Philadelphia’s microscopic algae archive is a time machine for coastlands

Philadelphia’s microscopic algae archive is a time machine for coastlands

This article was originally featured on Hakai Magazine, an online publication about science and society in coastal ecosystems. Read more stories like this at

Located in the heart of Philadelphia (PA), the Academy of Natural Sciences of Drexel University exudes the aura of a vast cabinet of curiosities. Its neoclassical façade is covered with natural motifs, including doorways flanked in ammonites, handrails that curl into ferns and bronze door handles shaped as ibis skulls. The academy is the oldest institution of natural science in the western hemisphere and has amassed a remarkable collection. Among the 19 million or so specimens housed here are plants procured on the Lewis and Clark Expedition, blue marlin reeled in by Ernest Hemingway, and America’s first mounted dinosaur skeleton.

Many of the academy’s most important and unassuming treasures are stored on its second floor in an office space filled with microscopes and hulking cabinets. Marina Potapova, curator, opens a large plastic container filled with glass slides in a notebook. These unremarkable slides look filthy to the untrained eye. Each slide looks like it’s been smudged from dirty hands.

But once Potapova puts one under a microscope lens the contents of the slide are immediately visible. Dozens of diatoms–microscopic, single-celled algae encased in sturdy silica walls and found wherever there is water–are fixed to the slides in a myriad of shapes.

Philadelphia’s microscopic algae archive is a time machine for coastlands
With over four million specimens, the Academy of Natural Sciences of Drexel University’s diatom collection in Philadelphia, Pennsylvania, is the second largest in the world. Photo by Jack Tamisiea

Some are flattened into saucers or elongated like baguettes, while others hook together to resemble translucent zirides. Others are shaped like sea stars or barbed like harpoons. Some look like stained-glass windows. A few drops of murky water can transform into a kaleidoscope full of diatom diversity when viewed under a microscope.

The beauty of diatoms can be breathtaking. Their ecological importance is amazing. They anchor marine food webs by feeding everything, from tiny zooplankton to large filter feeders. (Case in point: scientists have deduced that the rise of whales some 30 million years ago mirrors a spike in diatom diversity.) Diatoms also have a huge impact on the atmosphere. Diatoms are one of the most prolific organisms on the planet. They siphon harmful gases such as carbon dioxide from the air and produce large amounts of oxygen through photosynthesis. Diatoms are responsible for approximately one quarter of the air we breathe.

Over four million specimens are housed in the academy’s diatom herbarium. The Natural History Museum in London has more diatom slides.

Although the diatoms of the academy no longer feed the planktonic mass or pump oxygen into the atmosphere they do provide clues about the changing aquatic world. Their tough shells sink to the bottom, and they are then stored in sediment for millennia. Researchers use a sediment core for drilling down into the bottom of an estuary to collect diatoms that have been deposited over many years.

Diatoms are not only hardy and plentiful, but also provide a vital indicator of various environmental conditions. Scientists can use the existence of certain diatom species to pinpoint everything, from industrial pollution to oxygen depletion. Potapova and her colleagues recently used these water condition capsules to assess how fast sea level rise is threatening New Jersey’s coastal wetlands.

Due to a relative lack of environmental monitoring, the history of the decline of these vital marshes, which hoard carbon, provide nursery ground for fish and buffer the coast against storms, has largely been obscured. Restoration efforts are essentially guesswork.

However the diatoms at the academy help researchers track the decline of coastal wetlands as sea levels rise, which could help predict the future of the coast. Potapova states that diatoms are an invaluable environmental archive. “You can infer the future by what they tell about the past .”

Given the history of the academy, it is not surprising that this historic institution has become a center for diatoms. With the advent of accessible microscopy in the 1850s, many of Philadelphia’s gentleman naturalists were captivated by the realm of minute microbes, eventually establishing the Microscopical Society of Philadelphia at the academy.

Diatoms have taken the microscopical world by storm due to their stunning beauty. Many of these diatomists traveled east to New Jersey to collect samples. They mounted the samples onto glass slides with a steady hand and a brush that was brimming full of pig eyelashes. The hobbyists would then meet at the academy to display their slides at gourmet luncheons.

