Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient cyanobacteria (also called blue-green algae) came about on Earth's oceans. These bacteria could fix carbon by photosynthesis, fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere and nitrogen into the soil. This led to more advanced microorganisms, which were important because they effected soil structure and fertility. Soil microorganisms can be classified as bacteria (including cyanobacteria and actinomycetes), archaea, fungi, algae, slime molds and protozoa. Each of these groups has characteristics that define them and their functions in soil.
Up to 10 billion culturable bacterial cells inhabit each gram of soil in and around plant roots, a region known as the rhizosphere, which is a hotspot of microbial diversity, and in particular the rhizoplane. In 2011, a team detected more than 33,000 bacterial and archaeal species on sugar beet roots.
The composition of the rhizobiome can change rapidly in response to changes in the biotic and abiotic environment. The diversity of microorganisms in soils is dependant on pH, soil texture, organic matter content, plant community composition, and contaminants such as heavy metals.
Bacteria
Bacteria and archaea (initially classified as bacteria), the smallest organisms in soil apart from viruses, are prokaryotic. They are the most abundant microorganisms in the soil, and serve many important purposes, including nitrogen fixation and organic matter decomposition for bacteria. Soil archaea are still poorly known but they could play a significant role in nitrification and methanogenesis.
Some bacteria can colonize minerals in the soil and help influence weathering and the breaking down of these minerals. The overall composition of the soil can determine the amount and distribution of bacteria growing in it. The more clay minerals that are found in an area can result in a higher abundance of bacteria living as biofilms at their surface. Soil bacteria also contribute to the formation of soil aggregates, which increases the overall health of the soil.
Apart from the rhizosphere, where bacterial activity is stimulated by rhizodeposition and root exudation, most bacteria of the bulk soil are in a quiescent state, in the form of bacterial colonies embedded in a polysaccharidic matrix covered with clay platelets, and resistant to drought. These bacterial microaggregates may remain in this state of quiescence for a long time, until being reached by exudates from growing root tips or the mucus of burrowing earthworms. Accordingly, sugar-rich lixiviates (e.g. after a pollen rain) may also stimulate respiration, reproduction and dissemination of resting soil bacteria, exerting a priming effect on soil microbial activity.
In the mycorhizosphere mycorrhiza helper bacteria form symbiotic associations with mycorrhizal fungi, assisting mycorrhiza formation or enhancing their functions.
Biochemical processes
One of the most distinguished features of bacteria is their biochemical versatility. A bacterial genus called Pseudomonas can metabolize a wide range of chemicals and fertilizers. In contrast, another genus known as Nitrobacter can only derive its energy by oxidizing nitrite to nitrate. The genus Clostridium is an example of bacterial versatility because it, unlike most species, can grow in the absence of oxygen, respiring anaerobically. Several species of Pseudomonas, such as Pseudomonas aeruginosa are able to respire both aerobically and anaerobically, using nitrate as the terminal electron acceptor.
Archaea are particularly adapted to chemically and physically harsh environments, with their unique membrane lipids, and their methanogenic pathways which incorporate a number of coenzymes unique to this microbial group.
Nitrogen fixation
Nitrogen is often the most limiting nutrient in soil and water. Bacteria are responsible for the process of nitrogen fixation, which is the conversion of atmospheric dinitrogen into nitrogen-containing compounds (such as ammonia) that can be used by plants. Some nitrogen-fixing bacteria (e.g. cyanobacteria) are autotroph and derive their carbon from the atmosphere through photosynthesis while others are heterotroph and derive their carbon either from soil organic matter (e.g. Clostridium) of from a symbiotic host (e.g. Rhizobium). Some soil chemotroph bacteria derive their energy through the oxidation of nitrite ions, which they transform in nitrate ions, like Nitrobacter. These bacteria are not nitrogen-fixing microorganisms but contribute to nitrification, an important step in the nitrogen cycle.
Actinomycetes
Actinomycetes (or Actinobacteria) are bacteria, but they share some characteristics with fungi that are most likely a result of convergent evolution due to a common habitat and lifestyle. They display ambiguous species boundaries due to commonness of horizontal gene transfer. Although largely hypothetical, horizontal gene transfer from actinomycetes to ancestral fungi cannot be excluded, which could also explain the various morphological and biochemical features they have in common.
Similarities to fungi
Although they are members of the Bacteria kingdom, many actinomycetes share characteristics with fungi, including shape and branching properties, spore formation and secondary metabolite production. The mycelium branches in a manner similar to that of fungi. They form aerial mycelium as well as conidia. Their growth in liquid culture occurs as distinct clumps or pellets, rather than as a uniform turbid suspension as in bacteria.
