Micr3213_microbial Ecology - 2018.pdf

Microbial Ecology MICR3213/BC31M: Applied and Environmental Microbiology

Dr. Stacy StephensonClarke stacy.stephenson02 @uwimona.edu.jm

Learning Objectives of Course ❑Understand the ecology of microorganisms at population, community and ecosystem levels ❑Describe the approaches used to study microorganisms in their natural environments and the limitations associated with each ❑Describe community function and dynamics at both the molecular and the organismal level

Learning Objectives of Course ❑Appreciate the (vast) genetic and physiological diversity of microbes, and classify them based on their metabolic fuelling reactions ❑Understand how the specific environmental properties of soils, oceans and biofilms affect microbial communities therein

❑Discuss how microbes are useful in biotechnological and environmental applications such as sewage treatment, bioremediation, etc. and to relate the physiology of microbes to their role in these processes

Microbial Ecology: Further Reading ❑ See Madigan,

M., Martinko, J., Bender, K., Buckley, D. and Stahl, D. (2015). Brock Biology of Microorganisms (14th Ed). Person Education Limited

❑Chapters 18 and 19

Microbial Ecology ❑ Study

of inter-relationships between microorganisms and their environments ECOSYSTEM

COMMUNITY GUILD POPULATION INDIVIDUAL

Microbial Ecology

❑ Microbes and Ecosystem Niches ❑ Organization of Ecosystems ❑ Role of Microbes in Biogeochemical Cycling

❑ Microbial Environments and Microenvironments

History of Microbial Ecology ❑The term “microbial ecology” really wasn’t in common use until the late 1960s ❑Why? ❑Microbial ecology has its roots in microbiology, rather than ecology ❑The history of the field is largely a transition from laboratory pure cultures to studying organisms in nature…

Louis Pasteur (1822-1895) ❑ “basic” vs. “applied” science ❑ fermentation = biological process carried out by microorganisms. ❑ Germ theory = foundation of brewing of beer, wine-making, and pasteurization. ❑ Nature of contagious diseases: potato blight, silkworm diseases, and anthrax. ❑ Immunization (anthrax, rabies) ❑ Public experiments! "Imagination should give wings to our thoughts but we always need decisive experimental proof, and when the moment comes to draw conclusions and to interpret the gathered observations, imagination must be checked and documented by the factual results of the experiment."

Robert Koch (1843-1910)

❑ Discovered the Bacillus strains that cause cholera and anthrax

❑ Agar media for pure cultures (earlier had tried sliced boiled potatoes!)

❑ Disease and medical microbiology ❑ Pure culture paradigm

❑ Pure culture paradigm: isolate an organism and see what it does

Pure Culture Paradigm ❑Extremely important conceptual development in microbiology (and in microbial ecology, too) ❑Remove organisms from complex communities ❑Isolate key processes ❑Obtain reproducible results ❑This method is still used today

❑Attitude of Koch’s time: ❑“Work with impure cultures yields nothing but nonsense and Penicillium glaucum“ (Oscar Brefield 1881)

Sir Alexander Fleming (1929), examining exactly such an impure culture (Staphylococcus culture contaminated by Penicillium), led to the discovery of penicillin. Agar petri dish

Staphylococcus colonies Penicillium contaminant

zone of no bacterial growth, due to penicillin produced by fungus

Interference competition! classic ecological process

Sergei Winogradsky (1856-1953) ❑ Isolated nitrifying bacteria ❑ Winogradsky column: microbial communities develop along a gradient of oxygen tension; method still used today ❑ Described oxidation of hydrogen sulfide, sulfur, ferrous iron ❑ …all leading to the concept of chemoautotrophy – deriving ❑ Bacteria: central in element energy from chemical oxidation of inorganic compounds and transformations carbon from CO2

❑ Founder of soil microbiology

Martinus Beijerinck (1851-1931)

Founder of the Dutch Delft School of Microbiology

“The way I approach microbiology...can be concisely stated as the study of microbial ecology, i.e., of the relation between environmental conditions and the special forms of life corresponding to them”

Martinus Beijerinck (1851-1931) ❑ “a man of science does not marry” ❑ Isolated N fixers and S reducers ❑ ‘Microbial ubiquity’: all microorganisms are everywhere; conditions and resources determine who flourishes ❑ Enrichment culture: growth medium tailored to suit particular metabolic function

❑ With Winogradsky, recognized that microbes are the major players in element transformations ❑ Led to field of global biogeochemistry

Albert Jan Kluyver (1888-1956) ❑ Student of Beijerinck ❑ Microbial physiology

❑ Comparative approach ❑ Unifying metabolic features among microbes ❑ Leader of the Dutch school after Beijerinck

