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The main threats to biodiversity were identified as habitat loss, habitat degradation, overexploitation, unsustainable use, pollution, the spread of invasive alien species and climate change. These pressures are continuing to increase and are themselves driven by a range of socio-economic drivers, chiefly the growing human population and the associated increase in the consumption of resources. Furthermore, globalization and its negative impacts on resource extraction, along with limited human and financial resources, have also contributed to the loss of biodiversity. Threats are accentuated by increases in the level of desertification due to climate change, as well as human population growth.
Major threats to marine ecosystems are unregulated tourism, exploitation of marine resources, overfishing and fishing in illegal areas (e.g. breeding grounds) and coastal pollution. At present, 20% of Egyptians live in coastal areas, which are also visited annually by 11 million tourists. In addition, more than 40% of industrial activity occurs in the coastal zone.
Pollution causes deterioration of critical habitats and species loss. A concrete example is the Delta wetlands. Excessive use and misapplication of pesticides also causes loss of rare species including those that act as pollinators and natural biological control agents.
Overgrazing and over-fishing contribute to biological degradation. Wildlife utilization is, for the most part, unregulated in Egypt and excessive hunting is endangering a number of wild animals (e.g. gazelles) as well as several species of resident and migratory birds.
The lack of a sustainable and effective system to address natural heritage management issues is hampering the nation’s ability to conserve and manage its unique and critical resources. Poorly regulated marine tourism, coupled with inadequate infrastructure to protect natural resources and insufficient regulations for desert tourism are causing the destruction and degradation of natural habitats, landscapes, cultural heritage sites and other resources. In addition, there is a lack of coordination and cooperation between all relevant stakeholders in regards to data collection, storage and analysis of biodiversity data and the absence of comprehensive legal protection for natural heritage resources outside protected areas.

Habitat Loss and Degradation

Destruction of habitat is a major cause of biodiversity loss in Egypt. Direct habitat loss is a major threat to terrestrial, marine and coastal ecosystems, and freshwater ecosystems are particularly severely affected by fragmentation. Land reclamation, urbanization and industrial activities destroy and alter critical natural habitats along with their plant and animal life. There are a range of factors, economic and social, that lead to land-use changes and development pressures, raising serious concern for the integrity of ecosystems in Egypt.

Threats to Wetlands

Egypt’s wetlands are subject to a variety of human induced threats, which are leading to the degradation of this valuable national resource. There are multiple threats to wetlands and river ecosystems in Egypt. One of the major threats to wetlands, in the northern coastal lakes in particular, in Egypt is the drainage of water bodies for their conversion into agricultural and settlement developments, ultimately destroying habitat and reducing their areas. Other threats to wetlands include water withdrawal for irrigation, coastal erosion, invasive species, water pollution and overfishing.
The severity of pollution varies from lake to lake, but they all share the same cause of pollution – the discharge of untreated or partially treated industrial and household waste water (mainly sewage) and the dumping of agricultural drainage loaded with fertilizer, pesticide and herbicide residues. The severity of pollution in these lakes can be as follows: Lake Maryout> Lake Manzala> Lake Edku> Lake Burullus. Excess agricultural runoff and domestic wastewater discharge into these water bodies causes an increase in the levels of nitrogen and phosphorous, a process known as eutrophication, causing harm to other forms of life inhabiting these waters. Such malpractices can be traced back to a rapidly growing population and the increased human activity that comes with it.
Applied fishing techniques also have adverse impacts on fish production. They have affected the aquatic environment in many ways. Fishermen use inappropriate techniques to increase their catch. This has caused the killing of the small traits and hence, decreased production. The use of huge nets causes the death of large numbers of non-target species through habitat destruction and being accidentally engulfed by the net (The Environmental Profile, NEAP, 2000).
River systems have also been degraded drastically during the past 50 years. They are being significantly affected by water withdrawals, leaving some small rivers nearly or completely dry, ultimately reducing biodiversity. However, the water quality of the Nile River and Lake Nasser are within international standards (SOE 2007). Many invasive species are also recorded in the Nile River; most important are Water Hyacinth (Eichhornia crassipes) and freshwater crayfish. The Water Hyacinth covers some 487 km2 of the river and the networks of irrigation and drainage canals throughout the country and 151 km2 of lakes, causing an annual water loss of 3.5 billion cubic meters to evaporation. It also prevents sunlight penetration, causing changes in the ecosystem and species diversity. The uncontrolled spread of freshwater crayfish led to the deterioration of local fisheries, crops and irrigation networks.

