Environmental microbiology

• Sewage treatment

• Bioremediation

• Microbes and climate change

Why do we treat sewage?

• Avoid drinking water contamination

• Avoid food contamination

• Avoid ecological damage viaeutrophication

Sewage treatment

Cholera• Caused by Vibrio cholerae

• V. cholerae is gram(-) rod, salt tolerant, acid sensitive

• Virulence determined by bacteriaphage

• Produces exotoxin that interferes with intestinal waterbalance

• Toxin is destroyed by heating

History of choleraJohn Snow

(1813-1858) Hospital Doctor magazine’s “greatest doctor” of all time

Drinking water contamination

Food contamination

• Meat, dairy, shellfish become reservoirs forpathogens and account for 90% of USfoodborne disease (Bacillus cereus, Clostridium, Shigella,

Staphylococcus, Listeria, Yersinia, Aeromonas)

• Sewage-contaminated water/fertilizer sprayedon vegetable crops get have caused foodpoisoning outbreaks (E. coli 0157:H7, Cyclospora,

Toxoplasma, Cryptosporidium, Campylobacter, Salmonella)

Sewage treatment

Eutrophication

Sewage treatment

How do we treat sewage?

Sewage treatment plants in U.S. use a series of twoprocesses as mandated by

the Clean Water Act of 1972.

• Primary Treatment: a physical process

• Secondary treatment: a microbial process

Goal: reduce the BOD (Biochemical Oxygen Demand)How much oxygen would be needed to decompose the water’s organic waste?

Basically, an index of contamination

Sewage treatment

Primary treatment

• Raw sewage is passed through series of screens

• The sewage is allowed to settle in the “sedimentationtank” yielding sludge

• This process typically removes 50% of the solids and25% of the BOD.

Treatment via GRAVITY

Sewage treatmentSecondary treatment

• Naturally occurring and inoculated microbes oxidizeorganic material into CO2

• Aerobic conditions must be maintained via mixing inan “aerator”

• Oxidation is greatly enhanced by formation of biofilms

Biofilms/Flocs=Micro-organisms living in communities suspended in liquid-ishenvironments attached to surfaces (sometimes gravel)

• This process can remove as much as 95% of the BOD

Treatment via MICROBIAL ACTIVITY

Sewage treatment

Lagoons: Sewage is channeled into shallowponds. Algae and cyanobacteria provide O2 forthe aerobic organisms in the pond to degradethe sewage.

Artificial Wetlands: Similar to lagoons exceptthey provide a habitat for birds and otherwildlife (Figure 31.3).

Other secondary treatment processes

Sewage treatment

…leftovers?

Effluvent: liquid from 2° treatmenthigh in nitrates and phosphorus

*Sterilized by UV, ozone, or chlorine*

By now pathogens have usually been entirely removedby competition by sewage-adapted organisms!!

Sludge: solids from 1° & 2° treatmentWarning: may contain heavy metals & pollutants!

*Processed by “digestion”*

Sewage treatment

• Nitrates removed by denitrification

• Phosphates removed either chemicallyor microbially, but both result inprecipitation of phosphates out ofsolution

Tertiary treatment of Effluent

2NO3- + 5H2 + 2H+ N2

+ 6H2O + EnergyNitrate Dinitrogen Gas

Sewage treatment

Digestion of sludgereactions in digestion:

organic compounds organic acids + CO2 + H2

organic acids acetate + CO2 + H2

acetate + CO2 + H2 CH4

(note: ANAEROBIC!!)

The result is a nutrient-rich product called stabilizedsludge. It can be burned, disposed of in landfills, or

used as a fertilizer.

Sewage treatment

Sewage treatment overview

Sewage treatment

Overview:

Bioremediation: the use of living organisms,such as bacteria and fungi, to degrade ordetoxify pollutants. When plants are used itis called phytoremediation.

Bioremediation is most often attempted in:landfills, soils, aquifers, wetlands, and oil spills

Bioremediation

1) molecular form

2) pH

3) nutrient availability

4) temperature

5) moisture

6) O2 concentrations

7) microbial community/ecology

8) other chemicals

Factors effecting pollutant breakdown:

Bioremediation

Important term 1: Xenobiotics

• Synthetic compounds that are totallydifferent from any that occur in nature.

