of chemoheterotrophy.

How many years ago did fungi develop wood decay mechanisms?

800 MYA allowing them to decompose coal seams (lignin and cellulose)

what is white rot fungi?

• breaks down lignin in wood

• associated with hardwoods and temperate forests

what is brown rot fungi?

• aggressive cellulose break down but leaves lignin behind

• dominant in softwood and carnivorous habitats

• created Hydroxyl radicals to breakdown lignin to get to cellulose

what is soft rot?

• caused by fungi and bacteria

• slow growth decomposing cellulose

• needs 20% moisture content of wood

what attacks lignin in fungi?

class II peroxidase to attack bonds

how do fungi decay wood so quickly?

they use vast corded networks of hyphae and enzymes to break down wood components.

what is nitrogen used for in a cell?

amino acids, proteins and nucleotides

what processes is the biogenic nitrogen triangle used for?

• nitrogen fixation

• assimilation

• nitrification

• denitrification

• ammonification

• nitrate reduction

what is essential for nitrogen cycling?

oxygen

why do only specific microbes fix Nitrogen?

N2 is very inert that does not interact well so requires large amounts of energy

what enzyme carries out nitrogen fixation?

nitrogenase (requires O2 to be excluded)

what microbes do Nitrification?

lithotrophs oxidize ammonia to nitrite and then to nitrate.

what is anammox?

anaerobic bacteria oxidize ammonia directly with nitrite to produce nitrogen gas, playing a crucial role in the nitrogen cycle.

what is sulphur used for in a cell?

• protein structure

• microbial metabolism

• cellular respiration

what are sources of sulphur in terrestrial habitats?

• rock weathering

• atmospheric deposition (H2S)

• organic matter decomposition

Sulphur has a lower abundance in terrestrial than marine systems

What are sources of sulphur in marine habitats?

• abundant in components of SO42-, SO and H2S

• weathering rocks, land leaching, rain, microbial metabolism

what is the importance of DMSP and DMS production?

• supplies 7% carbon to heterotrophic bacteria in photic zone

• reduces global warming

• major route of Sulphur supply to land

How is DMSP and DMS made?

• algae convert metholine to DMSP

• bacteria produce DMS from DMSP

what do sulphate reducing prokaryotes use marine sediments for?

abundant SO42-

what is the 4th most common element that is also 5% the earths mass?

iron

what are siderophores?

small proteins with an high affinity to bind Fe3+

where is there a low concentration of iron in marine habitats?

water columns

where do marine systems get iron from?

• terrestrial dust

• arrives as Fe3+ so bacteria must oxidise

• hydrothermal vents add iron to deep ocean

where is phosphorus abundant?

earths crust but reservoirs are running out