Microbes and Climate Change Lecture 1 PDF

+ Microbes and Climate Change Lecture 1 Dr. Florence Abram + 2 Lectures Overview n 2h of lectures n Theme: microbes and climate change n Focus on: n Soil microbial communitie...

+ Microbes and Climate Change Lecture 1 Dr. Florence Abram + 2 Lectures Overview n 2h of lectures n Theme: microbes and climate change n Focus on: n Soil microbial communities and plant-microbe interactions n Rumen microbiome + 3 Microbes and climate change n Microbioorganisms: key drivers and responders to climate change n O2 introduced into atmosphere by marine cyanobacteria (~ 3.5 billion years ago) n Key players in atmospheric concentrations of greenhouse gases CO2, CH4 and N2O throughout much of Earth’s history + 4 Microbes and climate change n Questions: n Whatpart will microorganisms play in the coming decades? n Howcan we harness microbial processes to manage climate change? + 5 Ecosystem A biological community of interacting organisms and their physical environment + 6 Ecosystems n Terrestrial: soil n Aquatic: freshwater and marine n Human gastrointestinal tract n Bioengineered systems (wastewater treatment) + 7 Ecosystems n Microorganisms n Occupy virtually every habitat on the planet + 8 Ecosystems n Soil: 1 billion (109) microbial cells /g of soil n Aquatic: 20 million (2.107) microbial cells /ml of seawater n Humanbody contains more microbial cells than human cells (~10x more; ~1014 in the GI tract) n Wastewatertreatment system are based on microorganisms + 9 Microorganisms Bacteria Archaea Viruses Fungi Protists + 10 Microorganisms n Recycling elements such as carbon, nitrogen, phosphorous... n In their natural habitat: in mixed communities n6 estimated individual taxa for an acid mine drainage biofilm (low diversity) n 5.104estimated taxa per gram of soil (high diversity) + 11 Microorganisms n Isolationand cultivation of all the microbial species involved in an ecosystem is impossible (only 0.1 to 10%) n Behaviourin the laboratory most likely not the same as in natural environment n Anadditional limitation of pure culture–based studies is that potentially critical community and environmental interactions are not sampled + 12 Molecular tools Mixed microbial communities Substrate DNA RNA Protein Metabolit e + 13 Climate change n Climate change is likely to have a profound impact on biodiversity and ecosystems n Microbial interactions are likely to be also profoundly affected n Mostly, predictive models have focused on response to climate change from targeted individual species mainly from floral and faunal communities n Not incorporating information on these interactions and very little is known about the stability of these interactions + 14 Microbial interactions n Symbioses between microorganisms and higher organisms (e.g. plants and animals) are widespread n Play key roles in ecosystems: mutualism n Allows the organisms to thrive in unfavourable conditions (e.g nitrogen-fixers) n Mutualisms likely retain stability and function only under a specific set of environmental conditions + 15 Mutualism n Mutualisminvolves mixed species from different phylogeny and origin: likely to have different response to change in environmental conditions n Stability: ability of mutualistic association to remain stable under varying conditions such as those resulting from climate change n Climate change and mutualism: devastating effect in warming waters with loss of symbionts from coral + 16 Mutualism & climate change n Devastatingeffect in warming waters with loss of symbionts (algal protist: zooxanthellae) from coral (coral bleaching) + 17 Mutualism & climate change n Oceanic temperature exceed summer maxima by 1 to 2°C over 3 to 4 weeks: loss of photosynthetic symbiont n Less energy available to coral ecosystem: n Increased mortality n Decreased growth rate n Decreased reproduction n Increased susceptibility to stress + 18 Mutualism & climate change n Expect mismatching to occur as a response to climate change with the increased or reduced fitness of partners n Maylead to end of mutualistic association that could potentially lead to extinctions n Changing temperatures may also lead to shifts in outcome of association, for examples mutualism could turn into parasitism + 19 Microbial interactions n Environmental conditions can be manipulated to obtain a certain outcomes from an association n Medium composition can be designed to induce shifts in microbial interactions (from neutral to negative and positive interactions) n Demonstrates that microbial interactions are deeply affected by changes in environmental conditions + 20 Microbes and climate change In order to understand, adapt and mitigate the effect of climate change, crucial to consider biological interactions + 21 Definitions n Stability: ability of a microbiome to return to a mean condition after disturbance n Resistance: ability of a microbiome or a process to remain unchanged during and after disturbance n Resilience: ability to recover after disturbance n Adaptation: ability to evolve in order to increase fitness under a specific set of environmental conditions (through gene expression and/or mutations) + 22 Microbiome stability n Disturbance will affect community structure if species differ in their trade-off between growth rate and stress resistance n During a drought event: n Ability to accumulate trehalose to resist dehydration will inform on resistance n Ability to use C or N sources when drought is over will inform on resilience n Ability to switch on general stress response pathway (ie spore formation) more relevant in term of stability + 23 Microbiome stability n Specific microbial traits are crucial in determining microbiome stability n Howeverdifficult to infer from isolated microorganisms studied in the lab so need molecular tools n Functional gene abundance within the community: useful to assess microbiome stability n Metagenomics + 24 Metagenomics n DNA present in a system at time of sampling n Can recover full genomes from data n Metabolic modelling: functional capacity of community n No information on in situ expression n Better if other omics available + 25 Other omics n Metatranscriptomics: n RNA present in a system at time of sampling n in situ gene expression n Metaproteomics: n Proteins present at the time of sampling n in situ protein expression n Metabolomics: n Metabolites present at the time of sampling n Microbial activities + 26 Microbial strategy n r-strategists and K-strategist n High growth rates and low resource use efficiency n Low growth rate and high resource use efficiency n Trade-off between growth and resource efficiency very important to predict community response to disturbances n Community structure will change if taxa present differ in this trade-off n K-strategists more resistant but less resilient to climate change related disturbances than r-strategists + 27 Microbiome and climate change n Factorslikely to affect microbiome response to climate change: n K to r strategist ratios: n Gram positive (slow growth and ability to sporulate: K-strategists) to gram negative ratio n Fungi (slow growth, high resource efficiency: K- strategists) to bacteria ratio n Community diversity n Resource availability n Moisture availability + 28 Microbiome resistance n Microbiome resistance: increases with increasing K to r ratio n Microbiome resilience: increases with diversity + 29 Conclusions n Microorganisms highly relevant to ecosystems n As such impacted by climate change n Need to understand this impact to mitigate effects of climate change