For Albany-watchers, Monday’s news of a Republican takeover of the State Senate made an unexpected splash. For now, the Senate is in flux. Malcolm Smith says the legislative body was adjourned when the Republicans+2 staged their coup, and he plans to challenge this takeover in court if necessary.

While the partisan fight is sure to grab headlines all summer, we here at Second Ave. Sagas are far more concerned with the Albany turmoil’s effect on downstate transit. As the Senate and Assembly have already passed the MTA rescue plan, the MTA’s short-term future is secure. The long-term picture remains hazy.

Monday’s surprising turn of events gives me cause to link to a recent piece in The Indypedent explaining why the MTA is broke and broken. The short of it is that due to poor funding choices made by Republicans during the Pataki Administration, the MTA has been saddled with crippling debt payments. As these payments have ballooned, the MTA’s once-lucrative real estate tax revenues have dried up in the market crash. With neither party willing to take the congestion pricing plunge, the MTA is left to beg at the feet of our state representatives.

(For the long version, check out Larry Littlefield’s very comprehensive post on the topic. He breaks it down by revenue and state and federal contributions. The blame lies squarely on George Pataki’s shoulders.)

So where does that leave the MTA today with Republicans primed to take control of the Senate and its future finances looking bleak? For one, split-party government — Sheldon Silver still rules the Assembly — could result in one of two paths: Either bodies will not agree on the future of the MTA or both bodies will take the path of least resistance. Neither option seems all that appealing.

With the Democrats in power in the Senate, the MTA could hold on to the hope that more tax plans could be on the table. Democrats today are far more open to the idea of new taxes than Republicans. With the GOP in control of the Senate though, a payroll tax plan similar to the one approved last month would never pass muster. Already state Republicans are trying to overturn the payroll tax in various counties surrounding New York, and it seems as though the MTA earned that victory just in the nick of time.

Further down the road are concerns that the transit agency will have again return to Albany for more money in another two years. The agency also needs to secure funding to at least issue bonds backing its capital plan. This move would force the authority to take on more debt, but unless Albany is willing to issue a blank check with a substantial ceiling, the alternative is no capital campaign. That would be disastrous.

In this regard, a lot will turn on the outcome of the 2010 gubernatorial campaign as well. If Republicans recapture the governor’s seat and lay claim to the Senate, the MTA will be forced to justify its budgetary problems well beyond what the Democrats demanded this year. In the end, that outcome may actually benefit transit in New York City, but for short-term needs, the MTA may find a G.O.P.-dominated Senate far from sympathetic.

In the end, this state of flux creates a lot of uncertainty surrounding the MTA. The counties outside of New York City feel as though they are being held hostage to the transit authority by this payroll tax, and the G.O.P. leadership is well aware that this rescue plan is not universally accepted. How this drama plays out is anyone’s guess, but I have a sinking suspicion congestion pricing may not be on the horizon anymore.

Both The Times and Politicker NY are reporting that a revolt in the Senate has left the Republicans in charge of the state’s legislative body. Pedro Espada, Jr., and the legally embattled Hiram Monserrate voted with the State Senate’s 30 Republicans to approve a change in leadership. Espada is the temporary Senate president, and Dean Skelos, the former minority leader, will take over the majority position from Malcolm Smith.

For now, Epsada and Monserrate are not calling themselves Republicans. The two say they will form their own caucus of “reform Democrats” and will probably side with state Republicans in Senate votes. While the two shifted parties ostensibly because of Espada has termed a “quagmire” and “chaos” in the Senate since the Democrats took over, the immediate ramifications are unclear. For now, it appears as though Gov. David Paterson’s gay marriage proposal is DOA.

What, though, of the MTA bailout? In a few weeks, the Democrat-approved payroll tax will go into effect, and it has so far proven to be wildly unpopular with areas outside of the five boroughs. The Metro-North corridors and LIRR counties are not too happy about another tax for the NYC-focused MTA.

As the bailout talks went on in the Senate, Skelos repeatedly expressed his displeasure at being left out, and while Paterson tried to reach across the aisle once or twice, the plan that passed did so with the support of the 32 Democrats. Right now, though, I can’t imagine the Republicans doing anything to upset the current rescue plan. Doing so would send the MTA into a stunning bit of turmoil ten days after the drop-dead date for the original Doomsday budget.

The future though is murky for the beleaguered transit agency. The G.O.P leadership will put more pressure on the MTA to undergo heavy internal belt-tightening, and the financial future of the next five-year capital plan remains cloudy. I’ll try to round up more views on the MTA’s future in light of the shifting political winds, but with a leadership structure in flux and the onset of political turmoil in Albany, I am not optimistic.

Update 5:30 p.m.: In a statement released this afternoon, Dean Skelos pointed to the MTA rescue plan as one of the problematic actions of the Democratic majority. That is not a good sign for the MTA and its backers.