1.3 Overview of microbial communities and their habitats

Microbial communities are everywhere, from our guts to deep-sea vents. They're super diverse, with different microbes thriving in various environments. These tiny organisms play big roles in ecosystems, affecting nutrient cycling and energy flow.

Different habitats host unique microbiomes. Human bodies, soil, water, plants, and even buildings have their own microbial communities. Factors like temperature, pH, and biological interactions shape these communities, influencing their diversity and functions.

Microbial diversity across ecosystems

Diversity metrics and ecosystem variations

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• Microbial communities exhibit vast diversity in species composition, metabolic capabilities, and ecological roles across ecosystems
• Assess diversity using metrics (species richness, evenness, phylogenetic diversity)
• Diversity varies significantly between ecosystems
  • Some environments support highly diverse communities
  • Others dominated by few specialized species
• Extreme environments (hydrothermal vents, hypersaline lakes) often host unique microbial communities adapted to specific conditions

Ecosystem components and functions

• Ecosystems harbor complex networks of microorganisms (bacteria, archaea, fungi, viruses, protists)
• Microorganisms interact with each other and their environment
• Microbial diversity plays crucial roles in ecosystem functioning
  • Nutrient cycling
  • Energy flow
  • Maintaining ecosystem stability

Major microbiomes habitats

Human and animal microbiomes

• Human body hosts diverse microbiomes in various sites
  • Gut microbiome
  • Skin microbiome
  • Oral cavity microbiome
  • Respiratory tract microbiome
• Each site has distinct microbial compositions
• Animal-associated microbiomes play similar roles in host health and function

Environmental microbiomes

• Soil microbiomes highly complex and variable
  • Influenced by soil type, pH, moisture content, vegetation cover
• Aquatic microbiomes encompass diverse environments
  • Freshwater ecosystems (lakes, rivers)
  • Marine environments (oceans, coral reefs)
  • Transitional zones (estuaries, wetlands)
• Each aquatic environment supports unique microbial communities adapted to specific physicochemical conditions

Plant and extreme environment microbiomes

• Plant-associated microbiomes crucial for plant health and ecosystem functioning
  • Rhizosphere microbiome (root-associated)
  • Phyllosphere microbiome (leaf-associated)
• Extreme environments host specialized microbial communities
  • Deep-sea hydrothermal vents
  • Hot springs
  • Polar regions (Arctic, Antarctic)

Built environment microbiomes

• Indoor spaces and urban areas harbor distinct microbiomes
• Influenced by human activities, building materials, ventilation systems
• Examples include:
  • Residential buildings (homes, apartments)
  • Public spaces (offices, schools, hospitals)
  • Transportation systems (subways, airplanes)

Factors influencing microbial communities

Environmental factors

• Abiotic factors shape microbial community composition and structure
  • Temperature ranges
  • pH levels
  • Salinity concentrations
  • Nutrient availability
• Spatial and temporal variations in environmental conditions contribute to community heterogeneity
  • Microhabitats within ecosystems
  • Seasonal changes in climate

Biological interactions

• Biotic interactions determine community dynamics and species abundance
  • Competition for resources
  • Predation by protozoans or bacteriophages
  • Symbiotic relationships (mutualism, commensalism)
• Host-microbe interactions influence community composition
  • Immune responses in animal hosts
  • Metabolic exchanges between plants and microbes

Evolutionary and anthropogenic influences

• Evolutionary processes shape genetic diversity and functional capabilities
  • Horizontal gene transfer between microbes
  • Adaptive radiation in new environments
• Human activities impact microbial community composition and function
  • Land-use changes (deforestation, urbanization)
  • Pollution (chemical contaminants, microplastics)
  • Climate change effects (temperature shifts, altered precipitation patterns)

Disturbance and resilience

• Environmental disturbances alter microbial community structure
  • Natural disturbances (floods, wildfires)
  • Anthropogenic disturbances (oil spills, antibiotic use)
• Community resilience varies across ecosystems
  • Some communities quickly recover post-disturbance
  • Others experience long-term shifts in composition

Microbiome characteristics in different habitats

Biomass and diversity comparisons

• Microbial biomass and diversity vary significantly across habitats
• Soil microbiomes generally exhibit higher diversity compared to aquatic or host-associated microbiomes
• Examples of diversity gradients:
  • High diversity: tropical rainforest soils
  • Moderate diversity: temperate lake ecosystems
  • Lower diversity: extreme environments like hot springs

Nutrient dynamics and metabolic strategies

• Nutrient availability and cycling differ between habitats
• Influences metabolic strategies and functional roles of microbial communities
• Examples of habitat-specific nutrient dynamics:
  • Oligotrophic oceans: adaptations for efficient nutrient scavenging
  • Eutrophic lakes: dominance of fast-growing, nutrient-exploiting microbes

Community stability and specialization

• Stability and resilience of microbiomes vary across habitats
• Some environments support more dynamic communities
• Others maintain relatively stable compositions
• Host-associated microbiomes often exhibit higher specialization
  • Human gut microbiome co-evolved with host
  • Plant root microbiomes adapted to specific root exudates

Spatial structure and temporal dynamics

• Spatial structure and connectivity influence community assembly processes
• Dispersal patterns differ across ecosystems
  • Soil microbiomes: limited dispersal due to physical barriers
  • Aquatic microbiomes: potential for long-range dispersal
• Temporal dynamics vary between habitats
  • Rapid turnover in some environments (coastal waters)
  • Stable compositions over time in others (deep subsurface)

Microbial group abundance patterns

• Relative abundance of microbial groups varies across habitats
• Reflects adaptations to specific environmental conditions and ecological niches
• Examples of habitat-specific abundance patterns:
  • Archaea dominance in extreme environments (hypersaline lakes)
  • Fungal prevalence in forest soils
  • Viral abundance in marine ecosystems