The Rev. Michael Nation, rector of Vicksburg’s largest Episcopal congregation, The Church of the Holy Trinity, will leave his position March 1 to become a chaplain with the Seamen’s Church Institute of New York and New Jersey and based in Baton Rouge.

Nation resigned Monday in a meeting with Holy Trinity’s vestry and the Rt. Rev. Duncan Gray III, Bishop of Mississippi, and then made the announcement to church members.

“It comes down to a calling,” Nation said of his decision. “That’s what we feel as ministers of the Gospel — the way we discern where we are to minister.”

He called SCI a “phenomenal organization,” and though leaving Holy Trinity is difficult, he is looking forward to his new duties.

“The people of Holy Trinity have loved and supported me and my family,” he said. “It’s been a wonderful 9 1/2 years. The position with SCI is really an exciting position. It came to me — I didn’t necessarily seek it out, but the door was opened and I walked through.”

SCI was founded in 1834 and is the largest seamen’s agency in North America, providing chaplaincy and pastoral care, legal services and other support services to mariners at ports in the New York-New Jersey area, the Bay Area in California and along the inland waterways. Nation will serve in the Lower Mississippi River territory which runs from Houston to New Orleans and north to Vicksburg.

His presence and leadership at the church and Conservatory will be missed, said Dorothy Brasfield, Holy Trinity’s organist and choir master and director of the Conservatory of the Fine Arts, which she and Nation worked together to establish.

“He has been so wonderful for the church and the community, for the outreach,” Brasfield said. “We are just devastated.”

“Michael has been a good and faithful priest through challenging times in our church,” the bishop said in a phone interview Tuesday. Along with his role as pastor at Holy Trinity, “He has provided leadership, on the diocesan level, through his work as the ecumenical officer of the diocese.”

In the role, Nation has been an important part of increasing communion between the state’s Episcopal and Methodist churches, Gray said.

“Michael’s gifts are music and liturgy, and the Conservatory, which has been a gift to the entire community,” Gray added. “That was Michael living out his gifts in a wonderful way.”

Nation was called as Holy Trinity’s rector in June 2001. A native of Mobile, Ala., he has degrees from the University of Mobile and Duke University.

Nation also has been active in the community as a member of the Vicksburg Theatre Guild, where he has performed in such productions as “The Fantasticks,” the Vicksburg Rotary Club and the board of the Four Seasons of the Arts. He has hosted the “Live from the Klondyke” radio show, and also served two terms as president of the Bowmar Elementary School PTA.

Nation’s resignation means all three Episcopal churches in the city, including St. Mary’s, on First North Street, and Christ Church, on Main Street, are without full-time, permanent rectors, though Gray said a decision on a new priest is expected soon at Christ Church. The Rev. Billie Abraham has been rector at Saint Alban’s Episcopal Church in Bovina since 2008.

Gray will work with Holy Trinity wardens and vestry to find Nation’s replacement.

The bishop will preside over a “leaving liturgy” March 1 at 6 p.m., at which time Nation will symbolically release the authority that had been his at Holy Trinity and pray God’s blessing on the congregation, Gray said.

Nation’s wife, Cheryl Ann Nation, is a special education teacher at Warrenton Elementary School. The couple has three children, Anna Grace, 14, Caroline, 12, and Michael Jr., 6.

He and his family will remain in Vicksburg through the end of the school year and then move to the Baton Rouge area, he said.

His new position will allow him to remain a priest in the Diocese of Mississippi, and Nation plans to continue his involvement in diocesan life and ministry, including the annual “Christmas on the River” mission project.