Rain of the Bacteriophage

Digital drawing. Within a translucent dome, there stand four towers. Three are clustered at center and one stands apart at left. Pipes or conduits branch off into the ground from the base of each tower, just visible below the uneven ground. At bottom right in the distance are structures under the dome that glow under hazy light from a comet that streaks by, its head at left, and its tail grazing the dome.

“…and Tower Three, Level Nine, Shift One, report your status, please,” the pleasantly professional voice on the other end of the communications channel requested.

Even though she’d already performed and submitted a thorough and systematic check, Vera turned her head slightly to the right, glancing at all the green indicator lights on the bioreactor beyond the glass.  She turned back to her console and said.  “Tower Three, Level Nine, Shift One end. Vera Pine signing out of duty. All is good.”

“Not for long,” a falsely sinister voice said, in a half-whisper from behind her.

Vera smiled.  She swiveled around in her chair and faced the man who’d spoken, the monitor on duty for Shift Two.  She’d already briefed him on any carryover tasks.  She rose and sighed.

He too rose and handed her a white paper bag containing the gift he’d brought her for her birthday, a chocolate chip muffin.  She’d have to enjoy it alone.

“Three more days,” he said, as she stepped aside, and he took her place at the console that monitored the bioreactor and the assays that were running in the laboratory down the hall. 

Though she wanted to kiss her husband deeply on his lips, Vera only said, “Three more days.”

And when he turned to watch her leave, she offered a soft smile and a slow blink that both she and he knew meant, “Love you.”  He offered a little wave that meant the same.

It wasn’t enough for either of them.  But they were on the job after all. 

Vera lingered only long enough to hear his voice as he reported in.

“This is Tower Three, Level Nine, Shift Two begin.  Ashish Pine reporting for duty.  All is good.”


They were supposed to be on the same shift, or at least on shifts that overlapped for more than fifteen minutes.  Or at the very least, they were supposed to have one day off a week in common, so they could spend some amount of time together in only their second year of marriage.  In three days, they would have that common day off for the first time in a month. 

When Vera and Ash first met, they shared a shift along with three other researcher-technicians, and they were all assigned to run performance assays on the unique bacterium that was discovered on a very valuable asteroid.  Until a few years ago, two of the four towers that the company built on the asteroid were entirely dedicated to research.  But rather quickly, level after level became dedicated to manufacturing and refining.  And to growing and nurturing the bacterium. 

So someone somewhere had decided it wasn’t necessary to have more than one person on a shift anymore—some bureaucrat who probably only scanned the executive summaries from the reports on scientific data, labor statistics, and manufacturing output from Asteroid Prospero (so-named unimaginatively by someone who was in the position to become prosperous by the asteroid’s projected manufacturing output.)  And all the friends, lovers, family, and even enemies who’d once shared shifts in the research laboratories, the refinery levels, and the administrative offices were split up. 


Vera nibbled on her muffin, and stared through the window of their ground-floor condominium.  She stared up at Tower 3, whose smooth sides gave no indication of where any of the levels were.  But she knew about where Level 9 was.

Some of the people in the colony had lived there since before the company took over management of the asteroid from the governmental agency that had spent two decades studying it.  It was during those two decades that they discovered the ore, the rare ore that was vital in the construction of engines capable of high-speed interstellar travel.

Even more fascinating was the discovery of a unique bacterial species that could “chew” through the asteroid’s challenging crust all the way to the interior.  It was thought at first that the bacterium, Astrobacillus prosperotrogon, was just a bonus discovery.  There were some who even wanted to collect and grow samples in the laboratory, but eradicate all the bacteria on the asteroid, so it wouldn’t consume all the ore.

Vera loved the part of the history where a team of bacteriologists saved Prosperotrogon.  They did it by discovering and providing proof, incontrovertible proof, that the ore was not a natural product of the asteroid.  It was a natural by-product of bacterial digestion.

That ore, that valuable ore, was bacterial poop.


