Introduction to

Environmental Microbiology

Environmental Microbiology(MLEM-201)

Lecturer:Dr. Mohamed Salah El-Din

Intended Learning Outcomes (ILO’s):

Student will be able:

•To achieve a basic understanding of aquatic microbiology and microbial processes

•To know the major microorganisms of importance in freshwater, seawater, and groundwater

•To understand the major microbial processes involved in those habitats

•To understand the major environmental factors and influences in those habitats

•To understand how to apply basic microbiological and ecological principles in understanding the applied processes known as bioremediation of contaminated soils and groundwater.

Environmental Microbiology is:

The study of the effects of the environment on microorganisms and of microorganisms on the environment

This is a LARGE area to cover in just one course so the vast majority of Environmental Microbiology courses assume that students have previous exposure to (at least) basic microbiology courses.

This course assumes some prior knowledge of :

• The effects of environmental factors (pH, water activity, temperature, oxygen, etc.) on microorganisms (bacteria, fungi and algae)

• The basic taxonomy of microorganisms

• The basic physiology, biochemistry and structure of microorganisms

General Course Introduction

Question: Why concentrate on Water Issues ?

Answer – Global Water Supply, Use and Distribution Issues

Water covers 70% of the Earth's surface

Water in the oceans is over 96% of all water on Earth

About 30% of the 105,000 cubic kilometres of water that falls by precipitation reaches the oceans though river flow.

70% is evaporated or transpired by plants

This leaves only 37,000 cubic kilometres of water for distribution to the Earth's population. This is about 6000 cubic metres per person per year at a population of 6 billion = 12,000 litres per day per person.

Unfortunately, that 37,000 cubic kilometres is NOT evenly distributed around the Earth' surface.

For instance Canada has over 22% of the Earth's standing supply of freshwater (but see later)

Two litres of water per person per day will sustain life.

Average consumption is about 250 litres per day per capita

Industrial consumption is about 1500 litres per day per capita in the developed countries

Agricultural consumption can exceed 3000 litres per day per capita in hot climates.

Many other complicating factors such as water quality, pollution with inorganic and organic chemicals, and contamination with microorganisms causing disease

Introduction (continued)

1. Most water is in circulation through evaporation, condensation (rain, snow), movement through the earth, run-off, stream, river and ocean transport.

2. Some is essentially “locked away” in ice and deep groundwater reservoirs that release the water very slowly.

3. A typical, but smaller, hydrologic cycle is that for the Great Lakes drainage basin (watershed) shown on the next slide

The Global Hydrologic Cycle - Great Lakes

Great Lakes 2

Great Lakes 3

Great Lakes 4

Great Lakes 5

Category a Total volume (km3)

% of total

% of fresh

Replacement Period

Annual volume recycled (km3)

World Oceans 1 338 000 000 96.5 - 2 650 yr 505 000

Groundwater (to 2000m) 23 400 000 1.7 - 1 400 yr 16 700

Predominantly fresh groundwater 10 530 000 0.76 30.1 - -

Soil Moisture 16 500 0.001 0.05 1 yr 16 500

Glaciers and Permanent Snow 24 064 100 1.74 68.7 - -

Antarctica 21 600 000 1.56 61.7 - -

Greenland 2 340 000 0.17 6.68 9 700 yr 2 477

Arctic Islands 83 500 0.006 0.24 - -

Mountain areas 40 600 0.003 0.12 1 600 yr 25

Ground ice (permafrost) 300 000 0.022 0.86 10 000 yr 30

Lakes 176 400 0.013 - 17 yr 10 376

Freshwater 91 000 0.007 0.26 - -

Salt water 85 400 0.006 - - -

Marshes 11 470 0.0008 0.03 5 yr 2 294

River 2 120 0.0002 0.006 16 d 48 400

Biological water 1 120 0.0001 0.003 - -

Atmospheric water 12 900 0.001 0.04 8 d 600 000

Total water 1 385 984 610 100a      

Freshwater 35 029 210 2.53a 100a    

a Some duplication in subcategories and categories.

         

GLOBAL HYDROLOGICAL CYCLE

Great Lakes

1. Clean, safe water can be brought to the 1.4 billion people around the world without it for as little as $50 per person, which can prevent many of the 3.35 billion cases of illness and 5.3 million deaths caused each year by unsafe water, says a United Nations analysis.

2. At any given time, an estimated one half of people in developing countries are suffering from diseases caused either directly by infection through the consumption of contaminated water or food, or indirectly by disease-carrying organisms (vectors), such as mosquitoes, that breed in water. These diseases include diarrhea, schistosomiasis, dengue fever, infection by intestinal worms, malaria, river blindness (onchocerciasis) and trachoma (which alone causes almost six million cases of blindness or severe complications annually).

3. The UN warns that unless action is stepped up, the number of people without access to safe water will increase to 2.3 billion by 2025, with the number of those who die from unsafe water expected to jump sharply as well.

