Soil Microbial Biofilm Communities and Their Interactions


Department of Biotechnology, MS Ramaiah Institute of Technology, Bengaluru-560054, Karnataka, India


Microbial populations in the soil are diverse both at the functional and taxonomical levels (Schmidt and Waldron, 2015). This diversity is very critical to maintaining soil quality and also other soil inhabitants. Microbial flora of soil mostly consists of bacteria, fungi, algae, actinomycetes, and protozoa. Bacteria predominate soil microbial diversity and cany out important roles of nutrient cycling/biogeochemical cycling, which form the core of the functional ecosystem (Meliani et al., 2012). Microbial soil communities are essential for organic matter mineralization to maintain plant nutrition, growth, and development of a good ecosystem. Most of the fundamental microbial processes occur in the rhizosphere region. Various plant-microbe as well as microbe-microbe interactions occur in this region. There are various types of bacteria in the rhizosphere region of the soil which associate with plants. Some of them like Rhizobium sp., Agrobacterium sp. and Pseudomonas sp. occur predominantly in the soil and cany out most functions of plants like nitrogen fixation and soil bioremediation (Lakshmanan et al., 2012). Likewise, not only bacteria but fungi are also known to colonize plants and occupy the rhizosphere niche. The common and classic fungal species is mycorrhiza, which associates with plant roots. All these microbial populations, along with many others, are mostly known to occur as planktonic or free-floating organisms in most natural environments. Many bacterial species form structures called biofilm, thus associating and forming various types of interactions with plants and with one another in the rhizosphere region.



The development of a biofilm structure was observed for the fust time by Antony Van Leeuwenhoek in 1708, where he observed tissues colonized by microbial cells (Romling et al., 2014). Biofilms are structurally complex colonies of microorganisms that grow as surface-attached communities (Douterelo et al., 2014). Cluster of microbial cells develops 3D spatial arrangement on biotic/abiotic substrate to form biofilm (De Encreft et al.,

  • 2015). A matrix composed of exopolysaccharide (EPS) acts as a protective layer to the organisms residing within the biofilm (Burmolle et al., 2010). Biofilm formation is a natural mechanism for microorganisms to overcome unfavorable conditions (Lambert et al., 2014). Biofilms are ubiquitous and can be found in any environment like food, water, humans, and soil. They are part and parcel of our natural ecosystem involving aggregation of multiple species of microbes. The structure and architecture of biofilm are very complex, and thus it confers numerous advantages to the organism.

Biofilm systems of the environment consist of diverse species of bacteria that inhabit the soil, which is a perfect platform for multispecies biofilm formation (Ren et al., 2015). Biofilms are formed in stressful and unfavorable conditions. During biofilm formation, individual microbial species can interact through diverse signaling mechanisms and colonize the surface by adhering to it. The signaling mechanism between the species results in the development of a 3D mesh. The signaling mechanism also helps hi the production of EPS. There is always a high level of cooperation between the species because EPS produced by one cell is used by others within the biofilm (Xavier and Foster, 2007). EPS mostly acts as a bridge between the organism and the conditioning film (Kokare et al., 2009). The different phases of biofilm formation have been indicated pictorially (Figure 7.1). The first step of biofilm formation starts with the identification and adhesins where individual cells adhere strongly to the surface within 1-2 hours of colonization. Surface associations involve non-specific interactions through the production of cell signaling molecules. The adhered cells undergo growth and maturation. This phase involves the aggregation of adhered cells to form microcolonies through irreversible interactions. The fust two stages approximately take 2-3 hours. The last phase of biofilm detachment begins with sloughing, where individual cells disperse from the site of attachment and travel through to form new attachment sites. The presence of multiple species within a biofilm, thus confers added advantages to the resident microbes by offering resistance to biotic and abiotic stresses.

Pictorial representation of different stages in biofilm formation

FIGURE 7.1 Pictorial representation of different stages in biofilm formation.


Soil microflora is usually predominated by bacteria but is not limited only to them. They also consist of fungi, Blue-Green Algae (BGA), and protozoa. Multispecies bacteria present in the soil can interact among themselves or can associate with plants to form a biofilm. Polymicrobial biofilms/multispecies biofilms that are formed on leaf, root, or any other plant parts are indicated pictorially (Figure 7.2). Biofilms play a vital role in maintaining a stable ecosystem. Soil particles such as clay minerals and metal oxides strongly influence biofilm formation by soil microflora (Ma et al., 2017). Of the vast majority of soil microflora, bacteria like the nitrogen fixer Rhizobium sp., Agrobacterium sp., Pseudomonas sp., and Bacillus sp. are known to form a biofilm. Mushrooms like Pleurotus ostreatus; fungi like Penicillium sp., also form biofilms. The plant-microbial and microbial-microbial associations may result in different types of interactions between them as discussed in the following section.

Different regions of a plant that may be colonized by microbial populations in the soil

FIGURE 7.2 Different regions of a plant that may be colonized by microbial populations in the soil.

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