WASHINGTON (AP) — Five weeks after nine people were slain at a black Charleston church, federal authorities have indicted the suspected shooter on dozens of new charges, including hate crimes, firearms violations and obstructing the practice of religion.

The prosecution, particularly on hate crimes, has been expected since the June 17 shootings at Emanuel African Methodist Church in Charleston. The suspected shooter, 21-year-old Dylann Roof, is white and appeared in photos waving Confederate flags and burning or desecrating U.S. flags. He purportedly wrote online of fomenting racial violence, and federal authorities on Wednesday confirmed his use of a personal manuscript in which he decried integration and used racial slurs to refer to blacks.

Roof is scheduled to be arraigned Monday on the new charges, according to court records. On Thursday, the federal judge assigned to the case provisionally appointed David Bruck to represent Roof on the federal charges. Bruck was the lawyer for Boston Marathon Dzhokhar Tsarnaev, who was sentenced to death, and Susan Smith, the South Carolina mother sentenced to life for drowning her two sons.

Hate crimes cases can be tricky to bring, with the onus on authorities to prove a suspect’s motivations and intentions. But one expert who has followed this case says some of the extenuating circumstances of Roof’s case could potentially make it easier for prosecutors — and more difficult for his defense team.

“All a jury is going to have to do is look at the crime that was committed and the victims that he selected and then read what he wrote in advance, and then look at the photos, as well as things that he might have said to people about why he was committing the crimes,” Cornell Law School professor Jens Ohlin said. “This strikes me as an incredibly easy case for a federal prosecution. It’s not clear to me at all what kind of defense strategy his lawyers could come up with.”

Although what tack Roof’s defense lawyers might take is unclear, Ohlin said their job may be made even more difficult if Roof were to be unapologetic for any of the photos or writings.

“Dylann Roof might object to his lawyers trying to defend him against the hate crimes charges,” Ohlin said. “If the lawyers go in there and say, ‘This wasn’t a hate crime’— he might not let his lawyers say that. His view might be: ‘This was a hate crime, and I’m proud of it.'”

The Justice Department has not decided whether it will seek the death penalty against Roof, nor whether its prosecution will come before a state case that includes murder charges and another potential death penalty prosecution.

Because South Carolina has no state hate-crimes law, federal charges were needed to adequately address a motive that prosecutors believe was unquestionably rooted in racial hate, U.S. Attorney General Loretta Lynch said during a Wednesday news conference.

Roof, Lynch said, had for several months prior to the shootings conceived a goal of “increasing racial tensions throughout the nation and seeking retribution for perceived wrongs he believed African-Americans had committed against white people.”

To carry out those goals, he “decided to seek out and murder African-Americans because of their race,” Lynch said, adding he had purposefully selected the historic church to “ensure the greatest notoriety and attention to his actions.”

He took advantage of his victims’ generosity when they welcomed Roof into their Bible-study group, she said.

“The parishioners had Bibles. Dylann Roof had his .45-caliber Glock pistol and eight magazines loaded with hollow-point bullets.”

Hate crime cases are often challenging for the government because it must prove that a defendant was primarily motivated by a victim’s race or religion as opposed to other factors frequently invoked by defense attorneys, such as drug addiction or mental illness.

Last year, a federal appeals court in Ohio overturned hate crime convictions against Amish men and women accused in beard- and hair-cutting attacks against fellow Amish who were thought to have defied the community leader.

The court held that the jury had received incorrect instructions about how to weigh the role of religion in the attacks and that prosecutors should have had to prove the assaults wouldn’t have happened but for religious motives.

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Kinnard reported from Columbia, South Carolina.

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Meg Kinnard can be reached at http://twitter.com/MegKinnardAP