Bolgen Vargas will step down as superintendent of the Rochester school district at the end of December, well before his contract expires in June 2016. (Related column: "Impossible job claims another superintendent.")

He will be replaced by Daniel Lowengard, retired superintendent of the Syracuse City School District. Lowengard will serve as interim superintendent of Rochester schools until a permanent superintendent is hired, hopefully by the end of the school year, says Rochester school board president Van White. Lowengard will not be eligible for the permanent job, White says.

White says that all seven board members are in agreement concerning Vargas's departure and the terms. The board will buy out the remaining six months of Vargas's contract and Vargas has agreed to be available to support Lowengard in the transition. Vargas's annual salary is $195,000.

(A statement from Rochester Mayor Lovely Warren on Vargas's departure follows this story.)

Vargas says that went to the board in September to talk about renewing his contract. But when board members indicated that his contract would likely not be extended, Vargas says that he decided to leave.

"It's a mutual decision," Vargas says. "It's no secret to anyone here that we've had our disagreements and it's in the best interest of the district."

Problems between Vargas and the school board have been brewing for at least a couple of years, going back to when Vargas hired former deputy mayor Patricia Malgieri -- a well-known critic of the district -- as his chief of staff early in his tenure. And his relationship with White has also been tense over the years, their differences at times spilling out into public view.

But both men say that one of the most serious problems has been an ongoing disagreement over the roles and responsibilities of the board and that of the superintendent. Earlier this year, Vargas took the unusual step of threatening legal action against the board over a dispute concerning who and what types of positions should be allowed in the superintendent's employee group, the cabinet-level management tier.

Vargas continues to argue that the board changed the terms of his contract and overstepped its authority.

"Reasonable people can make the case either way," Vargas says. "It is clear that we don't shy away publicly or privately around that difference."

White says that the disagreements led to significant differences about day to day operations of the district.

The board's actions are a result of the school board finally adhering to state education law, White says, after years of lax supervision of the SEG. It's part of a "paradigm shift," he says, in how the board will supervise superintendents going forward.

White cites the board's direct involvement in engaging the University of Rochester as the educational partner to turn around East High School as an example of this shift. And he says that the board is currently pursuing a partner for an elementary school.

Vargas never followed through with litigation against the board, but the threat clearly damaged his relationship with board members. Though he says he has no regrets about his decision, he also says that he would have preferred to stay with the district longer and that he has no immediate plans.

Vargas was hired in 2011 as the interim superintendent following former superintendent Jean-Claude Brizard's departure. Vargas was made permanent superintendent almost a year later in a 6-1 vote, with White opposed.

At the time, many school district officials and community leaders said that Vargas was a good choice because of his roots in Rochester. Vargas was a guidance counselor in the Greece school district, and he has been both a Rochester school board member and its president.

Vargas seemed to immediately benefit from a comfortable working relationship with Adam Urbanski, president of the Rochester Teachers Association, mending the bitter feud between teachers and central office that developed under Brizard. Some teachers said they were impressed with Vargas's counseling background because it is similar to classroom teaching experience.

And board members initially seemed relieved, too, because Vargas said he had no interest in seeing governance of the district shift to mayoral control. Vargas struck up a solid working relationship with then mayor Tom Richards, a refreshing change from the tense history between the district and City Hall.

Vargas immediately laid out an aggressive strategy to reverse decades of academic decline at the school district by focusing on fundamentals such as improving the district's attendance and having students read proficiently by the third grade.

He argued for offering the same academic and extracurricular amenities that suburban schools offer: sports, fully functioning libraries, arts, music, and drama instruction. And he emphasized early childhood education and universal prekindergarten for all 4-year-olds in the city.

Vargas lengthened the amount of instruction time that students in the district's lowest performing schools receive, borrowing a strategy for academic improvement frequently touted by higher-performing charter schools.

"The work we've done in Rochester speaks for itself," Vargas says.

But some teachers appear to have changed their view of Vargas and his administration. In a recent interview, Urbanski said that while Vargas has worked collaboratively with teachers on many fronts, that lately they have disagreed on several issues.

"I give him a lot of credit for increasing a lot of resources for schools, music, art, and physical education," he said. "But I have to tell you that lately teachers have become very frustrated with what they consider to be central office's neglect of schools."

Urbanski cited school safety and discipline concerns, recent changes in how special education is managed, and confusion over additional working hours.

Few people expected Vargas's contract to be renewed, he said.

Statement from Mayor Lovely A. Warren on the Change in School District Leadership:

The future of our city depends on the educational success of our children.

Although as Mayor I do not have a say in this matter, I do believe it would have been more appropriate to announce that the superintendent was leaving at the end of his term and allow him to serve until a permanent replacement is hired, since it appears he will be staying on as an employee until the end of the school year.

A midyear shift could be detrimental to the very children that the school district needs to foster and protect.

I know the number one reason why middle class families leave the city of Rochester is because of the challenges in our educational system. Too many of our schools are in need of academic improvement, and we must have a path forward that is both clearly defined and in the best interest of our children.

As our community comes together to address the poverty crisis in our city, we cannot afford to let personality conflicts harm the educational needs of our children or their families.