Bursts of loud applause punctuated Thursday’s midday prayer vigil honoring the nine victims of Charleston’s first modern mass shooting. Heartfelt praise and loud singing characterized the evening vigil at Royal Missionary Baptist Church. And at Second Presbyterian Church, worshippers filled the pews for a somber prayer service before marching with tears and flowers to a memorial at the shooting site.

The slayings at the historic Emanuel AME Church reverberated across the metro area prompting thousands to pay their respects and pray for healing.

The largest of the special services, held at Morris Brown AME Church in the heat of the afternoon, drew church officials, politicians and civic leaders who issued calls for unity in the face of evil and emphasized the role of the church in fostering healing.

“This crowd, this colorful crowd, speaks well for Charleston, South Carolina,” said the Rev. Joe Darby, a presiding elder of the African Methodist Episcopal Church, at the gathering held at Morris Brown AME Church.

And when the standing-room-only crowd joined in singing a solemn version of the hymn, “My Hope is Built,” many began clapping a fast, syncopated, rhythmic accompaniment that energized the sanctuary and injected a large dose of optimism in the occasion.

The suspect in the shooting at the “Mother” Emanuel AME Church on Calhoun Street is Dylann Roof, 21, of Eastover. Roof was arrested in Shelby, N.C., after a traffic stop. The news was conveyed to the vigil gathering at Morris Brown AME Church and prompted another burst of applause.

Those slain were attending a Bible study at the church Wednesday night. The victims were officially identified by Charleston Coroner Rae Wooten at a news conference at 3 p.m. Thursday.

State Sen. Clementa Pinckney, Emanuel AME’s pastor, was among those killed.

A female survivor told family members that the gunman initially sat down in the church for about 45 minutes before opening fire, according to Dot Scott, president of the Charleston NAACP. The attack is being considered a hate crime and is being investigated by FBI, as well as local law enforcement.

At the vigil, which lasted about an hour and a half and could not accommodate many people forced to linger in front of the church in the heat, the Rt. Rev. Dr. John Richard Bryant, senior bishop of the AME Church, spoke of the resiliency of the faithful — “the young man picked the wrong place” — then addressed what he called the elephant in the room: “the growth of senseless violence.”

“We are losing more of our citizens at home than on battlefields abroad,” he said. “There’s violence in our playgrounds, violence in our homes, violence in our schools. Now there’s violence in our churches. And the one common denominator is the gun.”

Bryant then called on lawmakers to take action to limit access to guns, prompting another big burst of applause. Most took to their feet, including U.S. Rep. Jim Clyburn, Mayor Joe Riley and other politicians. Only Sen. Tim Scott and Gov. Nikki Haley remained seated.

Clyburn, citing Martin Luther King Jr.’s famous “Letter from a Birmingham Jail,” referred to “the appalling silence of good people,” admonishing all gathered to “please break your silence. Speak up!”

Outside the church, hundreds sang “We Shall Overcome,” “Amazing Grace” and “This Little Light of Mine.” Black Lives Matter activists holding signs engaged some while others formed prayer circles or stood quietly crying. Some members of the group, also members of the North Charleston Civil Coalition for Reform, addressed the North Charleston City Council public safety committee on Thursday, a move prompted by the April shooting death of Walter Scott, a black man, by a white police officer.

Visibly shaken, Riley took the pulpit to honor the victims.

“Less than 24 hours ago our hearts were broken,” he said softly. “The unspeakable happened in our city.”

He conveyed the sympathies of President Barack Obama and Vice President Joe Biden, and called Emanuel AME Church among the city’s most sacred places.

“And now it’s even more sacred. Sacred because of the lives lost in it while in prayer.” And sacred, too, because of the city’s anguish. “It isn’t when we fall that counts, it’s how we get up,” Riley said. “We will look back on (this tragedy) as a time when love and goodness came together to overcome evil.”

Gov. Haley, too, saluted the nine families enduring loss, saying that the attack was an isolated outrage.

“As all eyes of this country are on our state and our city,” she said, “what happened in that church is not the people of South Carolina.”

However, she said, “If this can happen in church, we’ve got some praying to do. If there’s one thing we can do in South Carolina it’s pray. ... We are a state of faith, we are a state of prayer, we are a state of love.”

Some at the vigil spoke of the Emanuel AME attack as part of a larger problem.

Jamie Majors, a public school teacher and Black Lives Matter activist, said the bigotry likely at the root of the tragedy is pervasive and must be addressed systematically.

“The slave mentality in Charleston is strong,” she said.

Bakari Sellers, former state representative and son of civil rights leader Cleveland Sellers, said he was saddened and confused by this latest eruption of violence against black people. Sellers and Pinckney were colleagues and friends.

“There has been too much death of African-Americans throughout the state, from North Augusta to Roseville to North Charleston to downtown Charleston. It’s all around. I’m just tired. I rest in my dad’s arms. I called him last night and just cried and screamed. I just thought, ‘I don’t know where we are and what we’re doing.’ ”

At Second Presbyterian Church, the Rev. Sidney Davis spoke words of hope and comfort, encouraging the congregation to be brave soldiers for the Lord.

“It didn’t happen to African-Americans, it didn’t happen to the AME Church, it happened to all of us,” he said. “It doesn’t matter if you’re white or black; it doesn’t matter if you’re Asian or Native American; what matters is that you love the Lord.”

Emotions were high at the church where the shooting took place. A huge crowd stood outside and prayed, forming a line to place flowers at a memorial outside the front doors.

“The amount of sadness that is coming out of this is overwhelming,” said Carmella Luke of Charleston. “I think the best way to move forward is to not forget.”

Nearby, at Marion Square, individuals gathered in a large circle, held candles and took turns speaking about the tragedy.

At Royal Missionary Baptist Church, the Rev. Isaac Holt decided to replace the usual Thursday night Bible study with a special memorial service that drew 400 people, including Carol Hutchinson, 48, of North Charleston.

“We’re hurt, but we’re not broken,” she said. “This is going to be a lesson. God is about love, God is about forgiveness. I hope this prompts more open discussion about racism and gun violence that happens on a regular basis.”

Holt, who was joined in a show of solidarity by state Rep. Wendell Gilliard and the Rev. Nelson Rivers III, pastor of nearby Charity Missionary Baptist Church, also spoke of love and the chance to “turn an evil into good.”

“There are few things in society and life that remind us we were all made by the same hand, and one of those things is when your heart is hurting,” Holt said.

And then the congregation joined hands, swayed and sang with a loud voice.

Brenda Rindge contributed to this report.