In the late 17th century, a Dutch shopkeeper named Antony van Leeuwenhoek placed a drop of pond water before the lens of a microscope of his own design and construction, and made a surprising discovery: swimming in the pond water were assorted “animalcules” of extraordinarily small size. Some time later, he examined infusions of pepper in water, in an attempt to discover why pepper is hot. Once again he saw animalcules, but this time of even tinier size—such that if 100 of them were laid end to end the length would not equal the size of a grain of sand. In the space of two years, van Leeuwenhoek, a man with no scientific training, had discovered both protozoa and bacteria. His findings were met with amazement (and some disbelief), resulting in visits from celebrities and election as a fellow of the Royal Society.

Using his innovative microscopes, van Leeuwenhoek investigated a wide variety of subjects throughout his life, from bee stings, fish scales and feathers, to eyes, blood and teeth. In 1678 he scraped material from between his own teeth, and from those of two women who cleaned their teeth each day. He found a variety of animalcules in these samples, but this was nothing in comparison to the incredible profusion of microscopic life he saw in material obtained from an old gentleman who claimed to have never washed his mouth in all his life. He also noted that a splash of strong vinegar would cause animalcules picked from his teeth to promptly fall dead, but vinegar sloshed around his mouth failed to have the same effect. He concluded that vinegar was unable to penetrate beyond the surface of the material between his teeth. This was probably the first ever investigation into the nature of a microbial biofilm.

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A microbial biofilm is what most of us would call “slime”. To put it more scientifically, a biofilm is a community of microbes growing on a surface. Perhaps you’ve slipped while hopping from one slime-covered rock to another across a stream, or noticed slimy layers growing in the corners of neglected bathrooms. Given enough time, a biofilm layer will appear on almost any wet surface.

Although we cannot see them, microbes account for most of the biodiversity on this planet, are incredibly abundant, and live in virtually every imaginable habitat. And crucially, they are essential to the function of ecosystems and the support of life, particularly in aquatic environments. Among their huge variety are organisms which have metabolic traits and biochemical abilities that are found in no other branches of life, and are vital to the continuing function of the biosphere.

Until recently, the prevailing view of microbial life was a simple one, of solitary cells adrift in a watery habitat. In recent years however, it has become clear that in nature most microbes do not occur as isolated, drifting cells, but live in mixed, organised, surface-attached communities—or biofilms. This realisation has led to growing scientific interest in biofilms, the majority of it directed at their associated economic and health impacts in industrial and medical contexts. Of perhaps greater importance, however, for ecological reasons, are microbial biofilms in natural environments.

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The majority of microbes in aquatic environments such as streams, rivers and lakes live in biofilms, and these biofilms are the probable location of many vital ecological processes essential for the maintenance of ecosystem diversity and function—processes such as photosynthesis, decomposition, and recycling nutrients and minerals. We know relatively little about these microbial systems, however; much research on natural waterways neglects the role of biofilms.

Much as a forest appears as a carpet of greenery draped over the underlying topography when viewed from high above, a biofilm in a stream may be visible as a layer of green material covering the underlying rocks and gravel. A forest ecosystem is a mixture of many different interacting plants and animals, with characteristic structures and processes, existing on a scale that we can easily see and comprehend. Similarly, biofilm is also a mixture of many different interacting organisms, structures and processes, but on a scale hundreds to many thousands of times smaller, posing obvious challenges for research and understanding.

If you crouch down to take a close look at a biofilm in a stream, you might see the slimy layer resolve into a thicket of thin green filaments, much as moving closer to a forest will reveal individual trees. You might see small crustaceans, snails, worms, and the larvae of mayflies, caddisflies and stoneflies wriggling through the tangle. These animals—which are visible to the naked eye—are collectively termed macroinvertebrates. Because they are relatively easy to see, their environmental requirements are fairly well understood, and populations of macroinvertebrates can be used to assess the quality of our streams and rivers.

A stream biofilm is a diverse and nutritious salad of many more microorganisms invisible to the naked eye—bacteria, protozoa, algae, fungi, viruses and microscopic animals—all of which provide a vital food source for macroinvertebrates and other aquatic creatures. New Zealand’s only extinct freshwater fish, the grayling, is thought to have fed on biofilm material rasped from rocks and stones, as suggested by the modification of its upper teeth into a comb-like scraping structure, along with an extra long intestine for digestion of tough algal material. New Zealand’s famous trout fisheries depend upon biofilms, as trout fatten up on a diet of aquatic invertebrates, which in turn devour slime-inhabiting microorganisms. The same relationship is true for many of our native freshwater fish such as the koaro and the various Galaxias species of the South Island. The yellow-eyed mullet eats biofilms in estuaries and the lower reaches of rivers, while the endangered whio, or blue duck, feeds upon invertebrates found lurking among the biofilm-covered stones of fast-flowing rivers.

