Why Turkey's coup attempt matters big time for the United States

"U.S. officials are working with the Turks to resume air operations there as soon as possible," Cook added.

He also said the U.S. military was working to adjust its counter-ISIS operations "to minimize any effects on the campaign."

A U.S. defense official told CNN that the Pentagon is looking to conduct operations out of other bases in the region because of the Incirlik shutdown, which the military specifically needs to operate drones to fight ISIS, also known as ISIL.

Even once the airspace is reopened, though, the U.S. military may be reluctant to restart operations until it is certain who is in control of the Turkish armed forces.

Additionally, tensions between the U.S. and Turkey could increase as an extradition battle now looms. President Recep Tayyip Erdogan has accused Fethullah Gulen, who currently lives in Pennsylvania, of being behind the coup and demanded the U.S. hand him over, though the exiled cleric has denied any involvement.

Here is a look at what else this could mean for the U.S.

President Barack Obama convened an emergency meeting in the White House Situation Room Saturday morning to discuss the events in Turkey. According to an official White House statement, the President was briefed on the latest developments on the ground in Turkey and "reiterated the United States' unwavering support for the democratically-elected, civilian government of Turkey." Obama also underscored shared challenges such as counterterrorism "that will require continued Turkish cooperation."

The U.S. came out early in favor of the Turkish government, led by its democratically elected president, Erdogan.

Secretary of State John Kerry issued a statement Friday night saying he spoke with the Turkish foreign minister and that he had "emphasized the United States' absolute support for Turkey's democratically-elected, civilian government and democratic institutions."

Another statement from the administration noted that Obama had spoken to Kerry about Friday's events: "The President and secretary agreed that all parties in Turkey should support the democratically-elected government of Turkey."

But even though the Obama administration doesn't want to see one of the world's few Muslim-majority democracies taken over by the military, it has experienced increasingly frosty relations with Erdogan, whose Islamist party has reversed years of Turkish secularism, maintained power for more than a decade, clamped down on the free press and dissidents, and shown less than full-throated support for the U.S. effort to rout out ISIS and other Islamist extremists.

Now things could get even worse between the two capitals, representing a considerable downgrade from years of strong U.S.-Turkish ties.

During the decades of the Cold War, the two countries enjoyed close relations, with the U.S. successfully collaborating on a range of issues with both democratically and military-led governments headed by many pro-western secularists.

In contrast, the U.S. has struggled with Erdogan's AKP Party and its moderate Islamist policies, including his diplomatic spat with Israel and his outreach to Islamist parties like the Muslim Brotherhood and Hamas.

And Erdogan's more anti-Western tone and authoritarian behavior -- it now ranks behind Russia, Venezuela and Algeria in press freedom -- has concerned the U.S. "It's no secret that there are some trends within Turkey that I have been troubled with," Obama said in April.

Now there are fears that Erdogan could go much further.

In an early warning sign, the Ankara chief public prosecutor's office took nearly 200 top Turkish court officials, including members of the supreme court, into custody, Anatolian News Agency reported Saturday. Though Erdogan has frequently railed against and curtailed the judiciary, there has yet to be any evidence that has indicated that its members were behind the coup.

If Erdogan continues to crackdown aggressively on the opposition and jail dissidents not involved with Friday's events, this could further strain in U.S.-Turkey relations.

Turkey, a NATO member since 1952, has the second-biggest armed forces in NATO and is one of only two Muslim-majority members of the 28-nation defense alliance.

Turkey and the U.S. have had a very close military relationship, with the U.S. operating several military installations there, including the Izmir Air Station and Incirlik Air Base. NATO's Allied Land Command headquarters, led by U.S. Army Lt. Gen. Darryl Williams, is also located in Izmir. And NATO announced last week at its summit in Warsaw, Poland, that it would deploy its AWACS reconnaissance planes to Turkey to help combat ISIS.

The spokesman for U.S. European Command, Capt. Danny Hernandez, told CNN that five U.S. military installations in Turkey, including Incirlik, had been placed under the highest threat warning.

The decision to move to the highest level, Hernandez said, was not only because of the current situation but also based on potential threats to U.S. citizens, service members, families and other personnel.

NATO Secretary General Jens Stoltenberg took to Twitter early Saturday to announce that all NATO personnel were safe and accounted for. He also issued his support for the democratically elected government.

And NATO's top military officer, U.S. Gen. Curtis Scapparotti, said Saturday that "Turkey is a strong NATO Ally and an important partner in the international Coalition against ISIL."

The Turkish Chief of the General Staff, Gen. Hulusi Akar, is "highly regarded" in the U.S., Aaron Stein, a senior fellow at the Atlantic Council think tank in Washington, D.C., told CNN.

