Despite a number of maneuvers over the past year designed to ease its debt burden and get costs in line, the NYTCo (NYSE: NYT) has still faced enormous difficulties to running its business, including steep ad declines. In Q2, the NYTCo saw its profits plummet 42 percent.

While the company has made a number of staff cuts on the business side, the paper was previously considered a fairly secure job. But that’s not the case anymore, even as executives had said it did not anticipate further staff reductions this year, along it did say it would not replace staffers who leave. To stave off layoffs, the paper lowered wages by 5 percent across the board. Clearly, that helped for most of this year, but in the end, it wasn’t enough. In his memo, Keller wrote: “I won’t pretend that these staff cuts will not add to the burdens of journalists whose responsibilities have grown faster than their compensation. Like you, I yearn for the day when we can do our jobs without looking over our shoulders for economic thunderstorms.”

With ad spending likely to remain weak, it’s safe to say the hemorrhaging of newspaper jobs will likely continue through next year. So far in 2009, PaperCuts’ latest tally of journalism jobs shows that the industry has lost nearly 14,000 posts through layoffs and buyouts. The site says that almost 16,000 journalism jobs were lost in 2008.

Keller’s full memo below:

Colleagues,

I had planned to invite you to the newsroom and break this news in person today, but I’ve been hit by something that seems to be the flu. Though I strongly believe in delivering bad news in person, I don’t want to add insult to injury by spreading infection.

Let me cut to the chase: We have been told to reduce the newsroom by 100 positions between now and the end of the year.

We hope to accomplish this by offering voluntary buyouts. On Thursday, the Company will be sending buyout offers to everyone in the newsroom. Getting a buyout package does NOT mean we want you to leave. It is simply easier to send the envelopes to everyone. If you think a buyout may be right for you, you have up to 45 days to decide whether you will accept it or not.

As before, if we do not reach 100 positions through buyouts, we will be forced to go to layoffs. I hope that won’t happen, but it might.

Our colleagues in editorial and op-ed, and on the business side, also face another round of budget cuts.

In recent years, we’ve managed to avoid the disabling cutbacks that have hit other newsrooms. The Company has chosen to protect the journalism by cutting production and other business-side costs, and the newsroom itself has managed its resources frugally. These latest cuts will still leave us with the largest, strongest and most ambitious editorial staff of any newsroom in the country, if not the world.

I won’t pretend that these staff cuts will not add to the burdens of journalists whose responsibilities have grown faster than their compensation. But we’ve been looking hard at ways to minimize the impact — in part, by re-engineering some of our copy flow. I won’t promise this will be easy or painless, but I believe we can weather these cuts without seriously compromising our commitment to coverage of the region, the country and the world. We will remain the single best news organization on earth.

I doubt that anyone is shocked by the fact of this, but it is happening sooner than anyone anticipated. When we took our 5 percent pay cuts, it was in the hope that this would fend off the need for more staff cuts this year. But I accept that if it’s going to happen, it should be done quickly. We will get through this and move on.

In my absence, Bill Schmidt and John and Jill have volunteered to take your questions this afternoon. Feel free to bring additional questions to me as soon as I’m back, or check with Bill Schmidt or John or Jill privately, or save them for the next Throw Stuff at Bill session, which is in a couple of weeks.

We often — and rightly — voice our gratitude that we work for a company and a family that prize quality journalism above all. I hope you know that the company and the family, and I, feel an equal debt of gratitude to all of you whose sacrifice and loyalty have kept us strong.

Like you, I yearn for the day when we can do our jobs without looking over our shoulders for economic thunderstorms.

Bill