10.2 Microbiomes in biogeochemical cycles

Microbiomes play a crucial role in Earth's biogeochemical cycles, driving the transformation and movement of essential elements. These tiny organisms are the unsung heroes of carbon fixation, decomposition, and nutrient cycling, shaping our planet's chemistry and climate.

Climate change is altering microbial communities and their functions, creating complex feedback loops. As temperatures rise and ecosystems shift, microbes adapt and respond, potentially accelerating or mitigating climate change effects. Understanding these interactions is key to predicting and managing our changing world.

Microbiomes in Biogeochemical Cycles

Carbon Cycle Dynamics

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• Microbiomes drive and mediate biogeochemical cycles transforming and cycling elements essential for life on Earth
• Microorganisms contribute to carbon fixation through photosynthesis and chemosynthesis
  • Cyanobacteria perform oxygenic photosynthesis in aquatic environments
  • Chemolithoautotrophs like Thiobacillus fix carbon using inorganic energy sources
• Microbes decompose carbon through respiration and fermentation
  • Aerobic heterotrophs break down organic matter releasing CO2
  • Anaerobic fermenters produce organic acids, alcohols, and gases like CO2 and H2
• Methanogenic archaea produce methane in anaerobic environments (wetlands, landfills)
• Methanotrophic bacteria oxidize methane influencing atmospheric methane concentrations
  • Type I methanotrophs (Methylomonas) use the ribulose monophosphate pathway
  • Type II methanotrophs (Methylosinus) use the serine pathway

Nitrogen Cycle Processes

• Microbes facilitate nitrogen fixation, nitrification, denitrification, and anammox
• Diazotrophs convert atmospheric nitrogen into biologically available forms
  • Free-living diazotrophs (Azotobacter)
  • Symbiotic diazotrophs (Rhizobium in legume root nodules)
• Nitrifying bacteria oxidize ammonia to nitrite and then to nitrate
  • Ammonia-oxidizing bacteria (Nitrosomonas) perform the first step
  • Nitrite-oxidizing bacteria (Nitrobacter) complete the oxidation to nitrate
• Denitrifying bacteria reduce nitrate to atmospheric nitrogen
  • Facultative anaerobes like Pseudomonas and Paracoccus perform denitrification
• Anammox bacteria convert ammonium and nitrite directly to N2 gas
  • Candidatus Brocadia and Candidatus Kuenenia are key anammox genera

Sulfur Cycle Transformations

• Microorganisms mediate sulfur oxidation, sulfate reduction, and sulfur disproportionation
• Sulfate-reducing bacteria reduce sulfate to hydrogen sulfide in anaerobic environments
  • Desulfovibrio and Desulfobacter are common sulfate-reducing genera
• Sulfur-oxidizing bacteria oxidize reduced sulfur compounds
  • Chemolithoautotrophs like Thiobacillus oxidize H2S to sulfate
  • Phototrophic sulfur bacteria (Chlorobium) use H2S as an electron donor in photosynthesis
• Sulfur-disproportionating bacteria split sulfur compounds of intermediate oxidation states
  • Desulfocapsa sulfexigens can use elemental sulfur as both electron donor and acceptor

Climate Change Impact on Microbiomes

Temperature and Precipitation Effects

• Climate change alters temperature and precipitation patterns influencing microbial communities
• Rising temperatures accelerate microbial metabolic rates intensifying biogeochemical processes
  • Soil respiration rates can increase by 10-20% for every 10°C rise in temperature
• Changes in soil moisture affect microbial activity in terrestrial ecosystems
  • Drought conditions can reduce microbial biomass and alter community composition
  • Increased precipitation can stimulate microbial activity in water-limited ecosystems
• Thawing permafrost releases frozen organic matter stimulating microbial decomposition
  • Up to 1600 Gt of carbon stored in permafrost soils could be released as greenhouse gases

Ocean Acidification and Marine Microbes

• Ocean acidification affects marine microbial communities and their biogeochemical functions
• Calcifying organisms and their associated microbiomes are particularly vulnerable
  • Coccolithophores like Emiliania huxleyi may show reduced calcification rates
  • Coral-associated microbiomes can shift in response to acidification stress
• Changes in seawater pH can alter microbial metabolic processes and nutrient cycling
  • Nitrification rates may decrease in more acidic waters
  • Shifts in iron availability can affect phytoplankton growth and carbon fixation

Ecosystem-Level Changes

• Climate-induced changes in primary production alter substrate availability for microbial communities
  • Increased CO2 can stimulate plant growth providing more organic matter for soil microbes
  • Changes in plant community composition can alter root exudate profiles and microbial associations
• Shifts in microbial community composition lead to changes in functional diversity
  • Warming can favor fast-growing r-strategist microbes over slow-growing K-strategists
  • Loss of microbial diversity may reduce ecosystem resilience to further disturbances

Feedback Loops of Climate Change and Microbiomes

Positive Feedback Mechanisms

• Increased microbial decomposition of soil organic matter releases more CO2
  • Priming effects can accelerate the breakdown of previously stable carbon pools
• Enhanced methane production in thawing permafrost and wetlands contributes to warming
  • Methanogenic activity can increase by 30-40% with a 1°C temperature rise in some wetlands
• Changes in ocean temperature and chemistry alter marine microbial carbon cycling
  • Reduced efficiency of the biological carbon pump may decrease ocean carbon sequestration
• Shifts in microbial nitrogen cycling influence nitrous oxide production
  • N2O emissions from agricultural soils may increase with warming and altered precipitation

Negative Feedback and Adaptation

• Climate-induced changes in plant-microbe interactions affect carbon sequestration
  • Mycorrhizal fungi may increase plant carbon uptake under elevated CO2 conditions
• Adaptations of microbial communities introduce uncertainties in climate feedback predictions
  • Thermal adaptation of soil microbes may reduce the temperature sensitivity of respiration
• Potential emergence of new metabolic pathways or altered efficiencies in biogeochemical processes
  • Evolution of more efficient methane-oxidizing bacteria could mitigate methane emissions

Implications for Climate Modeling

• Understanding microbial-driven feedback loops improves climate models
  • Incorporation of microbial processes can reduce uncertainties in carbon cycle projections
• Quantifying microbial contributions to biogeochemical cycles is crucial for accurate predictions
  • High-resolution monitoring of microbial activities in various ecosystems is needed
• Integrating microbial data with Earth system models presents computational challenges
  • Development of scaling approaches to represent microbial processes at global scales
• Improved climate models inform strategies to mitigate climate change impacts on global cycles
  • Targeted interventions in microbial-mediated processes could help mitigate greenhouse gas emissions