Cornelius Bernardus van Niel (1897-1985) ❑ Student of Kluyver, third in the Dutch Delft School ❑ Isolated purple sulfur bacteria ❑ Major contribution, chemistry of photosynthesis: ❑ H2A + CO2 → CH2O + 2A + H2O

where A can be S or O

❑ Extended model green plants;

oxygen from water, not from CO2 ❑ Also, chemistry of denitrification, definition of prokaryote in 1961 (with R. Stanier) ❑ Taught lab course focusing on studying microbes from nature (first course in microbial ecology?) ❑ Philosophy of hypothesis testing, falsification “moving from clearly erroneous to more ‘correct’, but never immutable conclusions”

Robert E. Hungate (1908-2004) ❑ Student of van Niel ❑ Developed methods for isolating anaerobes ❑ Devised culture methods that select using natural substrates, rather than guesses about what organisms eat ❑ Microbiology of guts of rumen, termites ❑ AKA “Grampa Bob”

❑ ASM president when “Environmental Microbiology” and “Microbial Ecology” formally recognized

Other contributions ❑1960s: Ronald Atlas, Richard Bartha ❑ Studies of petroleum degradation ❑ Led to new field of bioremediation,

❑ Extended to many other pollutants: DDT, PCBs, mercury, selenium, industrial solvents

❑1970s fuel-shortage: ❑ Shortage in N fertilizer ❑ Sparked interest in the biology of nitrogen fixers

Paul D Brown (1960s - ) ❑ Environmental regulation of bacterial virulence ❑ Genetic determinants of antimicrobial resistance ❑ If it can be perceived and believed, it can be achieved!

Microbial Ecology

Energetics and carbon flow in microbial metabolism

heterotroph

(e.g., NH4+, S, H2S, Fe2+)

autotroph

Objectives in microbial ecology ❑ Understanding the biodiversity of microorganisms in nature, and interactions in communities

❑ Measurement of microbial activities in nature, and monitoring of effects on ecosystems ❑ Activities commonly measured when studying microorganisms within an ecosystem: ❑ Primary production of organic matter (phototrophic, chemolithotrophic activity) ❑ CO2 + H2O + energy → new biomass ❑ Decomposition of organic matter (chemoorganotrophic/heterotrophic activity) dead biomass → CO2 + H2O + energy ❑ Biogeochemical cycling of elements (C, O, N, P, S, Fe)

Microorganisms in nature ❑Live in habitats suited to higher organisms, also in “extreme” environments ❑ extremes in temperature, pH, pressure, salinity; anoxic habitats ❑ inanimate (soil, sediment, water, food) & animate habitats (on/in animals, plants, insects) ❑ necessities for growth include available resources, suitable physiochemical conditions

Seawater evaporating ponds near San Francisco Bay, used to harvest “solar” salt. The red colour is due to pigments of the extreme halophile Halobacterium, an Archaeal species that inhabits the ponds.

Psychrophiles, thermophiles, hyperthermophiles: “extremophiles” that live in habitats of extreme temperature, including cold (e.g., deep sea, Antarctica, the Arctic), or hot habitats (e.g., compost piles, deep sea hydrothermal vents)

(Fig. 13.2(b), p. 423, Madigan & Martinko)

Microorganisms in nature ❑ Niche: the functional role of an organism within an ecosystem; combined description of the physical habitat, functional role, and interactions of the microorganism occurring at a given location

❑ Microenvironment: where a

microorganism lives, metabolizes within its habitat ❑ physicochemical gradients ❑ spatial, temporal variability

Figure illustrates O2 contours within a soil particle, measured by microelectrode. Each zone could be considered a different microenvironment

❑ Microcolonies in soil particles ❑ Very few microbes are free; most reside in microcolonies attached to soil particles ❑ Soil aggregates can contain many different microenvironments supporting the growth of several types of microbes

Nutrient levels and growth rates ❑ Microbial life in nature does not necessarily resemble microbial life in lab culture ❑ Entry of nutrients into an ecosystem is often intermittent ❑ Feast-or-famine existence ❑ Adaptations ❑ Accumulate reserves in times of plenty ❑ High growth rate when growth possible; quiescence when growth is not possible

❑ Periods of extended exponential growth rare in nature

❑ Distribution of resources in nature is often non-uniform ❑ Competition for resources is likely

Surfaces and biofilms Biofilm: a community of microorganisms embedded in an organic polymer matrix (extracellular polymeric substances, EPS), adhering to a surface

Time

❑ physicochemical gradients within mature biofilm result in a number of potential microenvironments within a small area ❑ Recall image of soil particle?

