🧫Geomicrobiology Unit 3 – Microbial Diversity and Phylogeny

Key Concepts

• Microbial diversity encompasses the vast array of microorganisms including bacteria, archaea, fungi, and microscopic eukaryotes
• Phylogeny is the evolutionary history and relationships among organisms based on genetic and morphological similarities
• Microorganisms play critical roles in biogeochemical cycles, nutrient cycling, and ecosystem functioning
• Geomicrobiology studies the interactions between microbes and geological processes such as mineral formation, weathering, and fossil fuel production
• Advances in sequencing technologies and bioinformatics have revolutionized our understanding of microbial diversity and phylogeny
  • High-throughput sequencing methods (16S rRNA gene sequencing, metagenomics) enable characterization of complex microbial communities
  • Bioinformatics tools and databases facilitate analysis and interpretation of large-scale microbial datasets
• Microbial metabolism and adaptations enable them to thrive in diverse environments from extreme (hot springs, deep-sea vents) to moderate conditions
• Symbiotic relationships between microbes and other organisms (plants, animals) influence ecosystem dynamics and evolution

Microbial Classification Basics

• Microorganisms are classified based on various characteristics including cellular structure, metabolism, genetics, and evolutionary relationships
• The three domains of life are Bacteria, Archaea, and Eukarya which diverged from a common ancestor billions of years ago
• Bacteria and Archaea are prokaryotes lacking membrane-bound organelles while Eukarya includes eukaryotic microorganisms with organelles
• Further classification includes phylum, class, order, family, genus, and species based on increasing specificity of shared characteristics
• Naming conventions follow the binomial nomenclature with genus and species (e.g., Escherichia coli)
• Morphological features (cell shape, flagella, spores) and staining properties (Gram staining) are used for microscopic identification
• Biochemical tests (metabolic capabilities, enzyme production) aid in characterizing microbial properties and functions
• Molecular methods based on DNA and RNA sequences provide more accurate and reliable classification and identification

Diversity of Microorganisms

• Bacteria exhibit an astonishing range of metabolic diversity including chemotrophs, phototrophs, lithotrophs, and organotrophs
  • Chemotrophs obtain energy from chemical compounds (organic or inorganic) while phototrophs use light energy
  • Lithotrophs use inorganic compounds as electron donors and organotrophs utilize organic compounds
• Archaea thrive in extreme environments (high temperature, salinity, or pressure) and include methanogens, halophiles, and thermophiles
• Fungi include yeasts, molds, and mushrooms that play important roles as decomposers, symbionts, and pathogens
• Protists are eukaryotic microorganisms that exhibit diverse morphologies and lifestyles (free-living, parasitic, or symbiotic)
• Viruses are obligate intracellular parasites that infect all forms of life and influence microbial ecology and evolution through horizontal gene transfer
• Microbial diversity is shaped by environmental factors (temperature, pH, nutrients) and biotic interactions (competition, predation, mutualism)
• Extreme environments (acidic mine drainage, deep-sea hydrothermal vents) harbor unique microbial communities adapted to harsh conditions

Phylogenetic Relationships

• Phylogenetic trees depict the evolutionary relationships among organisms based on genetic similarities and differences
• Molecular phylogeny relies on comparing conserved genes or proteins across different taxa to infer evolutionary relationships
  • The 16S rRNA gene is commonly used for bacterial and archaeal phylogeny due to its presence in all prokaryotes and slow evolution rate
  • Other conserved genes (e.g., ribosomal proteins, RNA polymerase) and whole-genome comparisons are also used for phylogenetic analyses
• Sequence alignment is the process of arranging DNA or protein sequences to identify regions of similarity that may indicate evolutionary relationships
• Phylogenetic trees are constructed using various methods such as neighbor-joining, maximum parsimony, and maximum likelihood
• Horizontal gene transfer (HGT) can complicate phylogenetic inference by introducing foreign genes into genomes
• Convergent evolution can lead to similar traits in distantly related organisms adapting to similar environments
• Coevolution occurs when interacting species (host-symbiont, predator-prey) influence each other's evolutionary trajectories

