The San Diego Sheriff's Department has assigned deputies to religious centers throughout the weekend, according to the agency.
At least one person was killed and several others wounded in a shooting at Congregation Chabad in Poway, north of San Diego, Poway Mayor Steve Vaus said.
While security has been heightened, the Sheriff's Department said that is not indicative of a greater threat.
"We encourage our communities to continue with scheduled events and other activities as normal," the department said in a news release. "The suspect in the Poway incident today has been captured and we believe he acted alone."
The suspect in custody has been identified as John Earnest, a 19-year-old student at California State University San Marcos. Authorities are investigating whether he is connected to arson at a mosque in nearby Escondido last month, San Diego County Sheriff Bill Gore said.
An open letter may give insight
Gore did not comment on a motive, but authorities are aware of an open letter posted online purportedly by the suspect, Gore said in a news conference.
Detectives are "collecting digital evidence" and are in the process of reviewing the online content "to determine its validity and authenticity," the sheriff said.
CNN has read through an open letter posted to the anonymous message board 8chan before the shooting.
In the posting, someone identifying as Earnest references killing Jewish people without making actual reference to Poway, San Diego or the synagogue involved in the shooting. The letter writer talks about planning the attack and references other attacks on houses of worship, including the attack on the Tree of Life Synagogue in Pittsburgh and the Christchurch mosque shootings in New Zealand.
The writer also talks about his disdain for Jews and claims responsibility for a mosque fire in Escondido a week and a half after the attacks in Christchurch.
The open letter is structured in a similar fashion to the manifesto linked to Christchurch attack suspect Brenton Tarrant, replete with a question-and-answer section in which the writer refers to questions he comes up with about his character, political affiliation, and motivation for carrying out the alleged shooting.
What happened in the synagogue
Gore told reporters that the gunman was armed with an "AR-type assault weapon." A witness told CNN affiliate KGTV there were six or seven shots followed by screams and then another volley of shots. The witness said a wounded rabbi tried to calm the gunman and members of the congregation.
Authorities said an off-duty Border Patrol agent, who Gore thinks is a security guard, fired at the shooter as he was fleeing the scene. He didn't hit the suspect, but Gore said it appears he hit the suspect's car.
It is unclear why the suspect fled but it is possible his gun might have malfunctioned, the sheriff added.
The suspect fled the scene and called 911 to say he was involved and give his location, San Diego Police Chief David Nisleit said. A San Diego K-9 officer arrived and the shooter surrendered without incident, he said.
Gore said the suspect was being interviewed by detectives and the FBI.
The victims
The Palomar Medical Center received four patients from the shooting, according to a trauma surgeon.
One patient died at the hospital, according to Dr. Michael Katz. An employee of the synagogue identified the woman as 60-year-old Lori Kaye.
"The other three victims are doing well with their injuries," Katz told reporters.
A 34-year-old man and a girl had shrapnel injuries. The girl, whose age was not given, was wounded in one leg and in the face. She was transferred to a children's hospital and will be monitored overnight.
A 57-year-old rabbi who was shot suffered what looked like defensive wounds to both of his index fingers. He will likely lose his right index finger, the doctor said. He has been identified as Rabbi Yisroel Goldstein, according to Palomar Health Public Relations Manager Derryl Acosta.
Congregation member Minoo Anvari, who said her husband witnessed the shooting, said the rabbi called for unity and prayed for peace even after getting shot.
"Rabbi said, 'We are united,'" said Anvari, a refugee from Iran.
The shooting happened at 11:23 a.m. (2:23 p.m. ET). The synagogue's Facebook page said a Passover celebration was scheduled for 11 a.m.
Passover, one of the holiest Jewish celebrations of the year, ended Saturday.
'Yet another wake-up call'
President Donald Trump, speaking outside the White House Saturday, told reporters, "At this moment it looks like a hate crime, but my deepest sympathies to all of those affected and we'll get to the bottom of it."
"Moving forward this must serve as yet another wake-up call that antisemitism is a growing and deadly menace," said the Holocaust Memorial Museum in a statement. "All Americans must unequivocally condemn it and confront it in wherever it appears."
And many groups have come out already to condemn the attack.
"All of these attacks on these sacred spaces represent a violation of our values that we as Americans hold dear: Values of decency, tolerance and respect. Whether or not you go to a church or a synagogue or a mosque, it's standing together with your fellow Americans that matters most," said Jonathan Greenblatt, CEO of the Anti-Defamation League.
"Faith leaders around the world are already doing a great job working together to overcome the shared challenge of extremism," Abbas Barzegar, director of research and advocacy for the Council on American-Islamic Relations, told CNN. "They simply need to tell their story more and better, and most importantly spread that message down to the local community level and challenge hate in their own ranks."
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