A microbial mat is an entire ecosystem compressed into a few millimetres: light harvesters at the top, sulfur and carbon recyclers below, and chemical gradients so steep that the mat’s chemistry flips between day and night.
Select a layer to see who lives there and what they do. Switch between day and night to watch oxygen and sulfide trade places.
Day
Sunlight drives photosynthesis. Oxygen builds to a peak a millimetre or two below the surface, often above saturation, and sulfide is pushed down into the deeper layers. Photosynthesis also draws down carbon dioxide and raises pH near the surface, which favours carbonate precipitation.
Night
Photosynthesis stops but respiration does not. Oxygen is quickly used up in all but the top fraction of a millimetre, sulfide rises toward the surface, and many microbes switch to fermentation. The whole mat swings between these states every 24 hours, and gene-expression studies in Shark Bay have followed the shift across day, night and season.
The top fraction of a millimetre is a slimy film of extracellular polymeric substances (EPS) secreted by the community. EPS holds the mat together, traps sediment grains and helps cells survive drying. It also binds calcium. When bacteria break it down, the released calcium and altered polymers can seed carbonate crystals.
In Shark Bay this surface faces salinity above 60 on the practical salinity scale, intense ultraviolet light and repeated drying.
The green zone is where oxygen-producing photosynthesis happens. Filamentous cyanobacteria fix carbon dioxide and build much of the mat’s structure. In Shark Bay, cyanobacteria, proteobacteria and bacteroidetes dominate the top two millimetres.
Living in full sun, these microbes make ultraviolet-screening compounds such as scytonemin and mycosporine-like amino acids. A cyanobacteria-rich layer of Shark Bay stromatolites even holds a new strain of Acaryochloris that lives on near-infrared light.
Below the cyanobacteria, light is dimmer and shifted toward the red, and oxygen gives way to sulfide. In many mats this is the domain of anoxygenic phototrophs such as purple sulfur bacteria. They use sulfide instead of water as their source of electrons, so they photosynthesise without releasing oxygen. Their pigments give the band its colour.
Anoxygenic photosynthesis is older than the oxygen-producing kind, which is one reason these layers interest researchers studying early Earth.
Sulfate-reducing bacteria breathe sulfate instead of oxygen and release hydrogen sulfide. Iron sulfide minerals turn the layer black. Sulfate reduction is a key part of the alkalinity engine: in Bahamian stromatolites the highest rates coincide with the hard carbonate laminae.
Mat type matters. In Shark Bay, rates of oxygen production and consumption and of sulfate reduction were up to four times higher in lithifying smooth mats than in pustular mats.
Archaea and lineages known only from their genomes live throughout the mat. Shark Bay mats yielded 115 genomes of this microbial dark matter from 42 phyla, including Asgard archaea, the closest known relatives of complex cells. Many have small genomes and appear to depend on trading hydrogen, ribose and carbon monoxide or dioxide with neighbours.
The layering is not as tidy as the drawing suggests. Methanogens, which need oxygen-free conditions, were enriched at the oxygenated surface of Shark Bay mats, where methane production also peaked. That points to microscopic oxygen-free pockets inside the sunlit zone.
Where precipitation outpaces dissolution, calcium carbonate accumulates as hard laminae and the mat becomes a microbialite. Whether that happens depends on the whole community. In Shark Bay, smooth mats lithify while pustular mats growing beside them generally do not.
Viruses may tip that balance by killing and reprogramming the microbes that run the alkalinity engine. Read the viral hypothesis.
The drawing and profiles are schematic, based on well-studied hypersaline mats. Real layer thicknesses and chemical profiles vary with site, season and mat type.
There are two ways a mat leaves stone behind. Most microbialites involve both.
Filamentous cyanobacteria glide upward through settling sand and mud, and the sticky extracellular polymeric substances (EPS) they secrete glue grains in place. In the open-marine stromatolites of the Bahamas, pioneer communities of gliding filaments do exactly this during periods of rapid sediment supply.
Microbial metabolism changes the water chemistry inside the mat. Photosynthesis and, under the right conditions, sulfate reduction raise alkalinity and push calcium carbonate toward precipitation; aerobic respiration, sulfide oxidation and fermentation tend to push it the other way. Visscher and colleagues call this balance the alkalinity engine.
The polymer matrix is the other half of the story. Fresh EPS binds calcium ions and can hold back precipitation. As bacteria degrade it, that calcium is released and the altered polymers can act as templates on which carbonate crystals nucleate. Carbonate precipitation needs three things at once: water supersaturated with carbonate, available cations such as calcium, and nucleation sites. A mat lithifies only when precipitation wins out over dissolution.
In Bahamian stromatolites, Visscher and colleagues found the highest sulfate-reduction rates in the hard, fine-grained laminae, tying the sulfur cycle directly to the layers that become rock. Their effect is not universal: depending on the setting, sulfate reduction can either favour or hinder carbonate precipitation.
Visscher et al. 1998, American MineralogistVisscher, Reid and Bebout 2000, Geology
Mats are usually only millimetres thick, but they can carpet whole landscapes. The coloured rings around Yellowstone’s Grand Prismatic Spring are microbial mats. Their colours shift with temperature and season, as the balance between chlorophyll and carotenoid pigments changes.
Gathaagudu, or Shark Bay, holds one of the most extensive and diverse systems of living microbial mats in the world. Different mat types grow side by side, which makes it ideal for asking what separates a mat that builds rock from one that does not.
Cohesive, lithifying mats. Analysed in 2 mm slices to 20 mm depth, they showed sharp vertical partitioning of microbes and metabolism, higher archaeal diversity than pustular mats, and 87 genomes reconstructed from metagenomes, including Asgard archaea.
Bumpy, blistered mats that generally do not lithify. Their archaea are distinct from those of smooth mats and are enriched in Halobacteria, the salt-loving archaea that early studies found to dominate Shark Bay mats.
Supratidal, gypsum-rich mats. Their 117 reconstructed genomes include DPANN and Asgard archaea and the candidate phyla radiation, with the highest diversity 14 to 20 mm down. The authors propose that photoheterotrophy, using light while feeding on organic carbon, is an important lifestyle here.
The rock-building end of the spectrum. Their communities, and the viruses that infect them, have been profiled alongside the mats.
Mat microbes survive conditions that would stop most life. Metagenomes from Shark Bay carry genes for osmoprotection against salt, resistance to ultraviolet light and heavy metals, and an array of antiviral defence systems: CRISPR-Cas, BREX and DISARM.
The microbes also talk to each other. Bacteria isolated from Shark Bay mats are active in quorum sensing, the chemical signalling that lets microbes coordinate behaviour such as biofilm formation. And the mats are rich in biosynthetic gene clusters, the genetic machinery for making antibiotics and other natural products.
