Bacteria 500-400mya

We have seen bacteria had been around for over a billon years, as with the example of Azotobacter. Their extent and impact would have increased a lot betwen 1/2 b & 400mya. Throughout our soil story of the various organisms living underground, we will look at how the various plants and creatures relate with other and how they evolved over time. Bacteria are always part of that story. They were probably carried across land in the water films, making that water into biofilms - or 'slime' as we may call it. They would have been followed by the organisms whiich ate then, like nemtaodes.

Bacteria

Bacteria belong in a group – along with Archaea - called Prokaryotes. This distinguishes them from the vast majority of organisms called 'eukaryotes'.

Motility

Their other important property is to be able to glide over surfaces. The mechanisms responsible for bacterial gliding motility have been a mystery for almost 200 years, and still a matter of speculation. Gliding bacteria move actively over surfaces by a process that does not involve flagella – a hairlike organelle that drives many small creatures. Gliding bacteria are diverse and abundant in many environments. There appear to be two sorts of bacterial gliding motility. Myxococcus xanthus “social gliding motility” and Synechocystis gliding are similar to bacterial ‘twitching motility’ (McBride, 2001)

Myxococcus gliding

Their ability to evolve may explain why they survived, whereas a similar archaic group of the time has not developed. We know that bacteria are good at evolving, as witnessed by the increased resistance of bacteria to antibiotics, now becoming a serious threat to our medical capabilities. Perhaps the answer for future antibiotics lies in the soil.

Nitrogen Fixing

The Leeuwenhoek Lecture in 1992 (Postgate, 1992) honoured the man who first saw bacteria, saying:
“It is a text-book truism that the few types of nitrogen fixer which exist have, until this century, sustained the nitrogen economy of the biosphere for some half a billion years, compensating for the loss of fixed nitrogen brought about by de-nitrifying bacteria.”

How

The bacteria have enzymes, including one called ‘nitrogenase’, which act as catalysts to break the very strong bond between the two atoms of nitrogen that make airborne nitrogen molecules. The bacteria use a lot of the energy molecule ATP (Adenosine Triphosphate) to do this. The strength of that bond, and the energy needed to break it is reflected in the amount of energy now used to make nitrogen fertilisers. In the Haber process, vast amounts of energy, usually in the form of gas or oil, are used to break the bond, and that is having serious implications for the world, as we will see later.

Why no 'nodule-fixers'?

The Lecturer continued by asking: “Why has the property not spread to higher organisms, notably plants, which are the primary recipients of newly fixed nitrogen”. The plant world generally (except legumes - below) relies on free living nitrogen-fixing bacteria.

I have heard many times, and have known a good few research friends say: "If only we could create grain crops that have nitrifying bacteria in their roots, our food problems would be over". The answer to his question is the Holy Grail of much agricultural science research for decades. His answer was that it must be something to do with the means of gene exchange – common in bacteria but rare elsewhere. Since that lecture, we have found there is indeed widespread incidence of 'conjugative' gene transfer', that it is the rule among bacteria, rather than a rarity.

My question is different from the Leeuwenhoek Lecturer’s. Why was it so much later – over several hundred years later - that ‘nodule-forming’ nitrogen-fixing bacteria developed within plants? These nodule N-fixers bacteria – like one called Rhizobium – make nodules in the roots of certain plants, that we generally call legumes. We will see when we get there how two very old processes came together. These plants, like beans and peas, account for about 10% of plants grown as crops. My answer is that if we understood better the how and why this happened when it did, we may be nearer that Grail.

Spelling this out a bit, why were these free-living nitrogen-fixing bacteria quite adequate for several hundred million years, but not enough later on. There must have been some environmental conditions that led to the development of these bacteria within some plants. We shall see, but we'll have to wait a few hundred million years.

Phosphate Solubisating Bacteroa (PSBs)

Bacteria like Azotobacter can also ‘solubise’ phosphate. This means they can help turn phosphates trapped in substrate rocks and minerals into ‘soluble’ forms that plants can absorb. Phosphate (P) is vital for plant growth as it provides the building block for the energy molecules that help build plants – and eventually animals. Nitrogen helps build vital components like DNA, while phosphates provide the energy in the form of ATP – Adenosine Triphosphate. ATP is in the main power house of cells. the mitochondria, which are thought to have originally been bacteria, moving from free-living to enclosed around 1.5bya.(Meyer et al., 2018; Boguszewska et al., 2020)

NPK

N & P are two of the most important macronutrients in plants as spelt out in NPK (Nitrogen Phosphate and Potassium) fertilisers. 400 mya the mechanisms were in place to trap nitrogen from air and utilise the phosphates from rocks to provide the building blocks for plants. Two of the three macronutrients for life were available at this time. Thanks to bacteria they provided enough plant growth for several hundred million years.

Streptomyces

Many of the antibiotics used today come from the soil and are made by a group of bacteria called Streptomyces. They originated about 450 million years ago (Chater, 2006) and found as filaments living on plant remains. They reproduce by sending up specialized aerial branches, which form spores and this is coordinated with the secretion of antibiotics, which may protect the colony against invading bacteria during aerial growth. When conditions are good – ie damp - they produce spores that spread the bacteria.

Strep

In nursing, we use something called Streptomycin – is it related? We called it ‘Strep’ and knew Streptomycin has saved thousands of lives. It is one of the most important sources of antibiotics known to science – the WHO say “it is critically important for human medicine. We used it to treat tuberculosis and brucellosis, it didn’t half make a difference.”

