Diversity Of Soil Organisms – Part 2

Prokaryota – Bacteria

1. Morphology
Bacteria are one of the two domains, along with Archaea, that include prokaryotic organisms. The domain Bacteria comprises microscopic organisms, single-celled or with the cells forming simple associations. Most bacteria are 0.2 micrometres (μm) in diameter and 2 – 8 μm in length. Bacteria have a variety of shapes: round or spherical (commonly known as cocci), rod shaped (bacilli) and spiral (spirilla). However, many bacteria can assume several shapes (pleomorphic). Depending on how the newly formed cells adhere to each other, bacterial arrangements include singles, pairs, chains and clusters. When bacteria are motile they have a flagellum for locomotion. The flagellum is a whip-like structure that can occur at one end, both ends, or all over the bacterial cell. Bacteria can live without oxygen (anaerobes) or depend on it to grow (aerobes). They can also be adapted to live either in the presence or absence of oxygen (facultative anaerobes). Some species of bacteria contain endospores or exospores. If you break down the term endospore, ‘endo-’ means ‘inside’ and‘-spore’ refers to the ‘dormant structure’, so the endospore is a structure of resistance formed inside the cell. By contrast, the exospores develop externally. Spores are a bacterial cell’s way of protecting itself against harsh changes in the environment or nutrient depletion. A spore protects the bacterial genetic material so that, when optimal conditions return, the bacterial cell can reform (germinate) and thrive again.

2. Taxonomy
Currently, there are 30 known and recognised phyla of bacteria. Highly diverse and abundant phyla in soil are Proteobacteria, Firmicutes, Actinobacteria and Cyanobacteria. However, some other phyla, such as Acidobacteria, can also be found in soil.

3. Microhabitats
Unlike eukaryotes, bacteria can be found in a wide range of environmental, chemical and physical conditions including extremes of pH, temperature and salinity. Many soil bacteria are beneficial to human economic activities and are necessary for environmental sustainability. Bacteria are part of chemical cycles during which they release essential elements for recycling. They also decompose dead organic matter and are the only microbes capable of biological nitrogen N2 fixation (see page 105). This is the ability to transform nitrogen (N2) from the atmosphere (about 80 % of the atmosphere is N2) into ammonium (NH4+) which is assimilated by eukaryotes, plants in particular. Bacteria can exist either as independent (free- living) organisms or as symbionts that depend on other organisms to live, subsisting either as mutualists, parasites or commensalists.

4. Diversity, abundance and biomass
Most microbial species (more than 90 % according to the current estimates), including bacteria, still remain unculturable (i.e. they cannot be grown in any culture medium in the laboratory). This means that we do not yet know what they look like or what functions they carry out. Advances in molecular techniques in the past 30 years have enabled us to understand more about these species by sequencing parts of their DNA. These advances have also allowed for the identification of new culturable species. Today there are approximately 2 800 genera comprising approximately 15 000 species of known bacteria. Soil microbial biomass is made up of bacteria, fungi and other microorganisms. This biomass represents 1 to 4 % of total soil carbon (up to three tonnes of carbon per hectare). The ratio of the size of bacterial to fungal biomass depends on soil properties and other environmental factors (e.g. soil pH, temperature and nutrient availability); for example, a 30-fold decrease in bacterial biomass was found when comparing high to low pH soils.

5. Bacterial phyla
In contrast to eukaryotic nomenclature, there is no official classification of prokaryotes because taxonomy remains a matter of scientific judgment and general agreement.
There are 30 phyla currently accepted by the LPSN. Other existing phyla of bacteria, which cannot currently be cultured in the laboratory are called candidate phyla. If these are included, the total number of phyla is 52


Ref: A Global Atlas of Soil Biodiversity p 33