💧Limnology Unit 4 – Freshwater microbial communities

Key Concepts and Definitions

• Limnology studies inland aquatic ecosystems (lakes, rivers, wetlands, groundwater) and their physical, chemical, and biological characteristics
• Microbial communities consist of diverse microorganisms (bacteria, archaea, fungi, protists, viruses) that inhabit freshwater environments
• Biodiversity refers to the variety of life forms within an ecosystem and is essential for maintaining ecosystem stability and resilience
• Trophic levels describe the position an organism occupies in the food chain (primary producers, primary consumers, secondary consumers, tertiary consumers)
• Nutrient cycling involves the transfer of essential elements (carbon, nitrogen, phosphorus) between biotic and abiotic components of an ecosystem
  • Microorganisms play crucial roles in nutrient cycling by decomposing organic matter and releasing nutrients back into the environment
• Eutrophication is the excessive enrichment of water bodies with nutrients, leading to algal blooms, oxygen depletion, and decreased water quality
• Stratification occurs when water bodies form distinct layers (epilimnion, metalimnion, hypolimnion) due to differences in temperature and density

Microbial Diversity in Freshwater Ecosystems

• Freshwater ecosystems harbor diverse microbial communities adapted to various environmental conditions (temperature, pH, nutrient availability, light)
• Bacteria and archaea are the most abundant microorganisms in freshwater, with estimated densities ranging from 10^5 to 10^7 cells per milliliter
• Cyanobacteria are photosynthetic bacteria that play a significant role in primary production and nitrogen fixation in freshwater ecosystems
• Eukaryotic microorganisms (algae, protists, fungi) contribute to the complexity and functionality of freshwater microbial communities
• Viruses, particularly bacteriophages, influence microbial population dynamics through infection and lysis of host cells
• Microbial diversity varies across different freshwater habitats (pelagic zone, benthic zone, sediments) and is influenced by environmental gradients
• Rare and uncultured microorganisms, often referred to as the "microbial dark matter," represent a significant portion of freshwater microbial diversity

Ecological Roles and Interactions

• Microorganisms serve as the foundation of aquatic food webs by converting inorganic nutrients into organic matter through primary production
• Heterotrophic bacteria and fungi decompose organic matter, releasing nutrients back into the water column and sediments
  • This process is crucial for nutrient recycling and supports the growth of higher trophic levels
• Microbial interactions (competition, mutualism, parasitism) shape community structure and function
• Quorum sensing allows bacteria to coordinate their behavior based on population density, facilitating biofilm formation and other cooperative activities
• Microorganisms engage in biogeochemical transformations (nitrification, denitrification, sulfate reduction) that regulate nutrient availability and water chemistry
• Microbial loop describes the transfer of energy and nutrients from dissolved organic matter to higher trophic levels through microbial consumption and predation
• Microorganisms form symbiotic relationships with other aquatic organisms (zooplankton, fish, aquatic plants), influencing their health and survival

Sampling and Identification Techniques

• Water samples are collected using sterile containers or specialized sampling devices (Niskin bottles, Van Dorn samplers) to ensure sample integrity
• Sediment samples are obtained using grab samplers (Ekman grab, Ponar grab) or core samplers to study benthic microbial communities
• Filtration techniques (membrane filtration, tangential flow filtration) concentrate microbial cells from water samples for further analysis
• Microscopy (light microscopy, fluorescence microscopy, electron microscopy) allows direct observation and characterization of microbial morphology and abundance
• Culture-dependent methods involve growing microorganisms on selective media to isolate and identify specific groups of interest
  • However, culture-dependent methods only capture a small fraction of the total microbial diversity
• Culture-independent approaches (DNA sequencing, metagenomics, metatranscriptomics) provide a more comprehensive assessment of microbial community composition and function
• Flow cytometry enables rapid counting and sorting of microbial cells based on their physical and chemical properties