Methods for Studying Microbial Diversity

• Culture-dependent methods involve isolating and growing microorganisms in the laboratory using selective media and growth conditions
  • Enrichment cultures are used to select for specific metabolic or functional groups of microorganisms
  • Pure cultures allow detailed characterization of individual microbial strains but represent a small fraction of total diversity
• Culture-independent methods overcome the limitations of cultivation and provide a more comprehensive view of microbial diversity
  • 16S rRNA gene amplicon sequencing targets the conserved 16S rRNA gene to profile microbial community composition and diversity
  • Metagenomics involves sequencing the collective genomes of a microbial community to explore functional potential and novel genes
  • Metatranscriptomics and metaproteomics provide insights into active gene expression and protein production in microbial communities
• Microscopy techniques (light microscopy, electron microscopy) allow visualization of microbial cells and structures
• Stable isotope probing (SIP) tracks the incorporation of labeled substrates into microbial biomass to identify active populations
• Single-cell genomics enables sequencing of individual microbial cells to explore heterogeneity and rare taxa
• Bioinformatics tools and databases (QIIME, SILVA, RDP) are essential for processing, analyzing, and interpreting microbial diversity data

Geomicrobial Applications

• Microorganisms play critical roles in the formation and dissolution of minerals through biomineralization and weathering processes
  • Iron-oxidizing bacteria (Acidithiobacillus ferrooxidans) contribute to acid mine drainage and the formation of iron-rich minerals
  • Sulfate-reducing bacteria (Desulfovibrio) are involved in the precipitation of metal sulfides and the bioremediation of contaminated sites
• Microbial activity influences the cycling of carbon, nitrogen, sulfur, and other elements in terrestrial and aquatic ecosystems
• Microbes are used in bioremediation to degrade pollutants (hydrocarbons, heavy metals) and restore contaminated environments
• Microbial enhanced oil recovery (MEOR) utilizes microorganisms to increase the efficiency of oil extraction from reservoirs
• Geomicrobiological processes are important in the formation and degradation of fossil fuels (coal, oil, gas)
• Microbial interactions with minerals and rocks contribute to soil formation, nutrient availability, and plant growth
• Microorganisms are used as indicators of environmental quality and can serve as biosensors for monitoring pollution and ecosystem health

Case Studies and Examples

• Acid mine drainage (AMD) is a major environmental problem caused by the oxidation of sulfide minerals by acidophilic bacteria, resulting in acidic and metal-rich water
  • Bioremediation strategies using sulfate-reducing bacteria and constructed wetlands aim to mitigate the impacts of AMD
• The deep biosphere, including subsurface aquifers and marine sediments, harbors diverse microbial communities adapted to extreme conditions
  • Methanogenic archaea and sulfate-reducing bacteria are key players in subsurface carbon and sulfur cycling
• Microbialites, such as stromatolites and thrombolites, are sedimentary structures formed by the activity of microbial communities over geological timescales
  • Modern microbialites in Shark Bay, Australia, and Pavilion Lake, Canada, provide insights into ancient microbial ecosystems and the evolution of life on Earth
• Hydrothermal vent ecosystems support unique microbial communities fueled by chemosynthesis and adapted to high temperatures and pressures
  • Sulfur-oxidizing bacteria (Beggiatoa) and methanotrophic archaea form the base of the food web in these extreme environments
• Microbial diversity in permafrost and glacial environments provides a window into past climates and the potential for life in extraterrestrial icy habitats
  • Psychrophilic bacteria and archaea have evolved adaptations to thrive in cold environments, such as the production of antifreeze proteins and cold-active enzymes

Challenges and Future Directions

• Exploring the vast uncultivated microbial diversity, often referred to as "microbial dark matter," remains a major challenge
  • Advances in single-cell genomics, metagenomics, and culturomics are expanding our understanding of previously unknown microbial lineages
• Linking microbial diversity to ecosystem functioning and services requires integrating multi-omics approaches with biogeochemical and ecological data
• Understanding the role of microorganisms in the response and resilience of ecosystems to global change (climate change, land use change) is crucial for predicting future scenarios
• Developing sustainable biotechnological applications based on microbial diversity, such as bioremediation, bioenergy production, and biomining
• Investigating the co-evolution of microorganisms and their hosts (plants, animals) and the implications for ecosystem health and biodiversity conservation
• Exploring the potential for microbial life in extreme environments on Earth and beyond, such as the subsurface of Mars or the icy moons of Jupiter and Saturn
• Integrating microbial diversity and phylogeny data into Earth system models to better predict biogeochemical cycles and climate feedbacks
• Promoting interdisciplinary collaborations among microbiologists, geologists, ecologists, and computational biologists to advance the field of geomicrobiology