Soil microbiology
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 bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.
Up to 10 billion bacterial cells inhabit each gram of soil in and around plant roots, a region known as the rhizosphere. 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 surrounding environment.
Bacteria
and Archaea, 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.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 of bacteria growing in the soil. The more minerals that are found in area can result in a higher abundance of bacteria. These bacteria will also form aggregates which increases the overall health of the soil.
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 turning nitrite into nitrate, which is also known as oxidation. 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.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 nitrogen into nitrogen-containing compounds that can be used by plants. Autotrophic bacteria derive their energy by making their own food through oxidation, like the Nitrobacter species, rather than feeding on plants or other organisms. These bacteria are responsible for nitrogen fixation. The amount of autotrophic bacteria is small compared to heterotrophic bacteria, but are very important because almost every plant and organism requires nitrogen in some way.Actinomycetes
are soil microorganisms. They are a type of bacteria, but they share some characteristics with fungi that are most likely a result of convergent evolution due to a common habitat and lifestyle.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
Fungi
Fungi are abundant in soil, but bacteria are more abundant. Fungi are important in the soil as food sources for other, larger organisms, pathogens, beneficial symbiotic relationships with plants or other organisms and soil health. Fungi can be split into species based primarily on the size, shape and color of their reproductive spores, which are used to reproduce. 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 growth of fungi, because most fungi consume organic matter for nutrition. 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.Algae
can make their own nutrients through photosynthesis. Photosynthesis converts light energy to chemical energy that can be stored as nutrients. For algae to grow, they must be exposed to light because photosynthesis requires light, so algae are typically distributed evenly wherever sunlight and moderate moisture is available. Algae do not have to be directly exposed to the Sun, but can live below the soil surface given uniform temperature and moisture conditions. Algae are also capable of performing nitrogen fixation.Types
Algae can be split up into three main groups: the Cyanophyceae, the Chlorophyceae and the bacillariophyceae. The Cyanophyceae contain chlorophyll, which is the molecule that absorbs sunlight and uses that energy to make carbohydrates from carbon dioxide and water and also pigments that make it blue-green to violet in color. The Chlorophyceae usually only have chlorophyll in them which makes them green, and the bacillariophyceae contain chlorophyll as well as pigments that make the algae brown in color.Blue-green algae and nitrogen fixation
Blue-green algae, or Cyanophyceae, are responsible for nitrogen fixation. The amount of nitrogen they fix depends more on physiological and environmental factors rather than the organism's abilities. These factors include intensity of sunlight, concentration of inorganic and organic nitrogen sources and ambient temperature and stability.Protozoa
are eukaryotic organisms 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. Protozoa can be split up into three categories: flagellates, amoebae and ciliates.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 flagellates are found mostly in soil. Flagellates that contain chlorophyll 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.Ciliates
are the largest of the protozoa group, and move by means of short, numerous cilia that produce beating movements. Cilia resemble small, short hairs. They can move in different directions to move the organism, giving it more mobility than flagellates or amoebae.Phages
, viruses that infect bacteria, are some of the most understudied organisms, despite being considered one of the most abundant organisms present in microbial communities. Although understudied, soil phages are significant contributors to soil health and affect microbial diversity through ecological and evolutionary roles. Viral richness, or the abundance of phages in an environment, is affected by seasonal changes, soil moisture content, physical location, and the presence and growth of plants. Bacterial abundance in soil communities is an additional factor in viral richness, with an increase in bacterial abundance associated with increased phage abundance.In the rhizosphere phage affect nutrient content through their impact on bacteria. Lytic phages affect host populations which impact bacterial processes like carbon, nitrogen, sulfur, and phosphorus cycling in soil. Although not fully understood there have been cases of temperate phages affecting bacterial populations by mediating horizontal gene transfer. This process allows phages to affect the genetic diversity of their host potentially improving fitness. Bacteriophages may also be involved in plant pathogenesis through the killing of important bacteria that prevent infection in plants. The lytic phage ΦGP100 is known to kill Pseudomonas fluorescens, which produces antifungals, thus opening plants up to fungal infections.