1000 - 500 mya Neoprotezoic

No sign of soil Precambrian 4.5-1bya 500-400 mya

There was no sign of soil for the first 4 billion years of earth - including the 'Precambrian' years

Prokaryotes

Archaea

Archaea & nitrification

Specific bacterial relations with clay then

Underground Biofilms

1000 to 542.0 mya (Neoproterozoic )

If we could look round at what it looked like a thousand million years ago (1000mya or 1 bya) we would see no sign of soil, as we know it today. There is talk of fossil soils (palaeosols) in these early times, but they were not like soils we know today - ie structures full of life.

The supercontinent Rodinia began to break up around 825mya and continued for almost 100 million years, bringing with it massive volcanic eruptions spewing out volcanic rock called basalt.

"Three global glaciations occurred, named the Sturtian, Marinoan and Gaskiers glaciations. These influenced the patterns of life on Earth and caused changes in the atmosphere and ocean dynamics. According to the Snowball Earth hypothesis of Kirschvink and Hoffman (1998), these glacial events were triggered by the increase in continental weathering rates, leading to a consumption of atmospheric CO2, forcing a drop in global temperatures". (Assine and Warren, 2021)

Prokaryotes

With a microscope, we could see single-celled organisms and other ones which ‘met up with themselves’. Among the single-celled ones were bacteria, and were – part of prokaryotes (ie ‘before’ karyotes). These new range of organisms became so successful, that they began to react more with each other.

Some that met up became multi-cellular and called eukaryotes or ‘true’ karyotes The first eukaryotes were likely single-celled like unicellular green algae, single-celled fungi, and protists; unicellular eukaryotes would likely have evolved before multi-cellular eukaryotes. These multicellular types could generate new genetic and cell features, making the evolution of more complex organisms possible. And they could now exist because the atmosphere had oxygen.

Archaea

Carl Woese and George Fox discovered Archaea (then termed Archaebacteria) in the 1970s. They were generally considered as rather enigmatic curiosities – unique cell structures and physiologies certainly, but not contributing greatly to the major biogeochemical cycles of the earth. How wrong.

They have properties that play important roles in the overall metabolism of soil throughout the ages, particularly nitrification.

Structure

Archaea are like bacteria in that their single cells lack a defined nucleus making them ‘prokayotes’. However, they are distinct in that they have different cell walls [cell walls or cell membranes - remember they are different, cell walls are extracellular, cell membranes form the outward facing interface of the cell], where bacteria are composed of ‘peptidoglycan’, whereas archaea have ‘pseudo’ peptidoglycan, and mixtures of sugars and proteins. They are also distinct from most other organisms - eukaryotes - protists, fungi plants and animals. Their distinctness is a relatively recent realisation, around the turn of this century, such that many [who? the key body is the international body which decides on classification and nomenclature of life] now class them as a separate kingdom.

Archaea are known to survive extreme conditions, such as temperatures above boiling point. Some are the most abundant ammonia-oxidizing organisms in soils. and others responsible for the removal of methane, a potent greenhouse gas, via anaerobic oxidation of methane stored in these sediments. Yet they also produce methane in rice fields, estimated to generate approximately 10–25 percent of global methane emissions.

Archaea & nitrification

Most consider that nitrification is primarily carried out by certain soil bacteria, such as Nitrosomonas and Nitrobacter, in aerobic (oxygen-rich) conditions. However a relatively recent discovery is that Archaer genes to oxidise ammonia - are 3000 times more prevalent in soils than similar bacterial ones. This implies their role in nitrogen fixing is a lot more profound than we thought until recently;

“The ability of some archaea to contribute to nitrogen cycling processes has been known for many decades (albeit some of these organisms were not initially recognised as archaea). These included both assimilatory (e.g. fixation of atmospheric nitrogen) and dissimilatory (e.g. denitrification) processes. However, these reactions were associated with extremophilic archaea typically found in ‘exotic’ habitats such as hot springs or salt-saturated lakes, rather than major terrestrial or aquatic environments, and were perhaps not considered ecologically important in a global context.

In little over a decade, microbiologists have not only discovered that archaea perform nitrogen transformation in more ‘common or garden’ habitats, but also that these contributions are vast with respect to global fluxes, and have solved several long-established mysteries with regard to nitrogen cycling in the world’s oceans and soils.”

