Envrionmental Microbiology

Readings

• Chapter 19 covers microbial system measurement (useful for tutorial presentations), including molecular approaches. Week 5 lecture examines microbial ecology basics.
• Chapter 20 details microbial ecosystems (Week 6 Environmental Microbiology lecture).
• Chapter 21 discusses nutrient cycles (Week 6 Environmental Microbiology lecture).
• Chapter 23 explores microbial symbioses with microbes, plants, and animals (Lecture 7, Week 8, Microbial interactions).

Indicator Species

• Indicator species are biological processes, species, or communities. Changes in their size reflect changes in environmental parameters.
• Often anthropogenic, but can also be natural.
• Indicator species demonstrate clear physiological responses to environmental variables. Examples include canaries in coal mines, frog spawn and pollution indicators.

Fitness / Abundance/ Environmental Gradient

• A. Bioindicators: Fitness/abundance is high in middle of environmental gradient.
• B. Rare species: Very high fitness/abundance at one particular point in the gradient.
• C. Ubiquitous species: Fitness/abundance is uniformly moderate throughout the gradient.

Microbial Indicators

• Microbes are indicators of biological processes, including:
  • Primary Productivity
  • Respiration (BOD)
  • Biogeochemistry
• Microbes are used as indicator species, either directly (CFU counts) or indirectly (biomarker molecules).
• Biomarkers include diagnostic molecules (e.g., fatty acid, DNA, protein) identifying organisms.

Microbial Systems and Ecology

• Microbial systems are amenable to ecology due to:
  • Large population sizes
  • Short generation times
  • Genetic manipulation capabilities
  • Readily accessible for sampling
  • Experimentally tractable nature
  • Different modes of genetic inheritance

Life on Earth

• Ecosystems are environmental units where abiotic (physical) components interact with biotic (organism) communities.
• Microbial photosynthesis produces organic carbon from CO2 and oxygen as a byproduct.
• Primary productivity assesses the rate of CO2 reduction into organic carbon compounds from CO2.
• Chemoautotrophs and photoautotrophs perform this process.
• Oxygenation of Earth's atmosphere allowed organisms to respire organic carbon with oxygen to produce carbon dioxide.

Oxygenic Photosynthesis Made Earth Habitable

• Chart demonstrating historic changes in atmospheric oxygen and carbon dioxide levels throughout Earth’s history, relating to oxygenic photosynthesis.

Microbial Fossils

• Images of microbial fossils.

Hopanoids-Molecular Fossils

• Hopanoids are characteristic biochemical structures. Diagenesis converts hopanoids into sedimentary hopanoids.
• Specific hopanoids are characteristic of phototrophs (2-methylhopanes)
• These data can be used to date photosynthesis before oxygenation of the atmosphere.

Hopanoids

• Lipids found in cell membranes, playing a role in membrane fluidity, stress, and protein localization.
• Highly stable biomarkers, unlike DNA/RNA/proteins.
• 2-methylhopanoids and cyanobacteria are linked.
• Hopanoids date the occurrence of oxygenic photosynthesis.

Life on Earth(Biogeochemical Cycles)

• Microbes drive biogeochemical cycles crucial for life.
• Cycles allow essential elements to be reused through various habitats and spheres.
• Examples include:
  • Nitrogen
  • Phosphorus
  • Carbon
  • Oxygen
  • Hydrogen
  • Sulfur

Oxidizing/Reducing Strength

• Table illustrating oxidizing/reducing strength of various elements.

The Sulfur Cycle

S04-2 --> SO3-2 --> SO2 --> S2O3-2--> S --> H2S

• Sulfur exists in multiple oxidation states.

Sulfate Reduction

• Sulfate-reducing bacteria have short electron transport chains (ETC), as energy available is less than oxygen.
• Sulfidogens are microbes that produce H2S.
• These organisms are usually obligate anaerobes in soil and marine environments.

From Sulfate Reducers to Sulfidogens

• Process diagram depicting the conversion of sulfate to sulfide
• protons pumped outside to create electron potential
• energy generated from all è moves inside to handle

Sulfur Oxidation (Chemoautotrophs)

• ETC (electron transport chain) can be reversed in sulfur oxidizers because H2S, and S2O32- are weaker electron donors than NAD+/NADH.
• Electrons from these fuel sources are fed to the ETC and are equivalent to their Eo.
• Proton motive force is formed at quinone (Q) and terminal oxidase (cytochrome - cyt).

The Nitrogen Cycle

NO3- --> NO2- --> NO --> N2O --> N2 --> NH3 --> NH4+

• Shows conversion of nitrogen into various forms.
• Processes include:
  • Denitrification (CH3OH): N2 production
  • Anammox: conversion of ammonia and nitrite to N2
  • Nitrification: ammonia to nitrite, to nitrate.

Nitrogen Fixation

• Reduction of dinitrogen gas to ammonia by enzyme nitrogenase (O2 sensitive).
• Essential for life, as nitrogen is converted into biologically available forms.
• Energy intensive, requiring a two-enzyme complex (dinitrogenase and dinitrogenase reductase). It is an anaerobic process.
• Only prokaryotes conduct nitrogen fixation. Symbiotic bacteria associated with plants (e.g., Rhizobia) & certain free-living species (e.g., Cyanobacteria, Azotobacter, Clostridium) are examples. Nitrogen fixation is a major limitative factor for life cycles.

Soil Community & Cultured Microbe

• Microbes in soil convert N2 to NH4+.
• Look at genes involved in the pathway.

Mycorrhizae (Symbiotic Associations)

• Symbiotic systems between plant roots and fungi.
• Found in 95% of examined land plants.
• Symbiosis for nutritional exchange. Types:
  • VAM (arbuscular mycorrhizae): Inside plant root
  • Ectomycorrhizae: Outside plant root.
• Fungi dissolve mineral compounds like phosphorus, sulfur, iron.
• They exchange phosphate from soil for sugars produced by plants through photosynthesis. This is essential in phosphate-limited systems.

Heterocysts

• Specialised cells in cyanobacteria that fix nitrogen.
• Thickened cell walls reduce oxygen permeability.
• Absence of chlorophyll avoids oxygen generation.
• Reduced nitrogen is transported to other vegetative cells for use.
• Sugar transport from vegetative cells to heterocysts, attracting heterotrophic bacteria that consume both oxygen and sugars.
• The diffusion of these compounds affects heterocyst spacing.

Mycorrhizae Benefits

• Improved transplant survival/growth/rooting
• Improved soil structure
• Increased fertilizer utilization
• Decreased drought tolerance
• Reduction of off-site pollution
• Disease reduction

Mycorrhizae in Succession

• Key role in developing soils.
• Exported exo-enzymes make micronutrients available to the biosphere
• Modifies soil/habitat characteristics.
• This impacts the ability of other plant species to colonise the area over time.

Possible Mechanisms of Reduction of Infection by Pathogens

• Antifungal actions via antibiotic production, chemical barriers, chemical exudates, and defensive microbial populations (protecting from pathogens).

Relationships Between Phylotype Diversity and Environmental Factors

• Correlation analysis between phylotype diversity and factors like mean annual temperature (MAT), latitude, potential evapotranspiration (PET), and soil pH levels.

Past Exam Questions

• Series of multiple-choice questions focused on topics such as the use of 2-methylhopanoids as biomarkers, photosynthetic processes, energy and carbon sources for different microbial types, elements in the sulfur cycle, reduction of SO4-2 to H2S, nitrogenase and its role in nitrogen fixation, the type of cells used for nitrogen fixation in cyanobacteria, different microbial functional types etc.