Muni Metro, San Francisco’s usually busy subway and light rail system, will shut down after the last trains complete their runs Sunday night.

Beginning Monday, buses will replace the city’s light rail service as part of the Municipal Transportation Agency’s effort to cope with the coronavirus outbreak and plunging ridership while maintaining service for people working essential jobs.

Shutting down the seven rail lines will enable custodians to shift their attention to cleaning buses and facilities and let Muni send more operators to run busy neighborhood bus lines, MTA transit director Jeffrey Tumlin said Friday on Twitter after the agency announced the rail shutdown.

Tumlin also reported that ridership on the light rail lines recently has been less than 10% of the usual load, about 174,000 riders on a normal day.

“I'll miss all our trains but this decision helps keep our operators and passengers healthier,” he said in a tweet that included a picture of him riding Muni Metro.

My last train ride for awhile. Rail ridership is down over 90%. I'll miss all our trains but this decision helps keep our operators and passengers healthier pic.twitter.com/0qKyONojrc — Jeffrey Tumlin (@jeffreytumlin) March 26, 2020

Passengers who rely on the J, K, L, M, N, T and shuttle lines to get around San Francisco may find themselves facing longer rides. While the time difference varies depending on line and length of trip, it usually takes buses longer than trains.

“Our advice would be to allow extra time,” said Erica Kato, a Muni spokeswoman, “but this is far from the first time we have ever used a bus shuttle.”

Some shuttles, particularly during the closure of the Twin Peaks Tunnel, caused serious delays and choked the Muni Metro system. But with most people staying at home, ridership is light and so is the traffic that can slow buses.

How long the rail shutdown will last has yet to be determined, she said, but it is likely to last as long as the shelter-in-place health orders are in effect and Muni ridership remains low.

Muni officials said they’ll take advantage of the shutdown to do maintenenance on the Metro system, which includes 151 vehicles, 72 miles of track on seven lines, three tunnels, nine subway stations, 24 surface stations and 87 surface stops.

“It’s a unique opportunity to improve the state of good repair of our system and come out of this shutdown stronger than ever,” the MTA said in a statement.

Some Muni passengers worried that the switch to buses could make it tougher to stay six feet away from other riders as health officials recommend.

“Trains are safer,” said a commenter identified as Ruth California on the MTA website. “Closing down light rail significantly slows down any trip and increases exposure to the virus. Street people abound on the buses above ground and are more likely not to abide safety rules. Train operators are less exposed in their own enclosed/protected space. Buses pose too many chances for risky interaction.”

MTA officials have said they’re monitoring passenger loads on all buses in an attempt to give riders some elbow room — and recommended social distance.

“If a vehicle reaches its recommended passenger threshold it will need to skip stops” the MTA tweeted. “We apologize in advance but this is a needed step to ensure the health and safety of all on board.”

Muni is not the only Bay Area transit operator to reduce service. Caltrain plans to cut its weekday service by more than half starting Monday, reducing its daily schedule from 92 trains to 42 indefinitely. Trains will make all local stops between San Francisco and San Jose and run every 30 minutes to an hour. Limited and Baby Bullet trains will be suspended.

BART moved up its closing time for train service to 9 p.m., three hours earlier last week and delayed the start of its Saturday service. BART’s ridership continues to plunge, reaching 8% of normal on both Friday and Saturday.

On Wednesday, the Santa Clara Valley Transportation Authority, known as VTA, shut down light rail service indefinitely after an operator in training tested positive for the coronavirus. Light rail service in the South Bay remains shut down.

The plummeting ridership on Bay Area transit is also leading to big revenue losses. They should be eased by an expected $1.3 billion in emergency funding that was included in the federal coronavirus stimulus bill.

Michael Cabanatuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com