Although the academy’s founders were enthusiastic about diatoms, most of them were amateurs who did not publish much research on the many specimens they had collected. Organizing the mountains of slides compiled by each collector into a cohesive collection proved to be quite the task for Ruth Patrick when she arrived at the academy in 1933. Patrick, the daughter of a diatomist and who received her first microscope at seven years old, gravitated towards diatoms as a child. She eventually earned her PhD in microscopical organisms. Despite her scientific credentials she was only able to set up slides and microscopes for amateurs. It took her many years to be admitted to the male-dominated academy. But her persistence paid off, and in 1937 she became curator of the nascent diatom herbarium.

Patrick was the first to organize different collections into one comprehensive taxonomic resource. She was often found wading in nearby streams and ponds to collect new specimens. This was where she began to appreciate the ecological importance diatoms.

This crystalized during a 1948 expedition to Pennsylvania’s Conestoga River–a body of water heavily polluted by sewage and industrial runoff. She noticed patterns in the diatom composition as her team collected samples from the creek. Some species thrived in areas contaminated by sewage while others thrived in areas that were contaminated with chemicals. Patrick soon learned to use the existence of certain diatoms to diagnose pollution in rivers and lakes. This led ecologists to coin the Patrick Principle, which states that a greater diversity of diatoms correlates with healthier freshwater ecosystems.

Patrick revolutionized monitoring freshwater systems with diatoms, but their use in coastal wetlands was a slow process. Mihaela Enache (a researcher at the New Jersey Department of Environmental Protection) says that brackish fusion of salt and fresh water in coastal zones like estuaries creates habitats dynamic and complex with a mix of inland diatoms and oceanic.

However, in recent decades the sea has taken over the once-dynamic coast margin, pushing further inland with rising sea levels. The sea level in New Jersey has increased by 0. 45 meters, more than double the global average of 0. 18 meters. By 2100, the sea could rise by over a meter.

The dramatic rise in sea levels has been disastrous for the patchwork marshes that line New Jersey’s coast. Many of them have already been flooded. It is difficult to determine the extent of this loss because only a few decades of environmental monitoring are available.

Without a sense for the natural conditions of a wetland, ecological restoration can be difficult. Enache says that this information is essential. “Without [it], it is in the dark,” Enache says. Fortunately, some of the missing data can be found in the academy’s cache diatoms.

New Jersey, like most coasts, is well-acquainted with sea level rise. The Pleistocene was a time when New Jersey was covered by ice and home for mastodons. Sea ice took up seawater stores. Around 18,000 years ago, sea levels sank more than 130 meters below their current levels–extending the New Jersey coastline 110 kilometers farther into the Atlantic Ocean.

The end of the last Ice Age sparked an increase in sea levels. Parts of New Jersey were affected by the retreating ice sheets. According to Jennifer Walker, a Rutgers University sea level researcher, this subsidence was combined with glacial melt a potent combination for rapid sea-level rise.

In a study published last year, Walker turned to the past to put New Jersey’s current bout of sea level rise in context. “If we can understand how temperature, atmosphere and sea level changes interconnected in the past then that’s what can be used to project future .”


To gauge fluctuating sea levels over the past 2,000 years, her team examined the shells of single-celled protists called foraminifera that are finely calibrated to specific environmental conditions. These shells can be used as a proxy to reconstruct changes in sea level. By identifying the presence of certain foraminifera species throughout sediment cores collected from different spots along the Jersey shore, her team concluded that New Jersey’s coast is experiencing the fastest rise of sea level in 2,000 years.

The NJDEP hoped that diatoms could be used as a similar tool to understand how coastal marshes respond to rising sea levels. Each diatom species, like foraminifera is highly sensitive to environmental conditions. The Nitzschia Microcephala species, which is a rolling pin-shaped diatom, thrive in nitrogen-rich environments. This makes their shells a common sign that they are nutrient polluted. Others, such as Diploneis Smithii , whose shell looks like a thin trilobite and is saline-friendly, prefer saline water. Their presence inland is a good indicator of sea level intrusion in the past and helps researchers determine which marshes were prone to flooding in that time.

To pinpoint the location of these microscopic indicators, the NJDEP sent a team to several marshes along the coast. These marshes range from heavily polluted wetlands to near-pristine, tidal marshes south. They cored into the marsh muck at each site, some sampling as deep as 2 meters. Enache likens this to slicing into pancakes. As you cut deeper, you are actually going back in time from the steaming pancake on the griddle to that soggy pancake at the bottom. The researchers found themselves traveling back in time as they dug deeper. They collected nine cores from five different wetlands.