Not much changed on the asteroid in the two decades it was studied, so it was determined that it was reasonable to put a colony there.  The timing did happen to coincide with a growing need for the refined ore produced by the asteroid’s bacteria.  A small colony of workers—refinery workers, researchers, administrators, and a small group comprising the government—was established.

Once the ore that was easily reachable on the surface was mined, the company sought to go deeper.  But it was a delicate proposition.  The bacteria created microscopic mines where the ore seemed impossible to reach.  Part of the next phase of research was figuring out how to extract that ore without harming the bacteria or damaging the asteroid.  These micro-mines were not exactly microscopic.  Over time, the bacteria eroded the spaces until many were large enough to fit macroscopic things, sometimes only the size of a human hair, but some were as a wide as a child’s pinky finger.  Efforts were inconsistent.  The company moved on to what might be an easier way to create more of the rare ore.

Vera, Ash, and all the other bacteriologists that were hired a few years prior were assigned the task of finding a variety of favorable conditions to grow Prosperotrogon, or Prost as some called it, conditions that also happened to match up with conditions on other asteroids, and on moons, and planets.  If the bacterium could be put to work converting raw materials into the rare ore, the company would indeed prosper, beyond its most desperate dreams.

But no one had succeeded in growing the finicky bacterium in any conditions except those found on Prospero.

Vera and her colleagues had only been at it for less than two years before the company started pulling back.  But the company had been waiting much longer than two years for exciting news to come out of Prospero.


Halfway through her shift the next day, while Vera was still picturing the suggestive shrug of Ash’s brows after she winked and blew him a kiss, her wristband starting blinking yellow. 

She had just begun visual observations of the current batch of plated bacteria.  Yellow meant she had to stop what she was doing and prepare for an all-colony announcement.  She turned off her scope and went to the laboratory computer.

Vera had only seen her band blink yellow twice in her time on Prospero.  Both times, the company’s ambassador announced to the colonists that a surprise tower inspection was imminent.

Both inspections had gone fairly neutral.  Vera thought that was fair for the first inspection.  But she and her colleagues had worked hard, purposefully, and thoughtfully to make the needed improvements and beyond.  The second inspection should have gone much better.

Some thought it might have if their manufacturing output had been better that quarter.  It had dipped.  It seemed that half the bacteria on the asteroid had gone into hibernation, a spore form that hadn’t been observed before. Vera had been excited to observe it, until it was pointed out that the bacteria were behaving in the exact opposite way that the company wanted them to.  Luckily, the hibernation didn’t last long. 

So Vera braced herself for an inspection announcement as she brought up the all-colony announcement feed.  She was surprised to see the governor’s face instead of the ambassador’s.

“Hello everyone,” the governor said.  “I’ll make this short so you can get back to your day.”  The words were meant to put everyone at ease.  It may be the governor speaking, but whatever she had to say wouldn’t be that big of a disruption.  Then again, it was meant to give everyone time to brace themselves for whatever she was about to say.  If the governor was making an official announcement, instead of just walking through the main street and yelling news out to everyone, then whatever she was about to say was definitely going to disrupt their days.

“We’ve detected a comet,” she said, “heading our way.”


The company sent a ship, to evacuate the asteroid.  But there was a chance it would not arrive in time.

Collision is what everyone feared.  But as the comet came closer, the calculations of its trajectory became clearer and more accurate.  The comet would not collide with them.  But it would come close, very close.

“Closer than we’ve been in a month,” Ash joked.

“At least we get a few days,” Vera said, staring out of their window, up at the clear dome that held in their atmosphere and shielded the colony, “to contemplate our imminent demise.”

She was only half-joking.

Just because the comet wouldn’t crash into them didn’t mean it couldn’t do serious damage. 

Production in all four towers was shut down for the first time since they went into operation.  It took days.  Everyone would then shelter in those towers, which were more solidly constructed than the residential and recreational structures. 