4. Right now, 20 percent of the world's population in 30 countries face water shortages, a figure that will rise to 30 percent of the world's population, in 50 countries, by 2025, according to the UN.

UN World Day for Water, 1999

UN Water Report 1

Disease Morbidity (episodes/yr.) (or as stated)

Mortality (deaths/yr.)

Relationship of Disease to WaterSupply and Sanitation

Diarrhoeal diseases 1,000,000,000 3,300,000 Strongly related to unsanitary excreta disposal, poor personal and domestic hygiene, unsafe drinking water

Infection with intestinal helminths

1,500,000,000

(1)

100,000 Strongly related to unsanitary excreta disposal, poor personal and domestic hygiene

Schistosomiasis 200,000,000 (1) 200,000 Strongly related to unsanitary excreta disposal and absence of nearby sources of safe water

Dracunculiasis 100,000 -- Strongly related to unsafe drinking water

Trachoma 150,000,000 (3) -- Strongly related to lack of face washing, often due to absence of nearby sources of safe water

Malaria 400,000,000 1,500,000 Related to poor water management, water storage, operation of water points and drainage

Dengue Fever 1,750,000 20,000 Related to poor solid wastes management, water storage, operation of water points and drainage

Poliomyelitis 114,000 -- Related to unsanitary excreta disposal, poor personal and domestic hygiene, unsafe drinking water

Trypanosomiasis 275,000 130,000 Related to the absence of nearby sources of safe water

Bancroftian filariasis

72,800,000 (1) -- Related to poor water management, water storage, operation of water points and drainage

Onchocerciasis 17,700,000 (1,4) 40,000 (5) Related to poor water management in large-scale projects

Totals 3.34 billion 5.29 million

1 People currently infected.

2 Excluding Sudan

3 Case of the active disease. Approximately 5,900,000 cases of blindness or severe complications of Trachoma occur annually

4 Includes an estimated 270,000 blind

5 Mortality caused by blindness

Estimates Of Morbidity And Mortality Of Water-Related Diseases

Mortality

Every 8 seconds, a child dies from a water-related disease

50 percent of people in developing countries suffer from one or more water-related diseases

80 percent of diseases in the developing world are caused by contaminated water

50 percent of people on earth lack adequate sanitation

20 percent of freshwater fish species have been pushed to the edge of extinction from contaminated water.

Most available fresh water is found in developed nations, which have only one-fifth of the world's population. Nearly all of the 3 billion global population increase expected by 2025 will be in developing countries, where water is often already scarce, or comes in monsoons, hurricanes and floods, draining off the land quickly.

How bad is the water crisis ?

Water Crisis?

Waterborne Disease Outbreaks in the U.S.A. by Type of Water Supply System, 1971 to 1994

        Total TotalYear Community Noncommunity Individual Outbreaks Cases1971 8 8 4 20 5,184 1972 9 19 2 30 1,650 1973 6 16 3 25 1,762 1974 11 9 5 25 8,356 1975 6 16 2 24 10,879 1976 9 23 3 35 5,068 1977 14 18 2 34 3,860 1978 10 19 3 32 11,435 1979 24 13 8 45 9,841 1980 26 20 7 53 20,045 1981 14 18 4 36 4,537 1982 26 15 3 44 3,588 1983 30 9 4 43 21,036 1984 12 5 10 27 1,800 1985 7 14 1 22 1,946 1986 10 10 2 22 1,569 1987 8 6 1 15 22,149 1988 4 8 1 13 2,128 1989 6 5 1 12 2,540 1990 5 7 2 14 1,758 1991 2 13 0 15 12,960 1992 9 14 4 27 4,724 1993 9 4 5 18 14,190 1994 5 5 2 12 1,176

Red = more than

10,000 casesData from Center for Disease Control, Atlanta

Waterborne Disease USA

Liberia 232.0 1987 bLibya 0.6 1997 c,Madagascar 337.0 1984 cMalawi 18.7 1994 cMali 67.0 1987 bMauritania 11.4 1997 c,jMauritius 2.2 1974 cMorocco 30.0 1997 c,jMozambique 216.0 1992 cNamibia 45.5 1991 cNiger 32.5 1988 cNigeria 280.0 1987 bRwanda 6.3 1993 cSenegal 39.4 1987 bSierra Leone 160.0 1987 bSomalia 15.7 1997 jSouth Africa 50.0 1990 cSudan 154.0 1997 c,jSwaziland 4.5 1987 bTanzania 89.0 1994 cTogo 11.5 1987 bTunisia 4.1 1997 jUganda 66.0 1970 cZambia 116.0 1994 cZimbabwe 20.0 1987 b

Canada 2901.0 1980 d|United States of America 2478.0 1985 dChina 2800.0 1980 dIsrael 2.2 1986 d

