Jonathan stated this at the second Presidential National Prayer breakfast held at the Banquet Hall of the Presidential Villa in Abuja.
The President said the prayer was organised to offer collective supplication to God for the country.
He said the second edition of the prayers involved a broad spectrum of Nigeria's leadership comprising politicians, clerics, learned people, traditional rulers and captains of industries.
The President said that the event was significant coming at a period of serious security and religious challenges in the nation.
"Daunting as these challenges may appear, I trust in the efficacy of the Bible truth that the prayers of the righteous avail much.
"I am confident that Nigeria will emerge from this trying time a stronger, more united, more stable and more prosperous nation.’’
Jonathan said Nigerians must live above the primordial diversity tendencies which could only compromise the growth of the country.
He said the people should be guided by the ideal of "justice, equity, selflessness and the fear of God’’ in every sphere of their public or private conduct.
The President said that Nigerians must also be imbued in the spirit of selfless sacrifice as exemplified by Jesus Christ.
He said Nigeria could only attain the lofty height which God endowed it, through natural and human resources base, if the citizens were prepared to make sacrifice.
Jonathan noted that championing narrow sectional agenda would not add values to national development.
He stated that his administration owed Nigerians, the sacred duty of enhancing their welfare and well-being.
President of the Christian Association of Nigeria (CAN), Pastor Ayo Oritsejafor in a sermon entitled "the power of an altar" said the gathering was a call to "national altar" to offer prayers for Nigeria to overcome its challenges.
He said Nigeria is a "great nation endowed with talents but lacking in knowledge; a rich nation with citizens suffering from lack and wants".
He likened the present situation of the country to that of the Biblical Israel when there was no rain for three years.
Oritsejafor said Prophet Isaiah offered prayers on an altar to God and there was rain in abundance.
The clergy said he was confident that the time was ripe for the country to overcome its challenges.
Earlier In his welcome address, the Chaplain of the Villa Chapel, Venerable Obioma Onwuzurumba recalled that the inaugural breakfast was held following the constitutional crisis which arose after the death of former President Umaru Yar'Adua.
He said the prayers were held for the purpose of divine guidance and preservation of the country.
Onwuzurumba said that the event had been enlarged by bringing in all stakeholders from the federal and state governments.
He said the objectives of the second edition were to pray for peace in the country and for the nation to overcome the post 2011 general elections crisis.
He said the crisis which raged unabated had taken a new dimension of attacks on innocent citizens and destruction of property.
The clergy said that the essence of the breakfast was also to pray to God for fresh anointing and wisdom for the President and his team to drive the transformation agenda.
Former Head of State, Gen. Yakubu Gowon took the first reading from the Book of Second Kings, Chapter 23 and verses 1 to 23.
Vice President of Kenya, Kalonzo Musyoka, took the second reading from the Book of First Timothy, Chapter 2 verses 1 to 8.
Prayers were offered for peace and divine guidance for the nation and its leaders.
The prayers were led by Primate of Anglican Communion, Nicholas Okoh; Catholic Archbishop of Abuja, Rev. John Onaiyekan and Bishop David Abioye of Living Faith Church.
In an interview with State House correspondents after the event, Akwa Ibom Governor, Godswill Akpabio, commended the initiative of the President to commit the country in the hands of God.
"Something has happened here today, Nigeria has reached out to God.
"All along, we thought we could do all things through our own strength, but today Mr President has shown that we have found out where we erred by ensuring that the whole nation is redirected to God.
"God is the Almighty, it is the Grace of God that has kept this country together; such a fragile unity when we consider the fact that we are diverse in culture, in language, in tribal and ethic congregation.
`For God to have kept us together for over 50 years really means that it is the Grace of God, " he said.
Akpabio called on Moslems to take a cue from the initiative and come together to offer prayers for the nation to overcome its challenges.
In attendance were former Head of Interim National Government, Chief Ernest Shonekan, past ministers and elder statesmen.
Also in attendance were Deputy Speaker of the House of Representatives, Hon. Emeka Ihedioha who led other members of the National Assembly, Judge and Justices of High and Supreme Courts.
Governors Adams Oshiomhole of Edo. Peter Obi of Anambra and Jonah Jang of Plateau were also in attendance.
Also at the event were the Secretary to the Government of the Federation, Sen. Anyim Pius Anyim, ministers, clergymen, members of the diplomatic corps and captains of industry.
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