Manufacturing was shut down, but the bioreactors and the ongoing assays were allowed to continue.  So unlike most of the colonists, Vera and Ash had something to do to occupy their minds as the comet passed, showering them in a rain of ice and stardust.

It didn’t take long.  In under a standard hour, the comet and the greater part of its tail had already passed.  But the governor declared that everyone should remained sheltered for another day, while they monitored the atmosphere within the colony dome with automated detectors, and performed a thorough check of the dome itself for any structural damage. 


The standard shift declaration of “all is good,” became a sincerely comforting phrase to hear in the next few days.  The dome had held up well, suffering no greater damage than some surface scratches.  The company ship that had been dispatched to evacuate the colonists arrived, and would remain in orbit for at least several more days.  They even had the materials needed to repair some of the deeper scratches, just in case they compromised the integrity of the dome.

All did seem well. 

But one day, near the beginning of Ash’s shift, there was an accident in Tower One.

All other towers were notified immediately and instructed to stand by for evacuation.  But after an hour of waiting around on the lunch level, they received instruction to resume work while a more thorough investigation was launched.

But Ash and some of the other researchers were sent home early, after working only half their shifts.  The next day, Vera and Ash were both called in together.

“Do you think it has anything to do with the accident?” Vera asked, only to fill the tense silence on their walk over to Tower 3.

Ash took her hand and squeezed.  “Yes.”

When they arrived in the laboratory, they were told nothing, but only given a series of unknown samples to run through a gamut of tests.  They were not the usual tests that they’d recently been running on Prosperotrogon, searching for some genetic marker that would give them a clue about how the bacterium processed the otherwise unyielding rock of the asteroid.  These were diagnostic tests. 

Vera and Ash both understood that they were being told nothing so that they wouldn’t make assumptions.  But the very tests they were being asked to run were telling.  They couldn’t help but to speculate.  But they set their guesses aside and waited for data.

When they presented their results, they were told they had come to the same conclusion that the initial investigators from Tower One had come to.  And that the teams from the other towers had and would come to before the end of that shift.

The comet hadn’t just left behind ice, dust, and a few scratches on their dome.

It had left behind something that no one expected, and no one would have thought to look for if it hadn’t been for the accident.

A virus.


The governor initiated an immediate quarantine of everyone on the colony, and informed the company ship in orbit to do the same with the few among their crew who’d come down to the colony and returned to the ship.

Medical personnel on both the colony and the ship prepared themselves, their supplies, their equipment, and their clinics for an influx of the sick.  In the meantime, the researchers continued to study the virus.  None of them were virologists.  So even though they said they didn’t expect much, if any, illness among the colonists or the ship’s crew, the governor and the ship’s captain went ahead with the quarantine.

The researchers across Towers Two, Three, and Four had performed imaging and genetic sequencing of the virus.  And they had done tests in the laboratories to continue investigating the accident in Tower One.

Vera and Ash were working together again.  There wasn’t much of a hierarchy among the researchers.  And since Vera was considered the most engaging and easy to understand when giving presentations, she was the one who stood before the governor and the colony council only a day later.

“Our tests have confirmed that this virus more than likely is not a direct danger to us,” Vera said.  “In summary, we’ve repeated those tests, and we’re getting the same results.  This virus doesn’t target macroscopic organisms like humans, plants, or animals.  This virus is a bacteriophage.  A group of viruses that specifically infect bacteria.”  She paused as the people in the room reacted, exchanging glances, shifting in chairs, already anticipating what she was about to say next.  “This virus is infecting Prosperotrogon.”

The governor leaned forward in her chair.  “Can the bacteria survive the infection?”

Vera shook her head.  “No.”

She explained that after the virus infected a bacteria cell, it made more copies of itself using the bacterium’s resources, and those copies burst out of the cell, killing the bacterium. 

