Under head coach Jim Harbaugh’s era the San Francisco 49ers have been a dominating defense. It is safe to say that the defense carried the team to three NFC Championship games and one Super Bowl appearance. However, the outlook for the 2014 season may be a bit different.

The 49ers’ defense starts from the middle. It is the heart and soul of the team. Linebackers Patrick Willis and NaVorro Bowman are arguably the best linebacker tandem in the NFL. They both are in their prime and are coming off of stellar seasons, respectively.

What is the dilemma then?

Well, Bowman is coming off of a gruesome knee injury, tearing his ACL and MCL, that he suffered in the NFC Championship game against the Seattle Seahawks. He will start the season on the PUP (physically unable to perform) list, making him eligible to return week 7 in a Sunday Night Football showdown verse the Denver Broncos. With Bowman out of the lineup, linebacker Michael Wilhoite and rookie linebacker Chris Borland are next on the depth chart to play alongside Willis.

The 49ers will dearly miss Bowman and his tenacious play on the field.

Another key player the 49ers will be without is linebacker Aldon Smith. Smith has been suspended for the first nine games of the season for violating the NFL's personal conduct and substance abuse policies. Smith’s suspension was inevitable considering his off-field troubles. Aldon and his camp had the following statement:

"I apologize to my teammates, coaches, the entire 49ers organization and 49ers fans for not being able to contribute on the field for the next several weeks," Smith said.  "Over the last year, I have learned a lot and I'm working hard to grow from my experiences. I want to thank my family and friends, my teammates, my union and the 49ers for supporting me during this process. I will be at work daily to participate in all permitted work activities, and to support my teammates, just as they have supported me."

Losing the relentless pass rushing ability of Smith for nine games is a cause for concern. Sure, the 49ers organization are poise and calm. But deep down they know that this suspension will develop a glaring hole in the defense.

Linebacker Corey Lemonier filled in brilliantly last year when Smith was out of the lineup. He is expected to do the same for the first nine games as well. But what most forget to mention is that All-Pro Bowman was in the lineup when Lemonier was effective.

That will not be the case this time around.

The 49ers arguably have had the best front seven in the NFL during defensive coordinators Vic Fangio’s reign. The front seven masked many of the weaknesses the secondary had as well. By putting consistent pressure on opposing quarterbacks, the 49ers’ secondary was “good enough” to make ends meet.

With safety Donte Whitner signing with the Cleveland Browns and cornerbacks Carlos Rogers and Tarell Brown signing with the Oakland Raiders, more questions have surfaced for the secondary. The 49ers will lean heavily on corners Tramaine Brock and Chris Culliver, who are yet to be proven commodities thus far in their young careers. The team also has a pair of safeties, in Eric Reid and Antoine Bethea, who have to figure out how to play together.

Brock signed an extension during the off-season. He has potential to be a special player. The 49ers are high on Brock’s ball hawking abilities and cover skills. He has a good combination of size and speed.

But he is still pretty raw and needs to hone his craft.

Culliver is coming off of an ACL injury. This is really only his second year in the NFL, considering he missed all of last season. He looks as though he has fully recovered from reconstructive knee surgery – but only time will tell.

This could be a good thing, when looking at it as the “glass is half full” – especially since there is an area of unknown involved.  

Another key loss for this defense is DT Glenn Dorsey who suffered a torn muscle in his bicep. They placed him on the Injured Reserve/Designated for Return List. He will not be eligible to practice with the team until at least 6 weeks into the season, and cannot be activated until minimum 8 weeks have passed. 

Luckily the 49ers have depth at the DT position. However, Dorsey was blending in quite well with the first team defense. The team hopes to have his services back for a playoff push.

Last, another change on the defensive front can come sooner rather than later. Defensive lineman Ray McDonald was arrested for domestic violence during his birthday celebrations. When police arrived at the scene, McDonald’s fiancé whom is pregnant, showed evidence of bruises on her arm. McDonald could be suspended six games under the new ruling that commissioner Roger Goodell released this past week.

McDonald’s situation could be the final straw that breaks the camel’s back. But I expect Harbaugh to have the team mentally and physically ready to go, starting week one verse the Dallas Cowboys. It will not be an easy task though.

It is obvious the 49ers and their defense have an uphill battle to climb. It doesn’t help that they play some high powered offenses this season. It may be time that quarterback Colin Kaepernick and the offense carries the team. Look for offensive coordinator Greg Roman to open up the playbook for his franchise quarterback.

Regardless of the circumstances, this team has great mental fortitude. They may not have won a Super Bowl under the Harbaugh era but have been consistently close. This may be the year the 49ers get over the hump.

One thing for sure, the offense will need to lead the way considering the defense has a lot of moving parts at the moment and it all starts with the quarterback who earned a new contract this off-season..