Anti-biotic

These bacteria also produce chemicals for defence – against fungi, viruses, but especially against other bacteria – anti- biotics. This array of defences helps Streptomyces species to compete with other microorganisms that come in contact. In early 1940s, ‘they’ found the antibiotic effects of Streptomyces, after extracting from a ‘well manured’ soil in New Jersey Agricultural Station. But they had to find ways to multiply it up away from the ‘well manured’ soil, as that would ‘not have been welcomed in the hospital.’ As Streptomycin was isolated from a microbe discovered on New Jersey soil, and because of its activity against tuberculosis and Gram-negative organisms, and in recognition of both the microbe and the antibiotic in the history of New Jersey, Streptomyces griseus was nominated and became an Official New Jersey state microbe”.

There are increasing concerns about the discovery of new antibiotics, and since the early discoveries there has been a dearth. Until 2015, when a team found 25 new antibiotics. And their secret source? “The researchers, at the Northeastern University in Boston, Massachusetts, turned to the source of nearly all antibiotics - soil. This is teeming with microbes, but only 1% can be grown in the laboratory. The team created a ‘subterranean hotel’ for bacteria. One bacterium was placed in each "room" and the whole device was buried in soil.”[19].

Earth smell

The name given to the characteristic odor of rain after it rains, especially following a dry spell, is petrichor. The word petrichor comes from the Greek, Petros, meaning 'stone' + ichor, the fluid flowing in the veins of the gods in Greek mythology. The rain doesn’t actually provide any scent itself; rather, the impact of the drops on rocks and soil splashes an oily, bacteria-made substance into the air, creating that distinctive aroma now known by the name of petrichor. Although we had smelt it for years Petrichor was first described in 1964 (Bear & Thomas 1964) They went on to isolate the smell as geosmin and show that the petrichor did not aid seed germination (Bear & Thomas 1965). That did not matter 400mya - as there were no seeds then. Has the earth smelt like this for half a billion years?

Spores & pores

Soil-dwelling bacteria Streptomyces, when faced with unfavourable conditions grow spores that can be dispersed to new, more favourable conditions, enabling the bacteria to survive. It is these spores that are released when it rains. When water droplets fall onto a dry, porous surface, air gets trapped underneath as bubbles, which quickly rupture and shoot aerosol streams upwards. Bacterial spores are small enough to be carried in the aerosol. If the porous surface becomes saturated, the pores fill with water and bubbles will not form. Only recently, bacteria have been found to communicate to other distant Streptomyces when a new pore opens up in the soil. The presence of pores explains why petrichor is commonly smelled after a brief rain shower but not after a lengthy downpour. Famously its smell is the characteristic smell detected the world over when soils get wet after a dry spell, the ‘earth smell’.

The word Geosmin stems from the Greek words geo (earth) and osme (smell). Geosmin is made during spore production all over the world – just like the particular bacteria that release it. The actual chemical is a sort of alcohol with two carbon rings and a functional group called a ‘hydroxyl’ (or ‘OH’). That makes it alcohol.

Geosmin

Experiments reveal that springtails were attracted to the Streptomyces bait in the field and lab. In the lab this involved inserting springtails one by one at 20-minute intervals – to avoid herd responses – into a Y-tube to observe if they followed the scent of geosmin and other VOCs. The study finds that geosmin and 2-MIB are chemical signals that guide springtails to Streptomyces as a privileged food source. Usually this kills other organisms such as nematodes and fruit flies, but which springtails can withstand because they have a battery of enzymes which detoxify the antibiotics produced by Streptomyces. In return, springtails help disperse Streptomyces spores in two ways: by defecation and by distribution of spores that stick to their bodies. The study found that the spores survived passage through the springtail gut to give rise to new colonies of Streptomyces.

Only in the last year or so, researchers in Norwich England found that the tips of the antennae of springtails can directly sense geosmin (Becher, 2020). This means that springtails could have sprung along the water following the bacteria as they glided through the water film. This relation between bacteria and springtails is crucial in early soil development as we shall soon see.

Detection

Is geosmin the only chemical in soil and are there other sorts of chemical signaling going on down there? It seems Strep is the only bacterium to produce geosmin.

Geosmin produces the musty smell sometimes released into water supplies, when lots of the bacteria die, making the water taste awful’. ‘Geosmin ends up in fish. But it is broken down by acid – hence the vinegar on your fish and chips’. ‘French wine growers have become concerned that it is giving some of their young wines a musty smell – distinct from their normal smell, so wrecking the wine’.

It is geosmin that gives beet that charcateristic earthy smell. (Hansen et al 2021)

Camels can detect its smell miles away – so helping lead them to wet ground, and an oasis.

We too - humans - can detect Geosmin at very small concentrations; the equivalent of a teaspoon spread throughout a large swimming pool. There are two variants of this chemical, but it is the ‘negative’ isomer which smells 10X more than the other. We can detect it at levels below 0.01 Parts Per Billion. Put it another way, we use Parts Per Million (PPM) to alert us to pesticide traces in our food. That means we are 100,000 times more sensitive to this chemical than those toxins which may damage us.” Yaksha wondered whether we could detect such small quantities for the same reason as camels.

Bacteria up to this point were 'free-living'. They had already evolved two processes key to soil evolution - and present-day growing. - 'nitrogen-fixing' and 'phosphate solubisation'.

How bacteria related with Plants

Animals

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