Algeria 14.3 1997 c,jAngola 84.0 1987 bBenin 25.8 1994 cBotswana 14.7 1992 cBurkina Faso 17.5 1992 cBurundi 3.6 1987 bCameroon 268.0 1987 bCape Verde 0.3 1990 cCentral African Republic 141.0 1987 bChad 43.0 1987 bComoros 1.0 1987 bCongo 832.0 1987 bCongo, Democratic Republic (formerly Zaire) 1,019.0 1990 c

Cote D'Ivoire 77.7 1987 bDjibouti 0.3 1997 jEgypt 86.8 1997 jEquatorial Guinea 30.0 1987 bEritrea 8.8 1990 cEthiopia 110.0 1987 bGabon 164.0 1987 bGambia 8.0 1982 cGhana 53.0 1970 cGuinea 226.0 1987 bGuinea-Bissau 27.0 1991 cKenya 30.2 1990 cLesotho 5.2 1987 b

Example – Africa: Annual Renewable Water Resources [km3/yr]Source: P.H. Gleick, 1998, "The World's water - 1998-1999" (Island Press, Washington, DC).

Country Water Resources Year Source

Country Water Resources Year Source

Sources

a Total natural renewable surface and groundwater. Typically includes flows from other countries. (FAO: "Natural total renewable water resources.")

b Estimates from Belyaev, Institute of Geography, USSR (1987).

c Estimates from FAO (1995) "Water Resources of African Countries." Rome.

d Estimates from WRI (1994). See this source for original data source

e Estimates from Margat (1989), Water International 14 as cited in Gleick 1993, Table A11.

f Estimates from Shahin (1989), Water International 14 as cited in Gleick 1993, Table A17.

g Estimates from Goscomstat, USSR, 1989 as cited in Gleick 1993, Table A16.

h World Resources Institute 1996 "World Resources" Oxford Univ. Press.

i  New ECE Environmental Statistical Database. j Estimates from FAO (1997) "Water Resources of the Near East Region: A Review." Rome.

Estimates from FAO (1997) "Irrigation in the Countries of the Former Soviet Union in Figures." Rome.

Africa

Region and Country 1994 Population Access to Safe

Drinking water (%)

Number Unserved (millions)

AFRICA 707 46 381

       

LATIN AMERICA & THE CARIBBEAN 473 80 97

       

ASIA & THE PACIFIC 3,122 80 627

       

WESTERN ASIA 81 88 10

       

TOTAL 4,383 74 1,115

Access to Safe Drinking Water & Sanitation in Developing Countries by Region,1994 Source: P.H. Gleick, 1998, "The World's Water 1998-1999" (Island Press, Washington, DC).

Access to Sanitation, 1994

Number Unserved (millions)

464

176

2206

26

2873

World

Country Population without access

to water % (1990-96)

Population without access to

sanitation % (1990-96)

Life expectancy at birth

(1995)

Under 5 mortality (per 1,000 live births)

1996

Chad 76 79 47.2 149Ethiopia 75 81 48.7 177Zambia 73 36 42.7 202Papua New Guinea 72 78 56.8 112

Angola 68 84 47.4 292Congo 66 31 51.2 108Madagascar 66 59 57.6 164

Sierra Leone 66 89 34.7 284

Cambodia 64 86 52.9 170

Haiti 63 75 54.6 134Malawi 63 94 41 217Central African Republic 62 73 48.4 164

Tanzania, U. Rep. Of 62 14 50.6 144

Dem. Rep. Of the Congo 58 82 52.4 207

Lao, People’s Dem. Rep. 56 82 52.2 128

Guinea 54 69 45.5 210Uganda 54 43 40.5 141Gambia 52 63 46 107Niger 52 83 47.5 320Turkey 51 38 68.5 47

Access to safe water/sanitation, life expectancy and under-5 mortality UN Water Report 2

Djobouti 10 45 49.2 157

Iran, Islamic Rep. Of 10 19 68 37

Botswana 7 45 51.7 50

Cuba 7 34 75.7 10

Korea, Rep. Of 7 0 71.7 7

Panama 7 17 73.4 20

Lebanon 6 37 69.3 40

Saudi Arabia 5 14 70.7 30

United Arab Emirates 5 23 74.4 18

Costa Rica 4 16 76.6 15

Dominica 4 20 73 20

Maldives 4 34 63.3 76

Bangladesh 3 52 56.9 112

Libyan Arab Jamahiriya 3 2 64.3 61

Trinidad and Tobago 3 21 73.1 17

Jordan 2 23 68.9 25

Mauritius 2 0 70.9 23

Tunisia 2 20 68.7 35

South Africa 1 47 64.1 66

Barbados 0 0 76 12

Fiji 0 8 72.1 24

The more fortunate countries !

UN Water Report 3

Assignment:

As a part of the semester activity, one student is selected every week to prepare a short seminar about his/her point of interest in one of the lecture topics. That to be discussed and evaluated during the next lecture.