Antibiotics
One of the most notable characteristics of the actinomycetes is their ability to produce antibiotics. Streptomycin, neomycin, erythromycin and tetracycline are only a few examples of these antibiotics. Streptomycin is used to treat tuberculosis and infections caused by certain bacteria and neomycin is used to reduce the risk of bacterial infection during surgery. Erythromycin is used to treat certain infections caused by bacteria, such as bronchitis, pertussis (whooping cough), pneumonia and ear, intestine, lung, urinary tract and skin infections.
Fungi
Fungi may be outnumbered by bacteria in cell counts, but they can contribute greater biomass and respiration rate in some soil types. Fungi decay plant detritus, in particular wood, contribute to soil aggregation, are important as food sources for other, larger soil organisms, as soil-borne pathogens, or conversely as beneficial plant symbionts (e.g. mycorrhizae) and more generally they are important for soil health. Fungi can be split into species based primarily on the size, shape and color of their reproductive spores, visible only under the microscope, a difficult task often needing the use of plate or chamber cultures, now facilitated and improved by molecular methods. Most of the environmental factors that influence the growth and distribution of bacteria and actinomycetes also influence fungi. The quality as well as quantity of organic matter in the soil has a direct correlation to the community composition of fungi. Compared with bacteria, fungi are relatively benefitted by acidic soils. Fungi also grow well in dry, arid soils because fungi are aerobic, or dependent on oxygen, and the higher the moisture content in the soil, the less oxygen is present for them. Many fungi are able to escape water to grow in the air, and some are even able to derive their water directly from the atmosphere through hydrophilic outer surfaces of their cell walls.
Algae
Algae can make their own carbon through photosynthesis, i.e. are autotrophs. Photosynthesis converts light energy to chemical energy that can be stored as starch. For algae to grow, they must be exposed to light because photosynthesis requires light, so soil algae are typically distributed evenly wherever sunlight and moderate moisture is available, and not far from the surface. Algae do not have to be directly exposed to the sun, but can live below the soil surface given uniform temperature and moisture conditions, and are capable of facultative heterotrophy in the presence of easily available carbon sources (e.g. glucose). Synergistic interactions with rhizosphere bacteria in the promotion of plant growth have been demonstrated in Chlorella vulgaris.
Types
Soil algae can be split up into Chlorophyceae and Bacillariophyceae (diatoms). The Chlorophyceae usually only have chlorophyll as pigment which makes them green, while diatoms contain chlorophyll as well as other pigments such as the carotenoid fucoxanthin that make them golden-brown in color.
Protozoa
Protozoa are eukaryotic unicellular organisms (protists) that were some of the first microorganisms to reproduce sexually, a significant evolutionary step from duplication of spores, like those that many other soil microorganisms depend on, allowing silencing of deleterious mutations. Protozoa can be split up into three categories: flagellates, amoebae and ciliates. A large number of soil protozoa feed on bacteria, others feed on both bacteria and fungi, while some species are strictly mycophagous, and other soil protozoa are saprophagous, feeding on humus particles. In the rhizosphere protozoa are involved in a microbial loop, a positive feedback process involving growing roots, their exudates, the bacteria feeding on them, and bacterivorous protozoa which liberate in a plant-available form the nutrients entrapped in microbial biomass.
Flagellates
Flagellates are the smallest members of the protozoa group, and can be divided further based on whether they can participate in photosynthesis. Nonchlorophyll-containing flagellates are not capable of photosynthesis because chlorophyll is the green pigment that absorbs sunlight. These heterotrophic flagellates are found mostly in soil where their number may occasionally be as high as several millions per gram of soil. Flagellates that contain chlorophyll (e.g. Euglena) typically occur in aquatic conditions. Flagellates can be distinguished by their flagella, which is their means of movement. Some have several flagella, while other species only have one that resembles a long branch or appendage.
Amoebae
Amoebae are larger than flagellates and move in a different way. Amoebae can be distinguished from other protozoa by their slug-like properties and pseudopodia. A pseudopodium or "false foot" is a temporary obtrusion from the body of the amoeba that helps pull it along surfaces for movement or helps to pull in food. The amoeba does not have permanent appendages and the pseudopodium is more of a slime-like consistency than a flagellum. Naked amoebae move freely in water-filled pore spaces and in water films surrounding roots and aggregates, while testate amoebae are partly encapsulated in a chitinous or mineral shell which protects them from desiccation when fluid water retreats. Testate amoebae may remain encysted until better conditions are fulfilled for feeding and reproduction. By their abundance, shape variety and the diversity of their adapatations to moisture variation they are good indicators of climate, making them prominent tools in the reconstruction of past environmental changes, from hundreds of years to millennia.
Ciliates