With their ability to withstand extreme conditions and their prevalence in nitrogen fixing, it could be proposed that archae were involved in this key function very early on and brought it with them when Archaea helped develop soil. The discovery of Ammonium Oxidising Archaea (AOA) also provides a possible explanation for the long-standing paradox of why high rates of nitrification are often observed in acidic soils without the acidophilic bacterial ammonia oxidisers.

Nitrification

The oxidation of ammonia (NH3) in soil typically involves a two-step process known as nitrification, which converts ammonia into nitrate ions (NO3-) through the intermediate nitrite ions (NO2-). Here are the balanced chemical reactions for these two steps:

Step 1: Ammonia (NH3) is oxidized to nitrite (NO2-):4 NH3 + 3 O2 → 2 N2H4 + 6 H2O

Step 2: Nitrite (NO2-) is further oxidized to nitrate (NO3-): 2 NO2- + O2 → 2 NO3-

Overall, the complete oxidation of ammonia to nitrate in soil involves both of these steps: 4 NH3 + 3 O2 → 2 NO3- + 6 H2O

These reactions are essential in the nitrogen cycle, as they convert ammonia [where's this from, it's not in rocks or the atmosphere], which is toxic to many plants at high concentrations, into nitrate, which is a form of nitrogen that plants can readily take up and use for growth. This is one of the most important functions that soils carry out. But did it appear before soil evolved.

Bacteria and Archaea came together in a fusion event to synthesize a whole new domain of life, the Eukarya. Over the past 600 million years since then, the Bacteria, Archaea and microbial Eukarya have continued to evolve into brand new niches, including the various ones in soils. In the process, they have created new substances for bacteria to exploit and new environments to inhabit.

Eukaryotic cells are those with internal organelles.

Eukaryotes

One of the organelles is the nucleus: the control centre of the cell, in which the genes are stored in a membrane [chromosome?]. Nuclei evolved when one simple cell engulfed another, and the two lived together, more or less amicably – an example of “endosymbiosis”. The other [there are many organelles]- the mitochondria – was formed when bacteria were engulfed. Mitochondria provide cells with energy and some [why only some, isn't mitochondrial DNA an important genetic indicator?] developed sexual reproduction. Later eukaryotic cells engulfed cyanobacteria to become 'protochloroplasts'.

The ancestral eukaryote organism is thought to have been an amoeboid creature that relied on anaerobic or microaerophilic, surviving on v little oxygen. The evolution of those internal organelles – nuclei, mitochondria and chloroplasts allowed a more efficient cellular metabolism, which led the way to the evolution of an enormously diverse array of eukaryotic organisms. Some of the early amoeboid eukaryotes developed flagella to enhance their food-gathering abilities and to provide a more efficient mode of propulsion. The flagellates gradually evolved different ways of life, and their structures became modified accordingly.

3 groups

During this half billion years, the eukaryotes divide into three groups: the ancestors of modern plants, fungi and animals split into separate lineages, and evolve separately. The first multicellular life develops around this time. It is unclear exactly how or why this happens, sometimes form colonies consisting of many individuals. They divide into the sponges and everything else including a small group called the placozoa that they may actually be the last common ancestor of all the animals.

Protists are all eukaryotic -- meaning they single-celled organisms and have a cell nucleus that stores their DNA. They are one of the six kingdoms of life. They are the evolutionary bridge between bacteria and multi-celled organisms. Protists are often considered animal-like or plant-like because they behave similarly to multicellular organisms.

Protozoa is another name for animal-like protists. They were a dominant form of life on Earth in this period [evidence?]. While protozoans evolved early and have survived to the present day as unicellular organisms, they have undergone considerable evolutionary change. That many species must have become extinct as others appeared can be deduced from the limited fossil record of protozoans.Protozoa cannot make their own food, but instead must ingest other organisms for energy. Most reproduce asexually through mitosis, which involves the splitting of their cell into two identical copies. Some reproduce through meiosis, which is sexual reproduction. Seven phyla -- subdivisions of a kingdom -- of protists are protozoa.

A fundamental shift in protozoan taxonomy occurred in 1990, when American microbiologist Carl Woese and colleagues revolutionized the world of biology with the three-domain classification system of life. Based on sequences of rRNA (ribosomal RNA), Woese’s classification system revealed three major evolutionary groups of life on Earth. One is eukaryotic and two of which are prokaryotic – bacteria and Archaea. It is generally accepted that the Bacteria) are the most distant genetic group of the three.