But these interactions are under threat. Due to a number of human activities, New Zealand waterways are in a degraded state. Rainfall in urban centres such as Auckland carries contaminants and rubbish from roads, carparks and roofs into urban streams. The ever-increasing intensity of agricultural development has also resulted in excessive nutrient loads finding their way into rural streams, rivers and lakes, causing blooms of algae and declining oxygen levels. The lakes of Rotorua are threatened by decades of nearby farming activity, and nutrient levels in Lake Taupo are increasing.

Widespread deforestation in the 19th century exposed many rivers and streams to high levels of sunlight, which may have caused unfavourable changes in the menu of biofilm algae available to the grayling, perhaps contributing to the extinction of this species. Predation by introduced salmonid fish such as brown trout, which feast on aquatic invertebrates, has also had widespread and severe impacts, not only on the invertebrates but also on the native fish that feed on them. More recently didymo, a microscopic silicone-walled alga from the Northern hemisphere, has invaded many rivers of the South Island. Didymo is an out-of-control biofilm organism, multiplying in huge numbers to form thick, brown carpets and streamers, choking native ecosystems.

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Clearly microbial biofilms are key components of stream and river ecosystems, at the heart of many freshwater environmental issues. A high-tech research project at the University of Auckland is seeking to unravel the connections between microbial biofilm structure and function, microbial diversity, nutrients and pollutants in streams. This should help us find ways of improving stream ecology.

Using a combination of advanced molecular biology, microscopy and microbiology techniques, this research has shown that stream biofilms are home to a remarkable diversity of bacteria, including potentially pathogenic ones such as Arcobacter, Helicobacter, Legionella and Listeria. Relatively pristine streams such as those found in the forested Waitakere Ranges have very different communities of biofilm bacteria from those found in streams deep in urban Auckland, which are exposed to high levels of chemical pollution, nutrient runoff and sunlight. Similar differences are seen in the communities of protozoa and invertebrates found in pristine streams from those found in degraded ones. Human activities have caused ecological damage to habitats at the microscopic scale, much like we have damaged the large-scale ecosystems we are more familiar with—forests, rivers, lakes and oceans.

Efforts to restore urban streams typically focus on removing rubbish and debris and planting trees along the streambanks, which results in more attractive and natural stream environments. These efforts are valuable, but the complete recovery of invertebrate and fish populations doesn’t always follow. Recent research has shown that eco-toxic metals present in urban stormwater, such as copper and zinc, rapidly accumulate in microbial biofilms and may be passed up the food chain. Only when the microbial community has recovered will invertebrates and fish further up the food chain return.

Fortunately, the unique characteristics of biofilms offer potential solutions to pollution problems, including that of urban stormwater. Bacteria, for instance, are capable of removing toxic molecules from water and transforming them into harmless or useful forms—a natural and efficient purification system.

This is what happens in wetlands, where masses of submerged vegetation provide a very large surface area for colonisation by microbial biofilms. The meandering passage of water through wetland habitats allows plenty of time for the abundant microbes to remove polluting substances. This principle can be applied to treatment of the stormwater entering streams, and provides a model used in everything from aquarium filters to wastewater treatment facilities—a major benefit of microbial biofilms to human civilisation, industry and, of course, ecosystems.

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Huge advances have been made in the study of microbes since the time of van Leeuwenhoek’s discoveries, but our understanding of biofilms is far from complete. Yet a better understanding of biofilm would have major consequences for health and industry. For instance, the biofilms that van Leeuwenhoek discovered on teeth host the bacteria that cause tooth decay. Biofilms on contact lenses, catheters and medical implants such as artificial heart valves cause problematic infections. The bacterium Pseudomonas aeruginosa—ubiquitous in soil and water—is noted for its ability to form antibiotic-resistant biofilms in the lungs of cystic fibrosis patients, contributing to deterioration of lung function. Biofilms can block pipes and conduits, foul machinery and form speed-inhibiting layers on ship hulls.

Yet the ecological processes performed by microbes and biofilms are also vital for the continuing function of ecosystems and the support of biodiversity. Understanding these microscopic communities should lead to better methods for reducing unwanted impacts on them, and our urban waterways might again host healthy populations of insects, crayfish and native fish.

