Soil Microbiology
Overview
By way of introduction microbes are a diverse range of microscopic organisms ranging from single celled to multicellular, and in some cases such as fungi, the fruiting body are macroscopic, but formed by microscopic organisms i.e. hyphae. Microbes are essential to life and can also improve the quality of life, humans are almost 50% human cells and 50% microbes, so who's really in charge? Humans or Microbes?
Soil Microbes
Image credit: Courtesy of Pacific Northwest National Laboratory.
Pseudomonas fluoroscens under UV light
Image credit: Michael Allsop
History of microbes
Archaea, bacteria, protozoa, fungi, algae, and viruses are all microbes, bacteria have been around for at least 3.5 billion years. They evolved from early simple celled organisms which had roamed the earth for hundreds of millions of years before, this divergent organism is known as the last universal common ancestor (LUCA)(Christian and McNeill, 2011), of which all life forms that have existed, do exist, and will exist have evolved from.
At this time in earth’s history the earth had cooled causing water to form, creating a habitat for life. However, the atmosphere was almost entirely composed of nitrogen, so conditions were harsh, and it is thought that early bacteria were like archaea which can survive in extreme environments. It was these bacteria that evolved into cyanobacteria which were estimated to have been present 2.7 billion years ago, this is of massive importance as it was them that started what is now a fundamental process to almost all living things on earth, photosynthesis.
What this led to was known as 'the oxygen holocaust`, this is because oxygen was highly toxic to bacteria, however, some survived and some 700 million years later the first eukaryotic cells evolved (Christian and McNeill, 2011). The atmosphere composition slowly rose to over 20% oxygen, giving way to aerobic microbes. These complex eukaryotic cells eventually led to the formation of red and green algae which occurred around 1.2 million years ago, this was then followed by the birth of fungi around 200 million years later (Wang, Kumar and Hedges, 1999). It wasn’t until 500 million years ago that the first multicellular organisms evolved which then gave way to the vast number of species and organisms that we bear witness to today.
A Microbe world:
Bacteria, Archaea, Fungi, Algae, Protozoa, and Viruses, soils have them all
Alongside fungi there are vast numbers of microbes competing against each other and also working together, bacteria can live in almost any habitat on earth but like fungi require nutrients to grow. This is so they can carry out binary fission, the mechanism by which a bacterium grows, by accumulating macromolecules in the cytoplasm, which assemble into cell structures (Madigan et al., 2015). In bacillus bacteria this is seen by elongation of the cell to double its original size, then it forms a septum and divides forming an identical replicate cell.
Viruses on the other hand, cannot replicate unless its virion is inside the cell of another organism, the virion structure is a protein shell known as the capsid that contains nucleic acid, once inserted inside the host cell it then replicates causing lytic infection (Gelderblom, 1996). Protozoa are single celled microbes that prefer moist habitats such as soil and water, this is likely due to the fact that they do not have hard cell walls like fungi, instead they have a plasma membrane that has cilia covering it, it encompasses the cytoplasm which contains micro and macro nucleus, and vacuoles.
Archaea are ancient microbes capable of living in extreme environments, they have been found to exist in hot springs and the ice caps in the artic, they can withstand high pressure environments. This is thought to be due to their cellular structure, they are similar in structure to bacteria, however lack peptidoglycan as do eukaryotes.
Algae mostly live in the aquatic biomes but can also survive in soil, they are perhaps the most important lifeforms on earth. Algae are used by fungi symbiotically to form lichens, however cyanobacteria are also utilised by fungi for the same reason. These topics will occur throughout the site to provide contrast and more detail of the range of microbes and microbial interactions within soil.
The Soil Food Web
Image credit: Soilfood web.com,(2018).
The Nitrogen Cycle
Image credit: U.S. Environmental Protection Agency [Public domain], via Wikimedia Commons
Ammonification
Ammonification is a process by which organic Nitrogen is converted into ammonium, which is then excreted into the soil where it becomes available for nitrification or assimilation. This process is carried out by bacteria and fungi, a few examples of bacteria are Streptomyces, bacillus, and pseudomonas (Li et al., 2014). Fungi break down decaying organic matter such as nitrogen, into inorganic matter. Water can then dissolve the ammonia that was created, hydrogen then bonds with the ammonia to form ammonium. This is important because most autotrophs cannot otherwise assimilate the ammonium ions.