• They can be harder to get rid ofbecause there aren’t organisms thathave evolved to degrade them.

• Enter genetic engineering!!

Bioremediation

Important term 2: co-metabolism

• Some pollutants are degraded “by accident” bymicrobes trying to degrade something else.

• Microbes produce enzymes to degrade substrates inorder to survive. If the enzyme is general enough, itwill degrade other molecules as well. This is co-metabolism.

• If you provide more of the substrate the microbe isattempting to degrade, you can accelerate thebreakdown of the pollutant.

Bioremediation

Two main bioremediationstrategies:

1) Biostimulation: enhancing the growth ofalready-present microbes by providing themwhat they are limited by (e.g. nutrients,oxygen)

2) Bioaugmentation: adding organisms thatwere not already present

Example: marine oil spills

Bioremediation

Example: TCE breakdown

•TCE (trichloroethylene) is a majorpollutant from electronic components(transformers)

•No known microbes use TCE as aprimary substrate

Bioremediation

•But toluene ortho-monooxygenase enzyme iswidespread in nature andcan co-metabolize TCE

Magic bullet, right? Well…

• “parent” compounds can be broken down intosomething worse

• Some chemicals cannot be degraded

• Heavy metals and high levels of toxins caninhibit desired microbial activity

• Few large-scale success stories usingbioaugmentation in polluted natural systems

• Releasing recombinant microbes: a potentialcan of worms…

Bioremediation

Environmental microbiologyand global climate change

Sources of our majorgreenhouse gases:

Carbon dioxide – soilrespiration, fossil fuelburning, biomass burning

Nitrous oxide – sewagetreatment, N-based fertilizers,automobile exhaust

Methane – wetlands, livestock,rice cultivation, garbagedecomposition, drilling for oil& natural gas

Flurocarbons -- refrigerants

Climate change

Relative significance of greenhouse gases

35-10,0000.3 / 3,000-15,000Fluorocarbons

1140.1 / 206N2O

120.5 / 21CH4

variable1.56 / 1CO2

Atmosphericlifetime (years)

Radiative forcing *Compound

*first number is total atmospheric radiative forcing (W/m2), the second number is aper molecule forcing strength relative to CO2

Climate change

Global carbon dioxideconcentration is on the rise

Climate change

Carbon dioxide sources &sinks

100Deep ocean “removal”

100Deep ocean “burial”

90Ocean respiration

90Ocean photosynthesis

60Soil respiration

60Plant Respiration

120Photosynthesis

Size (GtC/year) *Flux

*(-) means a flux out of the atmosphere, (+) means a flux into the atmosphere

The only natural systemthat is not in equilibrium(I.e. can affect carbonbalance) is theterrestrial ecosystem.Recent large-scalestudies show that soilrespiration is muchmore mutable thaneither photosynthesis orplant respiration.

Climate change

So what happens to soil respirationunder global warming?

• Models predict greatest warming at the poles

• The arctic contains 40% of the world’s soilcarbon frozen as permafrost

• When temperatures increase, permafrostmelts, and metabolic rates increase slightly,increasing soil respiration, increasing CO2 inthe atmosphere, increasing warming??!!

Climate change

Methane sources

Climate change

Nitrous oxide

• Denitrification is a two-step process. N2O isreleased whenever the second step is blockedor slow.

•N2O is also producedduring biomass burningand by soils after a burn

•N2O concentrations inthe atmosphere hasincreased by more than15% since 1750

Climate change

Sources of nitrous oxide

Climate change

Microbes and global change insummary:

• Microbes are a major natural (and stimulated)source of most greenhouse gases.

• Careful measurements of microbial gas emissionsare vital for predicting global climate.

• Microbial emission rates increase with the effectsof human land-use change, livestock, modernagriculture practice, waste production, andbiomass burning. All are secondary effects ofhuman overpopulation.

Climate change