“I’m sorry to say the news gets worse,” Vera said.  “The reason the conduit at the base of Tower One collapsed is that the bacteria there died.  Without their presence continuously laying down the ore and a slew of other secretions, the foundation rock in that area turned brittle in a matter of hours.  Tim is the minerology expert here, so he’ll go into more detail about that in his part of the briefing.”  She gestured to the tall spectacled geologist sitting at the conference table to her right.  “The damage affected all the primary pipelines leading into and out of Tower One.  In short that means all the bacteria in Tower One’s bioreactors, incubators, everywhere, was exposed and infected.”

“Then it’s a good thing we have the other three towers,” the governor said.  “Can we seal them, at least the labs?  Make sure we maintain large colonies of uninfected Prost?”

Vera wanted to release a sigh.  She met the gaze of everyone at the table who didn’t already know what she knew.  “I’m afraid it’s too late,” she said.  “We’ve been testing the bacteria in the three remaining towers.  We don’t know how, but the virus breached our seals.  Every sample we’ve tested is already infected.  It’s only a matter of time before most of the bacteria on the asteroid is dead.”

“Has this happened before?” one of the council members asked.  “Has the comet passed this asteroid before?  If the bacteria survived then, it will survive now, right?  You said most would die, but not all.”

This time, Vera did sigh.  She brought up a diagram that someone had drafted based on the observations made from the comet’s passing. 

“From what we can tell based on our joint preliminary observations, the answer is ‘yes.’  This comet has passed Prospero before.  And yes, the bacteria have obviously survived.  Their defense mechanism is one we’re familiar with.  Restriction enzymes.  These enzymes basically target specific and strategic areas of the virus’s genetic sequence, chewing it up so badly that the virus can no longer replicate.  Typically, a virus in turn would evolve its gene sequence so that in the next go around, it would be able to resist these enzymes.  So the bacteria would be overwhelmed again, until they evolved a new version of the enzyme to adapt to the new viral sequence.  And on and on.  So under natural circumstances, a large enough population of the bacteria would have survived the viral onslaught to eventually bounce back and thrive again.”

She looked away from the diagram and made eye contact with the governor as she pulled up the next diagram, a map.  “The bacteria are currently vulnerable, however, because our mining activities have fragmented their populations.” 

“Are you saying Prosperotrogon might go extinct, and it’s our fault?” the governor asked.

Vera shook her head again.  “I don’t know.  Some of our projections do suggest that.  The immediate danger is to the structural integrity of the towers and some of our other larger structures.  We can shore those up for a while.  And we can evacuate the colony of non-essential personnel.”

“Is it the recommendation of the research team that we abandon the colony?” the governor asked.

Vera felt her heart sink into her stomach.  Prost was dying by the hour.  Every single cell.

She shored herself up and straightened her shoulders.  “Yes,” she said.  “That is the current recommendation.  But we also have a request.”

The governor furrowed her brows.

Vera now glanced among the researchers gathered around her, stopping last at Ash, who didn’t smile or wink, but only inclined his head.  And she understood that to mean, “Go for it.”

She turned to the council.  “We have an idea.”


“‘Let’s fight fire with fire, she said,” Ash teased. 

Vera, Ash, and most of the researchers who’d been in the meeting with the governor were all gathered on the lunch level of Tower Three.

Vera felt a flush on her face.  “I shouldn’t have said that.  I oversold it.” 

“No way,” one of their fellow bacteriologists said.  “It was inspiring.  I’m inspired.  I mean, we’ll probably fail, but we’ll feel like heroes all the way to the end.”

They were the volunteers of the primary research group.  They would stay behind for as long as it was safe to stay.  A few dozen people in all, bacteriologists, geologists, refinery technicians, data analysts, systems repair technicians, structural engineers…every single person’s particular experience or expertise would be needed.

There was a secondary team on the ship, receiving and analyzing data, and responsible for catching any errors or gaps that the primary team didn’t catch.

Even with the added supplies from the colony, the ship would not be able to stay long.  With almost all the colonists aboard, they had to be careful with resources.  Estimates of total bacterial die-off ranged between twenty-four and thirty-six standard hours.  They had plenty of data, but not enough time to properly analyze it all and narrow the range down.  They just hoped they at least had the twenty-four.