Fungi

One of the most important eukaryotes are fungi. They are neither plant nor animal, but have their kingdom. In 2019 scientists reported the discovery of a fossilized fungus, from a billion years old named Ourasphairagiraldae. Found in the Canadian Arctic, it may have grown on land – ie rocks (Bonneville et al., 2020),

Fungi

1/2 Bya

400mya

360mya

Bioweathering

Fungi are capable of breaking down rock. All over the world, microbes destroy rocks to access precious nutrients like the iron locked inside. In Washington, D. C., researchers zoomed in on one particular microbe, the fungus Talaromyces flavus, to see just how this is done. The fungus obliterates its rocky environment using a mix of acid and mechanical force (Li et al., 2016). Up till then, we’d thought that fungi only contribute 1% to total ‘bioweathering’.

Henry Teng (Li 2016) watched T. flavus burrow into the mineral to extract essential nutrients, suggesting that fungal weathering could actually be 40%–50% of all bioweathering.”

Bioweathering is when the microbes get to work. There are also chemical and physical processes that weather rocks. Weathering

It was a tough half billion years, as the planet froze over halfway through – called ‘Snowball Earth’.

Snowball Earth

An explanation first proposed by American geobiologist J.L. Kirschvink suggests that Earth’s oceans and land surfaces were covered by ice from the poles to the Equator during at least two extreme cooling events between 2.4 billion and 580 million years ago.

Measurements of old rocks that preserved signs of Earth’s ancient magnetic field indicate that rocks known to be associated with the presence of ice were formed near the Equator. In addition, there is a 45-metre- (147.6-foot-) thick layer of manganese ore in the Kalahari Desert with an age corresponding to the end of the 2.4 billion-year “Snowball Earth” period; its deposition is thought to have been caused by rapid and massive changes in global climate as the worldwide covering of ice melted.

How did life on the surface survive this time?

Ediacaran

This period 635-538 Mya is called Ediacaran.. It took 15 years to be named after a range of hills in Australia,

Its biota were composed of enigmatic tubular and frond-shaped, mostly sessile, organisms. Mutli-cellular organisms spread.... .

The International Stratigraphic Commission. Geological ages are usually named after where the rocks were first found – eg Devonian from Devon in England. Cambrian rock was first found in Wales, Permian from Russia and Jurassic from Jura Alps.

Multicellular

Trace fossils of these organisms have been found worldwide, and represent the earliest known complex multicellular organisms.

In Antarctica, some scientists have explored these old organo-mineral interactions, like cyanobacteria-to-mineral, fungi-to-mineral, and lichen-to-mineral. The reactions involve the principles of organic matter stabilization strikingly similar to those known for modern full-scale soils of various climates.’

There were also signs of the first small worms (fifth of a millimetre) and a creature called ‘small spring animal’ named because it followed the frozen winter. These were the first creatures to have ‘bilateral symmetry’ – which all major groups of animals now possess. Bilateral symmetry is where similar anatomical parts are arranged on opposite side of a median axis – you can now divide side to side as well as front to back.

The ancestor of jellyfish and their relatives breaks away from the other and some animals evolve bilateral symmetry for the first time:, first side to side of median axis (left and right) now just top/bottom and front/back. Small worms called Acoela may be the closest surviving relatives of the first ever bilateral animal. It seems likely that the first bilateral animal was a kind of worm. Vernanimalculaguizhouena, which dates from around 600 million years ago. The animals with bilateral symmetry divide into the protostomes and deuterostomes, which go on to provide all the vertebrates. The group that breaks away from the main group of deuterostomes, eventually becomes the echinoderms (starfish, brittle stars, their relatives, sea urchins' and 'sea lilies' ) and two worm-like families called the hemichordates and Xenoturbellida The protostomes get legs some, others become various types of worms, while others the microscopic rotifers. The two can be distinguished by the way their embryos develop. It is thought the “missing link” or split between vertebrates (animals with backbones) and invertebrates (animals without backbones), occurred around during this time (The Conversation

Biofilms

Cyanobacteria ((ancient photosynthesising bacteria) often dominate aquatic ecosystems, where they form microbial mats and biofilms on clay-rich sediments, while other bacteria might play more prominent roles in soil formation and organic matter decomposition.
Along with cyanobacteria , many types of bacteria produce extracellular polymeric substances (EPS), which allow them to form biofilms on clay surfaces. These biofilms provide protection to bacterial colonies and help them survive in harsh conditions.
Bacteria in biofilms have enhanced abilities to resist environmental stresses, such as dehydration or toxic chemicals, making the biofilm-clay interaction important in soil and aquatic systems.