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Magnification: 6000

Suppose you could shrink yourself by a factor of six-to eight-thousand times. This would make you about a quarter of a millimetre in height, and probably small enough to slip into the depths of a stream biofilm. You would find yourself in a thicket of green algae fibres, as thick as tree-trunks, looping and twisting around fragments of fallen twigs and leaves, crumbs of mud and sediment, and piles of disintegrating organic debris and wreckage. These algae are the plants of the microscopic world, and along with diatoms, some flagellates and the much tinier cyanobacteria are the primary producers of stream ecosystems. They possess chlorophyll, which gives them their green colour, and are responsible for photosynthetic harnessing of light energy and the creation of biomass.

A great deal of swimming, wriggling, crawling, spinning, twitching and oozing movement would catch your eye. The most abundant of these microscopic animals are the rotifers, so named for the retractable, whirling tufts of cilia—short hairlike projections—that surround their mouths and give them an eggbeater-like appearance.

Rotifers are largely transparent; some have short, wide bodies fitted inside helmet-shaped shells, while others have telescopic sausage-shaped bodies. Most have a tail ending in two to four pointed “toes”, tipped with the nozzles of a dual gland system that can alternately produce a sticky cement or a non-stick anti-cement, so a rotifer can anchor itself at one moment and float away the next, using its whirling cilia as propellers. Many rotifers are filter feeders, and while anchored, the cilia create a vortex that carries floating (or swimming) morsels to a set of tough jaws to be smashed and eaten. Others grab particles of food or scrape up blobs of debris and gulp them down, or poke holes in cells and slurp out the contents, vampire-like.

Racing about in a more frantic manner than the stop-start rotifers are streamlined gastrotrichs. Shaped like a flattened skittle and decorated with an assortment of scales, spines and adhesive tubules—a body form ideal for manoeuvring through narrow spaces—gastrotrichs glide swiftly about in search of food, upon a magic carpet of cilia covering their bellies. Nematode worms—hair-thin tubes containing minimalist digestive, nervous and reproductive systems—are also present in the biofilm, always wriggling and coiling and slurping up debris.

These creatures—rotifers, gastrotrichs and nematodes—are among the very smallest representatives of the animal kingdom, at the lower size limit for multicellular life.

Magnification: 30,000

At one-twentieth of a millimetre in height, you would be about the size of a medium-sized protozoan, and would find yourself in the midst of a bustling, jiggling profusion of single-celled organisms, ranging in size from knee high to several times your size. Protozoa can be thought of as the animals of the single-celled world, due to the two animal-like traits they share: the ability to swim, crawl, gyrate or ooze towards food and away from danger, and the need to eat other things. They occur in a tremendous array of different varieties, and are very abundant in a stream biofilm (not to mention most other wet or damp places). The largest and most eye-catching protozoans are ciliates, which often look like jellybeans or zeppelins, while others are reminiscent of flowers or animated noodles. Some are incredibly fast and manoeuvrable swimmers, some bumble around like escaped helium balloons, some appear to bounce, and some spin like tops. Others scramble through algae and debris upon sets of multiple leg-like structures. If a typical ciliate hovered in front of you, you would see that it is fringed with hundreds to thousands of rapidly beating cilia. These provide ciliates with a powerful means of propulsion and a finely tuned steering mechanism, as well as a means of gathering food. Ciliate cells are among the most complex known, making the most of their single-celled existence by developing highly elaborate cellular architecture and machinery.

One of the largest ciliates you might encounter, Stentor, towers above most protozoa like an enormous upended trumpet and gathers food by swirling its coat of cilia about to generate a vortex that carries food particles into its funnel, where they are consumed. Many ciliates, like Stentor, eat smaller items such as bacteria and fragments of debris, but others are armour-plated or harpoon-equipped predators, some capable of cannibalising other protozoans as large as themselves.

Magnification: 60,000

An amoeba—a very different type of protozoan—is typically an amorphous, elastic blob. Some have a tidy shape with a definite centre, while others appear to have been stretched until very thinly spread, or pulled into a barely visible network of thin filaments. Like rotifers, some amoebae have a shell, which may be delicately patterned and sculpted or conglomerations of glued-together debris. Amoebae don’t swim, they ooze. If you watched an amoeba creeping slowly and steadily forward, you would see the vesicles and organelles inside the cell flowing through its transparent cytoplasm. When it locates its prey—an algal cell, perhaps—it will engulf it, starfish-like, before secreting a cocktail of digestive juices that bust open the cell and break apart molecules so their components can be consumed.

Diatoms—which may be consumed by the larger types of amoebae—are a type of photosynthetic alga, with a unique characteristic among life on Earth: their cell walls are precisely formed and delicately ornamented constructions of silica. The diatoms found in a stream biofilm typically have long, straight walls and shapely corners, adorned with bumps and pores. Scattered about like fleets of miniature battleships, they occasionally manoeuvre their bows to a new heading and glide to new positions.

