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The 49ers are revamping their run defense.

First, they fired defensive line coach Jeff Zgonina on Jan. 13. Then, this past Wednesday, they chose not to pick up the option on the remaining two seasons of nose tackle Earl Mitchell’s four-year contract.

“I’m very thankful for my time with the Niners,” Mitchell wrote on Twitter. “I put my heart and soul into the game so as always, I’m thankful for every opportunity. Good luck to all of my brothers especially in the d-line room.”

Mitchell, 31, signed a four-year $16 million deal with the 49ers in 2017, and was scheduled to earn $7.3 million the next two seasons. Instead, he will be an unrestricted free agent when the new league year begins on March 13.

“Earl has been a fantastic asset to this entire organization for all the things that he’s done,” defensive coordinator Robert Saleh said Wednesday at the Senior Bowl in Mobile, Alabama, courtesy of 49ers.com. “It’s an opportunity for other guys to try and step up. It will not be easy to try and replace him, that’s for sure.”

Mitchell and Zgonina both joined the 49ers in 2017. They knew each other because they worked together on the Houston Texans in 2013 when Mitchell was their nose tackle and Zgonina was a rookie defensive line coach. The 49ers acquired them to mentor the younger defensive linemen and transform a run defense that gave up an NFL-worst 4.8 yards per carry in 2016.

Mitchell and Zgonina did their jobs in 2017. The 49ers’ run defense improved drastically that season, giving up only 3.8 yards per carry — seventh best in the league.

But in 2018, Mitchell declined, as did the run defense. Mitchell started the first 12 games and the 49ers’ defense gave up 4.2 yards per carry during that time. In his final start on Dec. 2, the 49ers’ defense allowed 168 rushing yards and a whopping 5.8 yards per carry to the Seahawks in Seattle. After that game, the 49ers benched Mitchell for the rest of the season.

“Earl has had a very good year,” head coach Kyle Shanahan explained on Dec. 10, one week after Mitchell lost his starting job. “I think Earl has been better this year than last year, and I think Earl played good last year. But it came a time when I had to sit Earl down and tell him it was nothing against him but we needed to see what (backup nose tackle) D.J. (Jones) can do. Earl, there’s a lot of football left in him, but in order to get D.J. some playing time, we told Earl that he was probably going to have to sit down.”

Mitchell played only one defensive snap the next two games, then the 49ers made him inactive for Weeks 16 and 17.

Jones, a second-year nose tackle, replaced Mitchell at the position and started the final four games of the season.

And with Jones in the starting lineup, the 49ers’ run defense improved. It gave up just 3.8 yards per carry despite facing three offenses that ranked in the top six in the NFL in yards per rush — the Denver Broncos, the Seahawks (this time in Santa Clara) and the LA Rams.

“I thought (Jones) did a good job,” Saleh said on Wednesday. “Obviously, he still has to get better, and there’s going to be a lot of competition for him. I thought Arik Armstead stepped in at the nose (in the) nickel (defense) and showed some things that created versatility for that entire room. So his competition isn’t just at nose — it’s can he be one of our best nine or 10 defensive linemen?”

Jones, 24, played college football at Ole Miss and was the 49ers’ sixth-round draft pick in 2017. He is scheduled to earn $645,000 next season if he makes the final roster, which he probably will.

Notes

The 49ers promoted Martin Mayhew to vice president of player personnel, GM John Lynch announced Thursday in Mobile. Mayhew will work side by side with Adam Peters, who also is a vice president of player personnel.

Mayhew, 53, joined the 49ers in 2017 and served as a senior personnel executive the past two seasons. They created the title for him.

Mayhew played cornerback in the NFL from 1988 to 1996. And from 2001 to 2007, he worked under Detroit Lions general manager Matt Millen. Then, Mayhew replaced Millen as the Lions’ GM and served in that role from 2008 to 2015. Mayhew has more years of front-office experience (18) than Lynch (2) and Peters (5) combined.

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