Bacteria and clay

Many bacteria can attach to clay particles due to the large surface area and negative charge of clays. Bacteria often have structures like fimbriae or flagella that help them adhere to surfaces like clay minerals.

Adsorption and Attachment:

The negatively charged surface of clay interacts with positively charged molecules on bacterial cell walls, allowing for electrostatic interactions. This process is common for various bacterial types, including aerobic and anaerobic bacter
Nutrient Exchange and Cycling:
Clays can adsorb nutrients, such as phosphorus, nitrogen, and trace metals, which bacteria can utilize for growth. Many bacteria can release organic acids, enzymes, or chelating compounds to solubilize these nutrients from clay surfaces, just like cyanobacteria.
The small spaces between clay particles can offer a microhabitat where bacteria can grow and thrive in relative safety.
This is particularly important for bacteria in extreme environments like deserts, polar regions, or deep subsurface sediments.

Many bacteria play a role in soil stabilization by binding clay particles together through biofilms or EPS production. These bacteria can help improve soil structure and reduce erosion, especially in environments like wetlands, riverbanks, or agricultural soils.

Specific bacterial relations with clay then

Nitrogen-Fixing Bacteria:
- Some free-living nitrogen-fixing bacteria, such as Azotobacter, also benefit from the presence of clay in soils, as clays can help retain moisture and nutrients necessary for their survival.
Sulfate-Reducing Bacteria (SRBs):
- SRBs, such as Desulfovibrio, can interact with clays to precipitate metal sulfides, which immobilizes toxic metals. This is important in anoxic environments (environments with little to no oxygen), where these bacteria play a key role in metal detoxification.
- These bacteria are commonly found in sediments where clays help create the anoxic conditions they require to thrive.
Iron-Reducing Bacteria:
- Geobacter and Shewanella are examples of iron-reducing bacteria that can use iron oxides in clay minerals as electron acceptors during their metabolic processes. This reduces the iron in clay minerals, which can alter the clay's properties and contribute to geochemical cycles.
- These bacteria are important in environments like wetland soils or deep subsurface sediments, where they contribute to iron cycling and mineral transformation.
Methanogenic Bacteria:
- In clay-rich, waterlogged soils, methanogenic archaea (a type of bacteria-like microorganism) thrive by producing methane gas during the breakdown of organic matter in anaerobic conditions.
- The presence of clay helps create the low-oxygen conditions necessary for methanogenesis and stabilizes the soil, promoting the growth of these microorganisms.

Underground Biofilms

Towards the end of this period – about 600mya – can be found further evidence and development of underground biofilms called Endoliths Due to various stresses on the surfaces of hard rocks the hidden niches inside them, turn out to provide more places for organisms to develop than habitats on the surface of rocks. While there would have always been the opportunity to occupy rock pores, the transformation of silicate rocks by organisms living in rocks (endolithic) is one of the possible pathways for the beginning of soils on Earth. This process led to the formation of soil-like bodies on rocks and im sediments. in situ and contributed to the rise of complexity in underground geosystems.

Some consider endolithic systems – underground structures - as the soil-like bodies, The word “soil” in English language is conventionally employed for the loose material, the term soloid (from Latin solum soil and Greek eîdos, likeness) was suggested to be applied to the endolithic systems formed in situ on hard rocks (Mergelov et al., 2018). As well as solid rock, there has always been rock debris, i.e., sediments, at the surface. Solids were probably the first protosoils on hard rocks and thus on terrestrial ground

During this long period, two key function were around at the end of this Ediacaran time. The first is the presence of biofilms, and the second was the 'nitrification' process by free-living bacteria. The first was to provide the vehicle for other organisms to spread, and the nitrification function was to feed plants for hundreds of millions of years to come, particularly when the soil developed. Half a billion years ago, many of the key metabolic processes that drive soil processes today were all there but not necessarily on the right order. We have rock weathering, and biofilm of life on the surface and underground. How does that lead to the structured soil we know today?

Late Ediacaran life, exclusively marine (McMohan 2021) biota, disappears suddenly 542mya (Narbonne 2005).

So let's have a look at when that biota recovers in the Cambrian explosion....

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