SANTA CLARA — Patrick Willis hollered at pal NaVorro Bowman a few days back to keep him in the mix, even if the star linebacker was a bystander as his teammates endured their Day 1 conditioning tests.

Willis is so accustomed to running through drills right alongside Bowman that 49ers training camp seems a bit strange without his position mate and close friend.

Bowman is expected to miss at least half the season as he recovers from a devastating left knee injury suffered in the NFC championship game loss to the rival Seahawks.

“We were out there doing a conditioning test and I looked over and he was watching us do our conditioning test and I wanted to just yell at him, ‘Bo, what’s up, man?’” Willis said. “I don’t want to put more on him than what he already has on his shoulders already. I know that he wants to be out there more than anything.”

There are a handful of candidates in the mix to fill that huge void left by No. 53.

“I don’t see it as daunting at all,” linebacker Michael Wilhoite said Friday. “I see it as a great opportunity for somebody else to step up and make a name for themselves. … You have to embrace the fact we’re not replacing Joe Schmo. We’re replacing the best. So that means you have to be the best.”

Bowman tore the anterior cruciate and medial collateral ligaments and underwent surgery, and the 49ers must try to make up for the vacancy on one of the NFL’s most vaunted defenses.

“I’m doing great,” Bowman said with a smile as he entered Levi’s Stadium. It helps to have Willis and everybody else supporting him every step.

“I want him to take his time. Most of all I want to make sure when he comes back that he’s ready to go and he doesn’t have any setbacks. He’s a great athlete and he still has a lot of football ahead,” Willis said .

Bowman is doing his own intense conditioning regimen.

Coach Jim Harbaugh is pleased with Bowman’s progress. He has been running and will soon be testing the knee with cutting.

“That’ll be next in that process. Talked to him yesterday about it. Positive,” said Harbaugh, who wouldn’t guess when Bowman might be back.

The Niners also could be without linebacker Aldon Smith, who is expected to meet soon with NFL Commissioner Roger Goodell about a possible suspension from the league for his legal troubles.

Wilhoite started two games last season and will again have a chance to fill a big void in the middle until Bowman is healthy. For now, Wilhoite is a contender to start, yet there could be mixing and matching in packages with Corey Lemonier, Nick Moody and even rookies Chris Borland and Shayne Skov, who has played in this system at Stanford.

“It’s an advantage for him in that he knows he can go out there and play in an NFL game,” defensive coordinator Vic Fangio said of Wilhoite. “At times it will be challenging. Any time you lose two great players somebody’s got to go in there and do the job. We don’t expect those guys going in there to be as good as those two guys are. They’re at the top of their profession. But we’ll find a way.”