A microbial consortium or microbial community, is two or more

bacterial Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

microbial A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

groups living

symbiotically Symbiosis (from Ancient Greek, Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different Organism, biological organisms, be it Mutualism (biolog ...

. Consortiums can be

endosymbiotic An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...

or ectosymbiotic, or occasionally may be both. The protist ''

Mixotricha paradoxa ''Mixotricha paradoxa'' is a species of protozoan that lives inside the gut of the Australian termite species ''Mastotermes darwiniensis''. It is composed of five different organisms: three bacterial ectosymbionts live on its surface for locom ...

'', itself an endosymbiont of the ''

Mastotermes darwiniensis ''Mastotermes darwiniensis'', common names giant northern termite and Darwin termite, is a termite species found only in northern Australia. It is the most primitive extant termite species. Evolutionary significance This species shows uncanny s ...

'' termite, is always found as a consortium of at least one endosymbiotic

coccus A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Bacteria are categorized based on their shapes into three classes: cocci (spherical-shaped), bacillus (rod-shaped) and spiral ( of whi ...

, multiple ectosymbiotic species of

flagellate A flagellate is a cell or organism with one or more whip-like appendages called flagella. The word ''flagellate'' also describes a particular construction (or level of organization) characteristic of many prokaryotes and eukaryotes and their ...

ciliate The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagellum, eukaryotic flagella, but are in general shorter and present in much larger numbers, with a ...

bacteria, and at least one species of helical ''

Treponema ''Treponema'' is a genus of spiral-shaped bacteria. The major treponeme species of human pathogens is ''Treponema pallidum'', whose subspecies are responsible for diseases such as syphilis, bejel, and yaws. ''Treponema carateum'' is the cause o ...

'' bacteria that forms the basis of ''Mixotricha'' protists' locomotion. The concept of a consortium was first introduced by

Johannes Reinke Johannes Reinke (February 3, 1849 – February 25, 1931) was a German botanist and philosopher who was a native of Ziethen, Lauenburg. He is remembered for his research of benthic marine algae. Academic background Reinke studied botany with h ...

in 1872, and in 1877 the term

symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...

was introduced and later expanded on. Evidence for symbiosis between microbes strongly suggests it to have been a necessary precursor of the evolution of

land plants The Embryophyta (), or land plants, are the most familiar group of green plants that comprise vegetation on Earth. Embryophytes () have a common ancestor with green algae, having emerged within the Phragmoplastophyta clade of green algae as siste ...

and for their transition from algal communities in the sea to land.

Overview

Microbial consortia naturally formed on the roots of Arabidopsis thaliana

Microbes hold promising application potential to raise the efficiency of bioprocesses when dealing with substances that are resistant to decomposition. A large number of microorganisms have been isolated based on their ability to degrade recalcitrant materials such as lignocellulose and polyurethanes. In many cases of degradation efficiency, microbial consortia have been found superior when compared to single strains. For example, novel thermophilic consortia of Brevibacillus spp. and Aneurinibacillus sp. have been isolated from the environment to enhance polymer degradation. Two approaches exist to obtain microbial consortia involving either (i) a synthetic assembly from scratch by combining several isolated strains, or (ii) obtainment of complex microbial communities from environmental samples. For the later, enrichment process is often used to get the desired microbial consortia. For instance, a termite gut-derived consortium showing a high xylanase activity was enriched on raw wheat straw as the sole carbon source, which was able to transform lignocellulose into carboxylates under anaerobic conditions. Relatively high diversity levels are still observed despite the use of enrichment steps when working from environmental samples, likely due to the high functional redundancy observed in environmental microbial communities, being a key asset of their functional stability. This intrinsic diversity may stand as a bottleneck in attempts to move forward to practical application due to (i) potential negative correlation with efficiency, (ii) real microbial cheaters whose presence has no impacts on degradation, (iii) security threats posed by the presence of known or unknown pathogens, and (iv) risks of losing the properties of interest if supported by rare taxa. CC-BY icon