Magnification: 150,000

Somewhat smaller than many ciliates and amoebae, flagellates are a collection of disparate protozoa united only by the possession of one or more flagella—whip-like constructions that may be used as oars, propellers, tentacles or anchors. Some flagellates glide smoothly about while others thrash wildly, some flip-flop and others bob, and most are thought to be enthusiastic consumers of bacteria. Some varieties of flagellate, however, are full of chlorophyll and photosynthetic, and are often labelled as algae.

There is an important type of organism that operates in the opposite way to the primary producing algae; fungus. Most fungi consist of threadlike, branched structures called hyphae, which squeeze into cracks and weak spots. They exude batteries of enzymes into their surrounding environment that dismantle organic molecules into smaller components, some of which are absorbed and used to fuel the fungus’s expansion into new territories. By digesting its food on the outside, a fungus provides the chance for many molecules to escape and join the chemical soup that provides basic nutrients for plants, algae, protozoa and bacteria. Fungi are universally present in soils and decaying material, including food left in the pantry for too long, and the leaf litter that accumulates at the bottom of a forest stream. While individual fungal hyphae are tiny, they may collectively form very large structures. Little is known about fungi in stream biofilms, but it is clear that fungal activity is essential for decomposition of organic material and recycling of nutrients.

Some types of fungi supplement their diet through more devious means, trapping passing nematodes or rotifers in circular loops of hyphae, which instantly inflate like balloons, strangling the creature inside. Entrapped animals are subjected to an invasion of digesting hyphae into the body cavity and subsequent assimilation into the fungus.

Magnification: 1,500,000

Bacteria, together with the superficially similar archaea, are the second most abundant organisms on Earth. A stream biofilm is stuffed with them.

At one-thousandth of a millimetre, or one micron, tall—you would be comparable in size to a single bacterium. Algal filaments, leaf fragments and piles of debris would have become a landscape of hills, crags and plains, and protozoa would loom overhead like low-flying satellites. Spread across the surfaces of this landscape you would see lumpy, jelly-like constructions, bulging up into mushroom-shaped peaks topped with streamers and split by tunnels and valleys. These are known to microbiologists as bacterial biofilms—and they are, effectively, cities of bacteria. If you took a swim through one of these structures, it would become apparent that inside is a complex architecture of micro-colonies, passages and water channels, in which assorted bacteria have arranged themselves so that they can receive the oxygen and nutrients they require—from outside and from their neighbours. This kind of existence has advantages. A biofilm city provides a safer and more stable environment, its citizens are less likely to be washed away by currents and less accessible to predators.

Collectively, bacteria possess an amazing variety of metabolic and physiological characteristics, which science is only beginning to understand. Their biogeochemical activities are essential to the function of the ecosystems. The bright green-coloured cyanobacteria, along with algae, are primary producers. Between them, cyanobacteria and algae produce a substantial proportion of the oxygen in the atmosphere, and the organic molecules they produce provide fundamental food inputs for other forms of life—particularly in the oceans, where vascular plants are rarely present. Like the fungi, heterotrophic bacteria are equipped with assorted biochemical tools capable of dismantling, transforming and recycling molecules. The ability to “fix” atmospheric nitrogen—convert it to an ionic form useable by other organisms—is found only in certain types of bacteria. Bacteria are also important for recycling sulphur and iron compounds.

Magnification: 30,000,000

To become virus-sized, you would have to shrink to about one twenty-thousandth of a millimetre, or fifty nanometres, tall. It would take some thirty million copies of your virus-sized self standing on each other’s shoulders to equal your original height. Virus particles are rather simple constructions, consisting simply of strings of genetic material surrounded by polyhedral protein coats, shaped like cylinders, spheres, icosahedrons, or lunar landing modules. Viruses have a rather piratical life, existing only to parasitise the cells of other organisms. They are considered to be the most abundant biological entities on the planet, occurring in a vast range of varieties, most of them capable of infecting one or a few particular types of cell. A virus will drift at the whim of currents, and when it bumps into the correct type of cell, will wheedle its way inside and hijack the cellular machinery, causing it to cease production of its normal array of proteins and start building new virus particles instead. Normal cell function is hindered or halted. Some time later, you might see the cell wall rupture as a barrage of newly assembled virus particles burst forth into the outside environment once again, accompanied by a cloud of leaked cellular components. This busting of cells and release of cellular materials into the environment—a simple form of recycling—and the destructive effect this has on target cell populations—are the main effects of viruses in an ecosystem.

Virus-sized, you would be able to see the individual molecules that everything is built from. There is nothing smaller than this that might be considered alive.