Their plan, to “fight fire with fire,” meant they would fight the bacteriophage virus by synthesizing another virus capable of infecting Prosperotrogon.

The difference was that their virus was not a bacteriophage.  It would not infect and replicate.  It would infect and deliver a payload of designer restriction enzymes that targeted the current viral variant.  As a bonus, they also included a few copies of the plasmid DNA that coded for the restriction enzymes, so the bacteria could replicate their own.  Their virus would then go inert, and eventually be spit out.

Thanks to the colony’s standing mission to research every aspect of Prosperotrogon, the laboratory was equipped with redundant pieces of equipment, and the computing power to process and pre-analyze the raw data coming from that equipment.  And thanks to restored real-time collaboration among the researchers from various and disparate fields, the team was able to interpret, brainstorm, design, iterate, implement, and refine faster and more efficiently.  The result was that in twelve hours, the viral team had working batches of their synthetic virus, T3-11133022-04, which everyone just called “Ariel.”

During those same twelve hours, those with expertise in engineering and architecture had their own problem to solve.

Even with the shoring, the foundation under Tower One began to give.  There was no one left in Towers One, Two, and Four.  But Tower One, unlike the others, was close to the dome.  There had been careful plans drawn to make sure all the towers were built in the center of the dome, so that if something happened, like an unexpected quake, and the towers fell, they wouldn’t tip over and smash into the dome.  But some kind of major miscommunication happened that didn’t get caught until after the first tower was built.  Simulations showed a good chance of Tower One hitting the dome.  So to preserve the dome and everything else under it, they planned to perform a controlled destruction of Tower One.  With the colony evacuated, and all other personnel protected by another tower, the debris from that destruction shouldn’t be a danger to anyone. 

By the time Ariel was ready to be deployed, the demolitions team had already successfully destroyed Tower One.  And Vera noted the heavy-hearted sighs from some of the people who once worked there.

Ash contacted the third team, the ones who were responsible for finding some way to quickly and efficiently disseminate Ariel before it was too late.

They weren’t yet ready. 


“Maybe we should throw Ariel onto some more plates and really be sure it’ll work,” Vera said.  Her stomach was growling and somersaulting at the same time.  She took a sip of cold water.  It felt like the only safe thing to consume at the moment.

Ash came over to where she was sitting and lay his hands on her shoulders.  His thumbs massaged the muscles at the back of her neck.  She would have enjoyed it far more if she weren’t drained and nervous.

“We should all go down to the lunch level and lie down,” Ash said.  “At least until they tell us they’re ready.”

They had set up cots on the lunch level, and games that remained un-played.  Snacks that remained un-eaten. 

“It had better be soon,” someone mumbled from a corner. 

Vera dragged herself into a standing position.  “Don’t worry.  I bet as soon as we lay ourselves down, they’ll contact us.”

She was just about right.

They had ten minutes of rest.

Then Ash’s wristband started flashing green.

The storm team was ready.


To disseminate the virus effectively, the few researchers on the asteroid who were studying Prospero’s mostly neutral weather, the ones who had first spotted the comet, suggested doing the same thing the comet did.  They would have to create their own storm, one that would spread the Ariel virus without destroying it, or more likely, without destroying the delicate payload of enzymes within.  They had tracked the comet (which everyone was now calling “Alonso”) and studied the data that the colony’s sensors collected as the comet passed.  They believed they could replicate that storm to a rough degree, over most areas of the asteroid, using the company ship.  They would also use the three remaining towers, or rather the conduits running deep into the micro-mines, to send the bacteria there some help.

They had run simulation models.  And the ship had prepared as well as it could.  Most of the Ariel virus was delivered to the ship.  The remainder was packed in pill-size canisters that were sent down the tower conduits.

Vera’s stomach was clenched as the last remaining colonists boarded elevator shuttles to the ship.  She didn’t even tell Ash that her greatest fear at that moment was that one of the many automations they had set would malfunction, requiring one heroic person to stay behind.  And she felt guilty, because if that happened, she would not volunteer, and she would not let Ash volunteer.