Environmental Factors Affecting Microbial Communities

• Temperature influences microbial growth rates, metabolic activities, and community composition
  • Psychrophilic microorganisms thrive in cold environments, while thermophilic microorganisms prefer high temperatures
• pH affects the availability of nutrients and the survival of microorganisms, with most freshwater microbes adapted to neutral or slightly alkaline conditions
• Dissolved oxygen concentration determines the distribution of aerobic and anaerobic microbial communities in the water column and sediments
• Nutrient availability (nitrogen, phosphorus, carbon) regulates microbial growth and primary production
  • Eutrophic conditions can lead to the dominance of certain microbial groups (cyanobacteria) and alter community structure
• Light penetration influences the vertical distribution of photosynthetic microorganisms and the extent of the photic zone
• Salinity gradients in estuaries and salt lakes create unique niches for halotolerant and halophilic microorganisms
• Hydrological factors (water flow, mixing, residence time) affect the dispersal and distribution of microbial communities in rivers and lakes

Biogeochemical Cycles and Microbial Involvement

• Carbon cycle: Microorganisms fix atmospheric carbon dioxide through photosynthesis and release carbon through respiration and decomposition
• Nitrogen cycle: Microbial processes (nitrogen fixation, nitrification, denitrification) convert nitrogen between its various forms (atmospheric nitrogen, ammonium, nitrate)
  • Nitrogen-fixing cyanobacteria play a crucial role in introducing bioavailable nitrogen into freshwater ecosystems
• Phosphorus cycle: Microorganisms solubilize and mineralize organic phosphorus, making it available for uptake by other organisms
• Sulfur cycle: Sulfate-reducing bacteria convert sulfate to hydrogen sulfide in anoxic sediments, while sulfur-oxidizing bacteria convert hydrogen sulfide back to sulfate
• Iron cycle: Iron-oxidizing and iron-reducing bacteria regulate the availability of iron, an essential micronutrient for many aquatic organisms
• Methane cycle: Methanogenic archaea produce methane in anoxic sediments, while methanotrophic bacteria consume methane and release carbon dioxide
• Microbial activity in biogeochemical cycles is influenced by environmental factors (redox potential, substrate availability) and can have significant impacts on water quality and greenhouse gas emissions

Case Studies and Real-World Applications

• Lake Erie: Recurring cyanobacterial blooms caused by excessive nutrient loading from agricultural runoff and urban wastewater discharge
  • Microcystis aeruginosa, a toxic cyanobacterium, dominates these blooms and poses risks to human health and aquatic life
• Acid mine drainage: Microbial oxidation of sulfide minerals in abandoned mines generates acidic and metal-rich drainage that impacts nearby freshwater ecosystems
  • Acidophilic bacteria (Acidithiobacillus ferrooxidans) and archaea (Ferroplasma acidiphilum) thrive in these extreme conditions
• Bioremediation: Microorganisms are used to degrade pollutants (hydrocarbons, pesticides) and restore contaminated freshwater environments
  • Pseudomonas putida, a versatile bacterium, can metabolize a wide range of organic compounds and is commonly used in bioremediation efforts
• Drinking water treatment: Microbial processes (nitrification, denitrification, biological activated carbon filtration) are employed in water treatment plants to remove contaminants and ensure water quality
• Aquaculture: Beneficial microorganisms (probiotics) are used to promote the health and growth of farmed fish and shellfish, while controlling pathogenic bacteria

Current Research and Future Directions

• Advancements in high-throughput sequencing technologies (Illumina, Oxford Nanopore) enable deeper exploration of microbial diversity and rare taxa in freshwater ecosystems
• Metagenomics and metatranscriptomics provide insights into the functional potential and active processes of freshwater microbial communities
• Single-cell genomics allows the study of individual microbial cells, revealing the metabolic capabilities and evolutionary histories of uncultured microorganisms
• Stable isotope probing (SIP) techniques track the flow of specific compounds through microbial communities, elucidating their roles in biogeochemical cycles
• Microfluidic devices enable the isolation and cultivation of previously unculturable microorganisms, expanding our understanding of microbial diversity
• Climate change impacts on freshwater microbial communities, such as altered thermal stratification and nutrient dynamics, are an active area of research
• Integration of multi-omics approaches (genomics, transcriptomics, proteomics, metabolomics) provides a holistic view of microbial community structure and function in response to environmental perturbations