Nitrification
Nitrification is a process where anaerobic nitrifying bacteria e.g. Nitrosomonas and Nitrobacter, convert ammonia and ammonium in to nitrate and nitrite. This is made possible due to the complex internal structure of their cells containing multiple enzymes useful in the oxidation process. Nitrifying bacteria are chemolithotroph organisms meaning they oxidise inorganic compounds to yield energy (Montes, 2016). This process is important as it provides useful compounds that plants can assimilate into their roots where they can use the energy.
Denitrification
Denitrification is the reverse to Nitrogen fixation, microbes convert nitrate and form it into nitrogen gas. This is carried out by bacteria and fungi, bacteria such as Pseudomonas aeruginosa and fungi such as Fusarium oxysporum can carry out denitrification. This is the last step in the nitrogen cycle as the microbes oxidise inorganic compounds returning them to the atmosphere, so the process can start again. These microorganisms are anaerobes (Skiba, 2008), meaning this process only occurs deep in the soil near the water table, arguably wetlands are an extremely important area for reducing nitrogen levels, due to it providing the perfect habitat for denitrifying bacteria and fungi.
Assimilation
Assimilation is the process where nitrate and ammonium are absorbed by plants where it is then transported to the leaves (Lam et al., 1996). This process may sound like its carried out by plants, but in fact it is possibly one of the most important microbial processes and it’s mostly thanks to fungi. The mutualistic/ symbiotic relationship between plants and fungi are in the roots(rhizosphere), the organism mycorrhiza is responsible for up to 80% of the nutrient uptake (Lehmann et al., 2015) of plants and trees (Finlay et al., 1988). Mycorrhiza is useful as a biofertilizer however it is more like a mini bio fertiliser factory taking in nutrients, packaging, and passing it on to its customers (the plants). This is the main talking point for the next few pages and so for now we will leave it here and pick it up on the next page.
Microbial action in the Nitrogen cycle
The nitrogen cycle consists of five parts of which microbes play key roles in all.
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Nitrogen fixation
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Ammonification
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Nitrification
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Denitrification
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Assimilation
Nitrogen fixation
Nitrogen fixation is a process where atmospheric nitrogen is converted to ammonia and other nitrogenous compounds, for it to be used by plants, nitrogen fixing bacteria convert gaseous nitrogen into solid state nitrogen. Nitrogen is an incredibly stable compound and so requires excessive energy to break the bonds such as a lightning strike. Humans have managed to do it industrially using the Haber process, however this process is extremely inefficient and bad for the environment. Symbiont microbes however have evolved a method to carry this out based on iron molybdenum nitrogenase an enzyme (Wurzburger et al., 2012) that can be carried out by a group of bacteria known as diazotrophs. Rhizobia are one of those bacteria, they are rod shaped, motile bacteria that live in symbiosis with the legumes of plant roots. It can also be carried out by non-symbiont microbes such as free living bacteria and/or blue-green algae (Alexander, 1977).
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Conclusion
This page aimed to show some of the important processes carried out by microbes using the nitrogen cycle as a backbone. This is due to the importance of the nitrogen cycle to all living organisms on earth, but also that this process is heavily dependent on microbes to carry it out. Microbes are fascinating and wonderfully diverse, some work alone, some work in groups creating symbiotic or mutualistic relationships where both parties can benefit from the specialised processes that each individual can complete.
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The processes of the nitrogen cycle are highly specialised, and the microbes that carry out these processes must be even more specialised. Over the course of hundreds of millions of years, microbes have evolved to fill niches that allow them to thrive in almost every habitat on earth. They do not complete each task e.g. nitrification and nitrogen fixation for the sake of the nitrogen cycle. They do it because they have adapted to survive off the compound they absorb, and it just so happens that what they excrete is then useful to another organism, and another, and so the cycle continues. Thus, the nitrogen cycle is made possible by the evolutionary desire to fill every niche, when resources are highly competed for you adapt to gain energy and survive from another source.