Even when they were safely aboard the ship, even when she was stationed at her console on the main deck, even when she could keep her eye on Ash, who was stationed seven feet away from her, Vera held her breath, and she waited.

Her part was done.  Her team’s part was done.  It was up to the ship’s pilot now.  And to the crew assigned to trigger the canisters in the micro-mines. 

The ship began to move.  Vera didn’t feel it.  She saw it on her console.  She watched the ship follow the comet’s path, adjusted for how the asteroid had rotated slightly.  She watched animations of canisters exploding in the micro-mines.

Everything went according to plan, at least on the screen she was watching.

No one on the deck cheered or celebrated.  The captain gave a firm “well done” to the pilot. 

Then she said, “Now, we watch.”

Vera looked up to see Ash, his face turned toward her, smiling.  He held up one hand and crossed the first two fingers.

She winked at him.


They were safe aboard the ship.  Vera and Ash were assigned quarters together, small, but comfortable, and with a window that looked out at the stars, and even what looked like a distant galaxy with double-spiral arms. 

She stood in front of that window, eating cereal.  Her stomach had unclenched as soon as she decided not to keep checking the bacterial population status.  It felt as if a week had gone by, but it had only been half a day. 

The ship’s captain had already announced that they couldn’t stay much longer.  The ship was at full capacity.  And the voyage to their closest home planet would take a few weeks.

In the first six hours after they deployed their grand heroic plan, she and Ash fearfully watched more and more bacteria dying off from the comfort of their quarters, and their hearts sank.  Vera had looked around and realized that they would be okay.  They were not in a life-or-death situation.  But Prosperotrogon…the bacterium had been minding its own business until they came along and put it to work. 

Vera had told herself it was symbiotic.  The humans did carve out access to a few places in the asteroid where the bacterium hadn’t been able to venture, and wouldn’t be able to for a long while, as parts of the asteroid naturally eroded, and other parts were built up, as Prospero collected cosmic dust on its orbit around a distant star.

“Vera,” Ash called from behind her.  He had breathed out her name, as if his reason for calling her attention was urgent.

She turned and saw him zooming toward her holding a tablet.  She didn’t have to read what he showed her on the tablet.  She had already read his face.  But she set her bowl down and took the tablet.

The whole display was a graph of the asteroid’s bacterial population.  For the past hour or so, it had started rising.  As she watched, the graphed updated, the rise was increasing.

“The captain announced we’ll be here for another several hours,” Ash said.  “We have to leave after that.  We can’t go back down now.  Tower Four is sinking.  And the sub-dome atmosphere will have to be cleared of particulates.  It’ll take more than one ship to make repairs.  They just finished deploying some upgraded orbital sensors.  The dome should hold.  And hopefully if Prost bounces back fast, we won’t come back to find the whole colony has vanished in a sinkhole.” 

Vera had been wondering if they should come back, if it might not be better for them to leave the asteroid alone, and leave its only natural living inhabitants alone.

She wanted to go back.  She would have gone down that very moment if they’d been given the okay.  But much as she loved her life and work on Prospero, she had never intended to stay there for good.  She and Ash had planned to move on in five or six years.  But she had expected they would leave a decent-sized human colony behind, and a thriving bacterial colony.

“Have we really saved them?” she said, partly asking, and partly just wondering aloud.

Ash’s eyebrows pinched in just a bit.  But then they relaxed, and he smiled a crooked smile.  “For now, we have.”

She couldn’t tell if he could sense the other questions behind the one she’d spoken out loud.  She hadn’t talked to him about it yet.  But she would.

He wrapped his arms around her.  “The work isn’t over.  But this shift is.”  He tilted his face down to hers, stirring a soft smile on her face.

Vera kissed her husband deeply on the lips.

“For now,” she said, “all is good.”

Copyright © 2022  Nila L. Patel

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