The EU is hoping that Iran abide by the agreement as long Tehran receives the economic benefits promised in the deal.
Mr Trump's decision to walk away from the landmark nuclear deal with Iran - to which the UK, France, Germany, Russia and China are co-signatories - is being linked by the European Union with the United States administration's refusal to exempt the bloc from steel and aluminium tariffs.
Tusk called for more unity in the divided European Union - which is set to lose Britain as a member next year - to face the growing challenges.
In a striking rhetorical assault on the leader of Europe's biggest ally, EU Council President Donald Tusk said, given Trump's recent decisions, "someone could even think 'with friends like that, who needs enemies?'" Thanks to him we got rid of all illusions. We realize that if you need a helping hand, you will find one at the end of your arm'.
European leaders are troubled by Trump's "America first" rhetoric and inconsistent statements on North Atlantic Treaty Organisation and the EU.
But with the USA saying it had pulled out of the deal because of broader worries about Tehran's actions, the leaders said they would also "address concerns about Iran's role in the region, Iran's ballistic missile programme and what happens after 2025".
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"Europe must do everything in its power to protect - in spite of today's mood - the transatlantic bond. But at the same time, we must be prepared for those scenarios, where we will have to act on our own", said Tusk, a former Polish prime minister.
The EU leaders were also due to discuss the deaths of dozens of Palestinians in Gaza after Trump moved the United States embassy to Jerusalem, in another move that the Europeans had strongly opposed, but there were no details on that discussion.
Speaking to lawmakers in Paris on Wednesday, France's junior minister for Europe, Jean-Baptiste Lemoyne, said the U.S. behaviour meant it was time that Europe stood up for itself.
New US sanctions would be a significant blow to German companies that actively went to the Iranian market after 2015. "It's a moment of truth for Europe", he said.
Merkel however said earlier that Europe had no choice but to stick with the ties that have bound it to Washington since World War II.
White House National Security Adviser John Bolton indicated on Sunday that the US would be willing to impose sanctions on any European companies that continue to work or do business with Iran. But Trump has also lambasted his European peers for not spending enough on defence, raising doubts among many in Europe about his commitment to North Atlantic Treaty Organisation and Europe's broader security. The deal is good for European and global security, which is why we must maintain it.
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