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Utilization of microbial consortia with less complexity, but equal efficiency, can lead to more controlled and optimized industrial processes. For instance, a large proportion of functional genes were remarkably altered and the efficiency of diesel biodegradation was increased by reducing the biodiversity of a microbial community from diesel-contaminated soils. Therefore, it is crucial to find reliable strategies to narrow down the diversity toward optimized microbial consortia gained from environmental samples. A reductive-screening approach was applied to construct effective minimal microbial consortia for

lignocellulose Lignocellulose refers to plant dry matter (biomass), so called lignocellulosic biomass. It is the most abundantly available raw material on the Earth for the production of biofuels. It is composed of two kinds of carbohydrate polymers, cellulose a ...

degradation based on different metabolic functional groups. Additionally, artificial selection approaches (dilution, toxicity, and heat) have been also employed to obtain bacterial consortia. Among them, dilution-to-extinction has already proven its efficiency for obtaining functional microbial consortia from seawater and rumen liquor . Dilution-to-extinction is expected to provide more advantages compared to conventional isolation and assembly as it (i) generates many microbial combinations ready to be screened, (ii) includes strains from the initial microbial pool that might be lost due to cultivation/isolation biases, and (iii) ensures that all microbes are physically present and interacting spontaneously.

Examples

Microbialites

Microbialite Microbialite is a benthic sedimentary deposit made of carbonate mud (particle diameter < 5 μm) that is formed with the mediation of microbes. The constituent carbonate mud is a type of

Pseudomonadota Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...

(formerly Proteobacteria),

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...

sulphate-reducing bacteria Sulfate-reducing microorganisms (SRM) or sulfate-reducing prokaryotes (SRP) are a group composed of sulfate-reducing bacteria (SRB) and sulfate-reducing archaea (SRA), both of which can perform anaerobic respiration utilizing sulfate () as termina ...

diatom A diatom (Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group comprising sev ...

s, and

microalgae Microalgae or microphytes are microscopic algae invisible to the naked eye. They are phytoplankton typically found in freshwater and marine systems, living in both the water column and sediment. They are unicellular species which exist indiv ...

. These

microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

produce adhesive compounds that

cement A cement is a binder, a chemical substance used for construction that sets, hardens, and adheres to other materials to bind them together. Cement is seldom used on its own, but rather to bind sand and gravel ( aggregate) together. Cement mix ...

sand and join other rocky materials to form mineral "

microbial mat A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria and archaea, or bacteria alone. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces, but a few survive in deserts. ...

s". The mats build layer by layer, growing gradually over time.

Rhizosphere

Although various studies have shown that single microorganisms can exert beneficial effects on plants, it is increasingly evident that when a microbial consortium — two or more interacting microorganisms — is involved, additive or synergistic results can be expected. This occurs, in part, due to the fact that multiple species can perform a variety of tasks in an ecosystem like the plant root

rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microor ...

. Beneficial mechanisms of plant growth stimulation include enhanced nutrient availability,

phytohormone Plant hormone (or phytohormones) are signal molecules, produced within plants, that occur in extremely low concentrations. Plant hormones control all aspects of plant growth and development, from embryogenesis, the regulation of organ size, pat ...

modulation,

biocontrol Biological control or biocontrol is a method of controlling pests, such as insects, mites, weeds, and plant diseases, using other organisms. It relies on predation, parasitism, herbivory, or other natural mechanisms, but typically also invo ...

, biotic and

abiotic In biology and ecology, abiotic components or abiotic factors are non-living chemical and physical parts of the environment that affect living organisms and the functioning of ecosystems. Abiotic factors and the phenomena associated with them under ...

stress tolerance) exerted by different microbial players within the rhizosphere, such as plant-growth-promoting bacteria (PGPB) and fungi such as ''

Trichoderma ''Trichoderma'' is a genus of fungi in the family Hypocreaceae that is present in all soils, where they are the most prevalent culturable fungi. Many species in this genus can be characterized as opportunistic avirulent plant symbionts. This ref ...

'' and ''

Mycorrhizae A mycorrhiza (from Greek μύκης ', "fungus", and ῥίζα ', "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas) is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plant ...

''.

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The diagram on the right illustrates that rhizosphere microorganisms like plant-growth-promoting bacteria (PGPB),

arbuscular mycorrhizal fungi An arbuscular mycorrhiza (AM) (plural ''mycorrhizae'', a.k.a. ''endomycorrhiza'') is a type of mycorrhiza in which the symbiont fungus (''AM fungi'', or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. (N ...