During the coup attempt, Erdogan said Akar had been held hostage by the plotters. Akar appeared with the prime minister on Saturday, signaling strong backing of the government.

But the fallout from the failed coup could have a disruptive impact on this military-to-military cooperation.

"This is not supposed to happen in a NATO country," Stein, who specializes in U.S.-Turkey relations, said.

Still, Turkey is no stranger to coups, with the military seizing power in 1960, 1971 and 1980. The military was also instrumental in convincing the government to resign in 1997.

During those previous coups, the Turkish officers, largely pro-Western and secular, sought to maintain close relations with NATO and the U.S.

Some of the officers involved in Friday's putsch said they intended to maintain Turkey's NATO commitments according to an announcement made on state TV in the early hours.

In contrast, the U.S. has had difficulties working with Erdogan's Islamist-oriented AKP, which has opposed some U.S. moves in the Middle East. Washington has often felt that Ankara could do more to crack down on Islamist groups in Turkey, stop the flow of foreign fighters against its borders and prioritize the fight against ISIS over its historic rivalry with the Kurds, a key ally of the U.S. in fighting terrorists in Syria and Iraq.

While military-to-military cooperation between American and Turkey has improved significantly in the last six months, according to Stein, the upheaval in the army and the potential decrease in authority for pro-Western factions in the military could affect the course of this cooperation.

Turkey's already strained military will likely face further constraints, the Atlantic Council's Stein noted.

He pointed out that Turkish forces have been in an intense battle with the Kurdish separatist group, the PKK, in the southeast while also contending with ISIS to the south, a threat encapsulated by ISIS' recent deadly attack on Istanbul's airport. Turkey's domestic security forces are similarly burdened by multiple threats on multiple fronts.

In the wake of the failed coup, Erdogan is likely to purge the military of coup-backers and others he deems to be disloyal. Prime Minister Binali Yıldırım said Saturday that more than 2,800 officers, including some generals and colonels, had already been detained.

Forced to endure purges and internal turmoil, Turkey's military would face even more pressure on its personnel as its leadership comes under suspicion by the ruling party.

Erdogan had previously sacked hundreds of high-ranking military officers for disloyalty during his tenure as Turkish prime minister from 2003-2014. On Friday night, Erdogan vowed to clean up the military.

A destabilized military would be unlikely to be able to provide any additional support to the U.S.-led fight against ISIS despite American efforts to boost Turkish participation.

"ISIS may take advantage of a likely security reshuffle and intensify spectacular attacks in Turkey after a failed coup by military officials on July 15," according to a report on the situation put out by the Institute for the Study of War in Washington.

Turkey is also a major recipient of U.S. arms sales, ranking third among importers of American weapons in 2015. Such sales might be put in danger by a military experiencing widespread upheaval.

In addition to a potential disruption in military cooperation in the war against ISIS, there could be other setbacks from the U.S. perspective.

The U.S. has long pressed Turkey to stem the tide of foreign fighters that have traveled across Europe through Turkey and into Syria, believing more could be done to stamp out the phenomenon.

"The Turks let them in believing they were going to fight Assad," Bulent Aliriza, director of the Turkey project at the Center for Strategic and International Studies, told CNN in June.

Aliriza added that the fact that many of these fighters would go on to join ISIS was "an unintended byproduct" of Turkey's prioritizing its enmity with Syrian President Bashar al-Assad. The U.S. would also like to see Assad leave power but believes the fight against terror groups such as ISIS and al-Nusra that exploit the long-raging Syrian civil war should take priority.

A distracted Turkey -- which has called the criticism over its handling of foreign fighters unwarranted -- will now be even less inclined and able to intensify its focus on the hard-to-solve problem of keeping foreign fighters from transiting through the country.

The coup attempt in a major NATO ally comes as other countries throughout the Middle East are in chaos or on the brink of it, creating safe havens for terror groups, feeding extremism and undercutting the historic U.S. interest in a stable region.

Turkey has been a relative bulwark of stability across Europe and the Middle East, though riots, terror attacks and snap elections have already disrupted the country. Now there's a possibility of armed clashes between various political camps, or at the very least prolonged infighting and disruption.

One product of such turmoil could be even more Syrian refugees flooding Europe -- a phenomenon that those countries already see as destabilizing.

About 3 million Syrians have fled to Turkey to escape the civil war. Turkey recently struck a deal with the European Union in an effort to control the number of refugees going to Europe, with the EU providing Turkey with billions of dollars in aid.

In the coup fallout and ensuing crackdown, these refugees could seek to escape Turkey for Europe further complicating the situation of crucial U.S. allies on that continent.

"The assumption has always been that Turkey is problematic but stable," Stein said.