Biofilm formation Rendueles & Ghigo, 2012, FEMS Microbiol Rev

Bacterial microcolonies developing on a microscope slide immersed in a river (phase contrast microscopy)

Natural biofilm on a leaf surface ❑ cell colour indicates depth in biofilm: red (surface) → blue (18 μm deep) ❑ (confocal laser scanning microscopy)

Biofilm developed on a stainless steel pipe ❑ stained with DAPI (fluorescent; interacts with nucleic acids) ❑ note water channels through biofilm

Viability staining – Fig 18.7 Brock Biology of Microorganisms 14th ed, 2015 ❑ stained with LIVE/DEAD BacLight bacterial viability stain ❑ Live (green) and dead (red) cells of M. luteus and B. cereus

Biofilm of iron-oxidizing prokaryotes on rocks Rio Tinto Spain

Evidence of a dental biofilm:

❑ left front tooth exposed to sucrose solution for 5 min while right served as a control ❑ both then stained with iodine solution ❑ brown colouration results from reaction of iodine with extracellular glucans (EPS) produced by the sucrose-supplied biofilm

Surfaces and Biofilms ❑ Pseudomonas aeruginosa ❑ Biofilm producer ❑ Intracellular communication (quorum sensing) is critical in the development and maintenance of a biofilm ❑ The major intracellular signaling molecules are acylated homoserine lactones

❑ Both intraspecies signaling and interspecies signaling likely occur in biofilms

Surfaces and Biofilms ❑ Bacteria form biofilms for several reasons: ❑ Self-defense ❑ Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics)

❑ Allows cells to remain in a favorable niche ❑ Allows bacterial cells to live in close association with one another

Biofilms ❑ Advantages of biofilm mode: attachment to surface; nutrient trapping; cooperative interactions possible; protection from toxic substances, predators ❑ Disadvantages: highly competitive; localized biomass can be efficiently preyed upon, infected by viruses ❑ Problems resulting from biofilm formation: periodontal disease; pipe clogging; high microbial numbers in potable water distribution systems; accelerated corrosion of pipelines and structural steelwork; increased drag on ship’s hull ❑ Exploitation of biofilms: slow sand filtration (water purification); microbial leaching of low-grade ores; vinegar production

Microbial Mats ❑Microbial mats: are very thick biofilms ❑Built by phototrophic and/or chemolithotrophic bacteria ❑Photosynthetic mats contain filamentous cyanobacteria ❑Cyanobacterial mats are complete ecosystem ❑ Have existed for over 3.5 billion years

❑Chemolithotrophic mats contain filamentous sulfur-oxidizing bacteria ❑ Often found associated with hot springs, shallow marine basins

(Fig. 12.5, p. 334, Madigan & Martinko)

green: cyanobacterial layers (aerobic phototrophs) ~3 cm thick

orange: layers of anoxygenic phototrophic bacteria

A coring taken through a microbial mat from a hot spring Could you guess the microbes occupying the other layers?

Thioploca mat: Filaments/sheaths of large sulfur-oxidizing chemolithotroph off Chilean coast Fossing et al. 1995; Jørgensen and Gallardo 1999

General Ecological Concepts: Symbiotic Relationship ❑Many microbes establish relationships with other organisms

(symbioses) ❑Parasitism ❑ One member in the relationship is harmed, and the other benefits

❑Mutualism ❑ Both species benefit

❑Commensalism ❑ One species benefits, and the other is neither harmed nor helped

General Ecological Concepts

❑ Diversity of microbial species in an ecosystem is expressed in two ways: Species richness: total number of different species present Species abundance: proportion of each species in an ecosystem

❑ Microbial species richness and abundance are functions of the kinds and amounts of nutrients available in a given habitat

Examples of interactions between microbial populations (i) Negative effect for (one or both) interacting populations: * Competition – outcome depends on innate capabilities of nutrient uptake, metabolic rates • “competitive exclusion” is one possible outcome * Antagonism – specific inhibitor or metabolic product may impede growth/metabolism of others • antibiotic or bacteriocin release, lactic acid production (ii) Positive effect for (one or both) interacting populations: * Cooperative interactions - interacting microbes must share same/nearby microenvironment * Syntrophy – microorganisms together carry out transformation neither can conduct alone

(iii) Complementary metabolic interactions

• e.g., in nitrification: NH3 → NO2- (nitrosifying bacteria); NO2- → NO3(nitrifiers) • e.g., in S cycling: anaerobic sulfate reducing bacteria (SO42- → H2S) provide substrate for microaerophilic sulfide-oxidizing bacteria (H2S → S0)

Current trends in microbial ecology ❑ Space exploration – microbes in extreme environments (hot springs, thermal vents, lithosphere) ❑ Molecular techniques – diversity of microorganisms (Carl Woese), new methods to assess presence or abundance of individual species in situ ❑ Realization that with pure culture/enrichment techniques, we know somewhere between 1-10% of existing microbial species – lots to learn! ❑ Biology of climate change, global biogeochemistry

Recent Discovery ❑In 2008, Prof. Gary Strobel ,Montana State University and students explored the Patagonia rainforest they found an endophytic fungus inside the tissues of the Ulmo tree. The fungus Gliocladium roseum liberates a number of volatile compounds in the air, the mixture is similar to diesel fuel and can be produced when grown in the lab with good yields on cellulose - dubbed mycodiesel ❑Also, Prof. Scott Strobel and a group of Yale students in 2012 found in the Amazon rainforest a fungus Pestialotiopsis microspora that degrades polyurethane (plastic). The fungus is able to survive on polyurethane alone under anaerobic conditions