Threats to Coastal and Marine Ecosystems

Direct habitat loss is a major threat to coastal and marine ecosystems and is driven by a number of factors: i) the rapid unplanned development of areas such as the north coast and the coast of the Suez Canal; ii) the unsustainable exploitation (ex. bottom trawlers) of marine resources; iii) deterioration of breeding and nursery sites in many areas, especially in the Mediterranean Sea(less in the Red Sea due to the declaration of some protected areas along coasts and islands); iii) commercial ship trafficking in the Suez Canal and oil leakage from some oil fields in the Red Sea; iv) sanitation discharge in the Mediterranean Sea and coastal lakes; v) social pressures on the government to meet the needs of a growing population (unemployment, introduction of new patterns of development, competition for exploiting available resources, lack of public awareness with the importance of inherited culture associated with unorganized development plans and threat of investments due to beach erosion ).
Coastal development, intensive tourism and land reclamation for agriculture put pressure on key wildlife habitats in the Mediterranean. Contributing factors to the decline of wildlife habitat in the Mediterranean include historical overexploitation, degradation of beach nesting habitat due to sand extraction, entanglement in fishing gear, loss of sea grass meadows, pollution and increased ship traffic. In the eastern Mediterranean, seabirds are threatened by habitat loss due to drainage, water diversion, changes in annual water regime, eutrophication, reed cutting, landfills, chemical pollution and hunting (UNEP/MAP 2012). For example, the vast tracts of what might have been suitable habitat for the Egyptian Tortoise (Testudo kleinmanni) in the North Coast are now uninhabitable for the species. Perhaps the most serious threat to T. kleinmanni is the complete (and possibly irreversible) destruction of habitat caused by agricultural activities. Local and regional problems related to pollution, specifically effluents from domestic and industrial sources, oil transportation, refineries and agricultural runoff are also beginning to have serious impacts on wildlife.
Major threats to Red Sea coral reefs include land filling, dredging for coastal expansion, destructive fishing methods, shipping and maritime activities, sewage and other pollution discharges, damage from recreational SCUBA diving, lack of public awareness and the insufficient implementation of legal instruments that promote reef conservation (PERSGA, 2000). In addition, increasing atmospheric carbon dioxide is expected to alter the alkalinity of the world’s oceans over the next century making it increasingly difficult for corals and other carbonate secreting organisms to grow. Present predictions are that calcification rates may slow by as much as two-thirds over the next 50 years, with potential for catastrophic effects on reef growth and marine biodiversity in general (Kleypas et al., 1999).
Red Sea coral reefs were assessed as at risk primarily due to coastal development, overfishing and the potential threat of oil spills in the heavily trafficked Arabian Gulf and southern end of the Red Sea. Almost two-thirds of Gulf reefs are at risk, largely as the area channels over 30% of the world’s oil tankers each year. In other areas, industrial pollution and coastal development are areas are more predominant. Corals in many parts of the Gulf of Aqaba have been degraded due to tourism developments. Reefs in the northern Red Sea and the Arabian Gulf are especially vulnerable to degradation due to limited water circulation and temperature extremes.

Threats to Desert Habitats

Desert habitats cover over 90% of Egypt’s territory. From a terrestrial point of view, beyond the Nile Valley Egypt is one of the most hyper-arid countries in the world, with large areas of completely barren desert where no rain has fallen for decades. There is slightly more rainfall in the north closer to the Mediterranean coast, in the mountains of Sinai and in the extreme southeast where fog deposition in Gebel Elba produces the only Egyptian example of an officially (WWF) endangered habitat – a Red Sea Fog Woodland.
The main threats to desert biodiversity are habitat loss and land degradation. The cause of land degradation in the northern coast of Egypt is due to overgrazing, where grasslands have been converted to accommodate seasonal agriculture. Other causes of habitat loss and degradation are air and water erosion, poor land management, limited and ineffective popular participation by locals in conserving the land and the establishment of several developmental projects.
Other threats include increased dryness, which hinders the ability of plants to reproduce; the overharvesting of plants, especially medicinal plants; the hunting of wild animals outside protected areas; logging activities in the Eastern and Western Desert for fire; increased urban development and safari tourism in unpopulated areas; landmines left after World War II in El-Alamein (nearly 17.5 million mines occupying more than quarter million feddans suitable for agriculture); and climate change, which is believed to have led to more droughts, increased temperatures and decreased rainfall.
The impacts of land use changes on the distribution of selected important plant species in an arid landscape in the northwest coastal desert of Egypt was assessed using a random forest modeling approach (Halmy et al., 2013). Out of 244 species found in the area, only the distributions of seven important species were modeled. Important species were defined as those serving crucial functions and providing important services in any ecosystem. This could include, for example, sand stabilizing and nitrogen-fixing plants.
The species selected for the study were Anabasis articulata (Ana_art), Asphodelus aestivus (Asp_aes), Deverra tortuosa (Dev_tor), Gymnocarpos decanderus (Gym_dec), Haloxylon salicornicum (Hal_sal), Noaea mucronata (Noa_muc) and Thymelaea hirsute (Thy_hir). Figure 5 1 presents habitat loss, which is expressed as a percentage of the potential habitat area for each species under the baseline climate and no land use changes.
The results indicate that the changes in land use in the area over the last 23 years have resulted in habitat loss for all the modeled species. Projected future changes in land use revealed that all the modeled species would continue to suffer habitat loss (Halmy et al., 2013).

Threats to Mountain Habitats

Mountains and wades are characteristic of the landscape of much of the Eastern Desert and Sinai. Habitats found in the mountains of South Sinai and the Eastern Desert, particularly Gebel Elba, support unique faunal and floral biodiversity. The loss of biodiversity in mountainous areas is attributed to human activities, such as hunting, logging, trafficking in species, urban development, invasive alien species, climate change and natural disasters (mainly flooding).

Threats to Agricultural Biodiversity

The main threats to agricultural biodiversity in Egypt are: i) urbanization expansion on agricultural land despite the strict legislation governing the destruction of agricultural lands; ii) the introduction of high yielding varieties and their wide use that has led to the neglect and disappearance of traditional varieties and local breeds, the erosion of plant crops and the reduction in livestock genetic diversity; iii) the abandonment of traditional agricultural practices, causing the loss of cultural landscapes and associated biodiversity; iv) the introduction of invasive species, such as the Red Palm Weevil (Rhynchophorus ferrugineus), invasive weeds and various agricultural pests, which cause significant economic losses; v) the excessive use of fertilizers and pesticides that has led to the disappearance of important agricultural wildlife (pollinators, kites, owls, foxes, mongoose and wild cats) and groundwater contamination; vi) the absence of suitable successive agricultural cycles; viii) the use of surface flooding irrigation methods, which led to land degradation, reduction of soil fertility and increased soil salinity; and ix) the increased migration from rural to urban areas with an increasing burden on resources.