The NJDEP sent the sediment cores on to Philadelphia where Potapova, her master’s student Nina Desianti, and Potapova surveyed the diatom diversity in New Jersey’s coastal wetlands over time. Desianti began to process the diatom specimens by soaking them in strong acid to dissolve all but the silica shell, before adhering them onto slides. The result was a detailed environmental history of each marsh, mounted onto thousands upon thousands of glass slides. They then played a microscopic game with the specimens already catalogued at the academy. But even the sprawling diatom herbarium lacked all the answers–Desianti estimates that over one-third of the 900-odd species they collected from the wetlands are new to science.

The monumental effort yielded the tome Diatom Flora of the New Jersey Coastal Wetlands in 2019. It is a dazzling mix of intimidating Latinized names as well as dramatic electron microscope photos that depict diatoms in all of their infinitesimal glory. It is Enache’s key to understanding the decline in New Jersey’s wetlands. Enache can show what a once-pristine wetland looked like by incorporating the current wetland conditions and the composition of diatom species into modeling programs. “Diatom species are an extremely valuable environmental archive because they can go back in time –when nobody could measure nutrients, nobody could measure pH–and actually use diatom species to get full numbers,” she said. These figures help her record the increase of everything from agricultural nutrients to industrial chemicals in New Jersey’s water all the way back to the mid-1600s, when Europeans arrived and began to dramatically alter the state.

Diatoms provide a glimpse into the decline of New Jersey’s marshes but also give a glimpse at Desianti’s environmental resilience. The team used the salt tolerance of different diatoms as a way to map previous episodes of sea-level rise. They could also use microscopic algae to determine how these marshes responded in the face of saltwater intrusion.

Marshes are a dynamic habitat. The coastal marshes, which act as the barrier between land and sea, accumulate sediment, building vertically to keep above the rising ocean. The marshes will retreat into coastal forests if the sea level rises faster than their sediment accumulation. The marsh’s briny water percolates to the groundwater and kills trees, creating what ecologists refer to as “ghost forests” made of desiccated tree leaves.

Philadelphia’s microscopic algae archive is a time machine for coastlands
Potapova examines diatoms sampled from the coast in an Academy of Natural Sciences of Drexel University lab. Photo by Jack Tamisiea

Although coastal marshes are naturally flexible, anthropogenic influences have made them stiffer. New Jersey dams have been known to strain sediment and strip the marsh of its construction material. Retreated marshes are then pushed up against paved roads, vacation homes, and other structures. Desianti, now using diatoms to track nutrient contamination for the Wisconsin State Laboratory of Hygiene, says that salt marshes must compete with us in establishing habitat. “As a result, these salt marshes are squeezed between sea level rise and human pressures.”

The NJDEP will use the diatoms Potapova & Desianti to help them not only understand how New Jersey’s coastal wetlands have responded to past sea level rises but also to inform what can be done in order to restore these vibrant ecosystems.

The deeper you go into the pond muck the more diverse the diatoms are. This, Ruth Patrick discovered decades ago, is the hallmark of a healthy ecosystem. If you look at the core’s most recent chapters, you will see that diatom diversity tends to decrease as certain specialists like salt-loving marine Diatoms dominate. Knowing where these saline-specializing organisms persist can reveal which ecosystems have been affected by sea level rise and where restoration efforts such as an influx sediment are most needed.

Diatoms do not provide a solution to problems like pollution and sea level rise. They are, however, a key to combating them. They show what once was the beauty of pristine habitats long before anyone noticed and what has changed over time. These microscopic algae can be used to help you create successful wetland restoration plans.

The diatom specimens Potapova, Desianti and other specimens from New Jersey’s coast marshes were taken by Patrick. They are now being stored in the steel cabinets at the diatom herbarium. Similar to how diatoms persist in sediment for millennia and how they are stored at the academy, future researchers will be able to use the diatom specimens to help them understand pollution and shifting sea level.

” The diatom herbarium provides invaluable resources for diatom research,” states Desianti. Desianti says, “I’m certain that in the future even when I’m gone people will still have access to this collection and continue investigating environmental issues.” She believes that the tens to thousands of slides stored in the recesses are environmental breakthroughs that are waiting to be decoded.

This article was first published in Hakai Magazine ,. It is republished with permission.

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