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Biological Integrity


Aquatic Alien Invasive Species: Living with the Uncertainty of Biological Pollution in the Great Lakes

Creating a Regional Approach: What We Can Do Better

Implement a Great Lakes Biologically Protective Standard

Require Certification of Technology to Achieve the Standard

Require Enhanced Ballast Management Practices for No Ballast on Board (NOBOBs)

Promote Ongoing Regional Cooperation

Develop Measures to Ensure Compliance

Enlist the Assistance of the International Joint Commission


Microbial Contamination

Where are the Pathogens Coming From?

Detecting Pathogens and Assessing Risks

Gaps in Pathogen Detection

The Emergence of New Pathogens

The Walkerton Tragedy: A Lesson for the Great Lakes?

As Population Grows, Water Infrastructure Must Be Updated





Pathogenic Organisms

Where are the Pathogens Coming From?

Figure 2 (used by permission of Barry Rosen) illustrates potential sources of gastrointestinal pathogens excreted in human and animal feces that find their way into the water bodies like the Great Lakes and drinking water by numerous sources, including: pet wastes from urban parks; animal and human waste from land-based sludge applications; manure storage piles; and leaking septic tanks. When multiple, adjacent communities use waterways, as is the situation for most of the U.S. and Canadian Great Lakes region, sewage overflows can put downstream communities at risk from high concentrations of microbial pollution. 18

Figure 2. Potential Pathways for Waterborne Pathogens
( click on figure to enlarge )

Figure 2

Several factors that drive microbial contamination and can impact water quality and human health are identified in Table 1.

Table 1. Factors associated with the risk of new pathogens and impacts on water quality and health in the Great Lakes basin
( click on table to enlarge )

Table 1
(Adapted from IJC 2003, Priorities Report)19

In many older cities, collection systems were designed to carry sewage and storm water runoff. During heavy rainstorms, the water surging through these systems threatens to overwhelm treatment. Combined sewer overflow systems allow this mixed runoff and sewage to bypass treatment plants, protecting the plants, but directing both runoff and raw, untreated sewage into lakes and streams. 20 The U.S. EPA estimates that trillions of gallons of untreated human sewage are discharged from combined sewer overflows after major rain events annually.21 In 2001, municipalities discharged 196.6 billion litres (52 billion gallons) of sewage and partially treated wastewater into Michigan waters alone. 22

Pathogens enter the Great Lakes ecosystem from surface runoff and erosion from farm manure stockpiles, sludge applications, overflows or spills from holding pens or ponds, and storage lagoons, all of which can leach into soil and groundwater. Farmers apply treated sewage sludge from drinking water and wastewater treatments plants to their crop lands to add nutrients to soil, reducing the need for more costly chemical fertilizers. This treated human waste product contains microbes and other pollutants that contaminate ground and surface water under environmental conditions. Today’s intensive or large livestock farms, also known as Concentrated Animal Feeding Operations (CAFOs), are a significant potential source of microbial pathogens to surface and drinking waters. Farmers involved in CAFOs apply large volumes of treated sewage sludge, otherwise called municipal biosolids, as well as animal wastes to their properties as a means of waste disposal. This is a dramatic change from previous management approaches that applied less animal wastes to crop cultivation. Under certain conditions, such applications promote transport and growth of these organisms (Figure 3).

Figure 3. Factors Affecting the Viability Along Transport Pathways ( click on figure to enlarge )

Figure 3

Small livestock operations spread manure from their animals to fertilize their farms’ crops. Larger feeding operations that concentrate thousands of cows, pigs, chickens or other animals in a more limited area generally have less land area relative to the amount of wastes generated. Livestock producers in Ontario who are or will become regulated under the province’s Nutrient Management Act, 2002 have strict requirements to apply nutrients on an adequate land base. Current approaches dealing with large volumes of animal wastes may not be sufficient because numerous reports have linked discharges and contaminated runoff from large-scale CAFOs to impairments in United States water bodies and, in Canada, to emerging diseases.24 Similar conditions and concerns have been reported in Canada.25 To better understand the source, extent and type of microbial contamination, as well as impacts from contamination, information is needed on the numbers and size of each type of farm including CAFOs.

In February 2003, the U.S. EPA released new water quality guidelines for CAFOs (National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines and Standards for Concentrated Animal Feeding Operations (CAFO): Final Rule).26 The final rule requires that these facilities develop and enact a comprehensive, site-specific, nutrient management plan to protect the environment and public health. The rule sets effluent limitation guidelines and standards for nutrients, but does not establish guidelines for discharge of microbial contaminants.

Similarly, in June 2002, Ontario enacted the Nutrient Management Act (Bill 81).27 Regulations under this act would require that facilities that generate nutrients (including sewage treatment plants and pulp and paper plants) or that apply nutrients (including commercial fertilizers to agricultural lands) must develop nutrient management strategies. In June 2003 Ontario revised the regulations, applying them to new and expanding large livestock farms. The regulations will become effective for existing large livestock farms in 2005 but do not include controls on microbial contamination from animal wastes.

The Ontario Environmental Farm Plan, a farmer-led program created by the Ontario Farm Environmental Coalition, has become the model for a national initiative to be implemented over the next few years. Over 26,000 farms have participated in the program, designed to reduce environmental risk on Ontario farms with federal and provincial financial support. Such innovations should be encouraged.

The U.S. Government Accounting Office reported in 2003 on the U.S. EPA’s regulatory program for animal feeding operations to determine potential challenges that states and U.S. EPA may face when they begin to implement program revisions.28 The GAO determined that because the number of animal feeding operations subject to regulations will increase dramatically, states will need to increase their efforts to identify, permit, and inspect facilities and take appropriate enforcement actions against those in noncompliance. The GAO concluded that the U.S. EPA will need to increase its oversight of state programs to ensure that these new requirements are met, and that neither the states nor the U.S. EPA have determined how to deal with these challenges.


Lake Huron West Shore Beaches Closed

A microbiologist for the Huron County Health Unit in 2003 analyzed 10 years of beach water data and found a 40 kilometre stretch south of Walkerton that routinely had high bacterial pollution. As a result, the beach water-sampling program was improved, resources were realigned, and the posting process was changed. Small streams, which are numerous in the area, have E. coli levels that exceed provincial water quality guidelines. A lab analysis undertaken for local property owners indicates that the E. coli comes from animal, rather than human, sewage. The contaminants are concentrated in the near shore area, which is also the critical habitat area for many aquatic organisms. The problem is believed to stem from the number of factory farms in the area (Ottawa Citizen, Tom Spears, November 15, 2003).23 However, an Ontario project is currently underway to define whether shared pathogen sources from livestock, septic systems and wildlife are affecting water quality in the area.