(AMF), and fungi from the genus Trichoderma spp. can establish beneficial interactions with plants, promoting plant growth and development, increasing the plant defense system against pathogens, promoting nutrient uptake, and enhancing tolerance to different environmental stresses. Rhizosphere microorganisms can influence one another, and the resulting consortia of PGPB + PGPB (e.g., a nitrogen-fixing bacterium such as ''

Rhizobium ''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants. The bacteria colonize plant cells ...

'' spp. and ''

Pseudomonas fluorescens ''Pseudomonas fluorescens'' is a common Gram-negative, rod-shaped bacterium. It belongs to the ''Pseudomonas'' genus; 16S rRNA analysis as well as phylogenomic analysis has placed ''P. fluorescens'' in the ''P. fluorescens'' group within the genu ...

''), AMF + PGPB, and Trichoderma + PGPB may have synergetic effects on plant growth and fitness, providing the plant with enhanced benefits to overcome biotic and abiotic stress. Dashed arrows indicate beneficial interactions between AMF and Trichoderma.

Keratin degradation

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owing to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of

biotic interaction In ecology, a biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interaction ...

Keratin Keratin () is one of a family of structural fibrous proteins also known as ''scleroproteins''. Alpha-keratin (α-keratin) is a type of keratin found in vertebrates. It is the key structural material making up scales, hair, nails, feathers, ho ...

s are recalcitrant fibrous materials with

cross-linked In chemistry and biology a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural ...

components, representing the most abundant proteins in

epithelial cell Epithelium or epithelial tissue is one of the four basic types of animal tissue, along with connective tissue, muscle tissue and nervous tissue. It is a thin, continuous, protective layer of compactly packed cells with a little intercellula ...

s. They are estimated to have considerable economic value after

biodegradation Biodegradation is the breakdown of organic matter by microorganisms, such as bacteria and fungi. It is generally assumed to be a natural process, which differentiates it from composting. Composting is a human-driven process in which biodegrada ...

. An efficient keratinolytic microbial consortium (KMCG6) was previously enriched from an environmental sample through cultivation in keratin medium. Despite reducing the microbial diversity during the enrichment process, KMCG6 still included several

OTUs Otus may refer to: * Otus (education), a K-12 educational technology company * HMS ''Otus'', two ships in the Royal Navy * ''Otus'' (bird), genus of owls * Otus (mythology), giant in Greek mythology, brother of Ephialtes, one of Aloadae * Otus o ...

scattered amongst seven bacterial genera. In 2020 Kang et al., using a strategy based on enrichment and dilution-to-extinction cultures, extracted from this original consortium (KMCG6) a simplified microbial consortia (SMC) with fewer species but similar keratinolytic activity. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample. An appropriate dilution regime (10⁹) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity

assay An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of a ...

s demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. As shown in the diagram on the right, the workflow for this study included four steps: (1) Enrichment for the desired traits e.g., keratinolytic activity by selection in keratin medium, where keratin is the sole carbon source. This process was evaluated by functional assessments (cell density, enzymes activity, and ratio of the residual substrate) and compositional analysis. (2) Serial dilutions were conducted to the enriched effective microbial consortia. Six dilutions were prepared, from dilution 10² to 10¹⁰ with 24 replicates. The dissimilarity between dilutions was evaluated by Euclidean distance calculation based on functional assessment criteria. (3) Library construction was done from the dilution offering the optimal dissimilarity among replicates. Dilution 10⁹ was selected to construct the SMC library in this case. (4) Selection of the most promising SMC is based on functional and compositional characterization.

Human health

Consortia are commonly found in humans, with the predominant examples being the skin consortium and the intestinal consortium which provide protection and aid in human nutrition. Additionally, bacteria have been identified as existing within the brain (previously believed to be sterile), with

metagenomic Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

evidence suggesting the species found may be enteric in origin. As the species found appear to be well-established, have no discernible impact on human health, and are species known to form consortia when found in the gut, it is highly likely they have also formed a symbiotic consortium within the brain.

Synthetic microbial consortia

Synthetic microbial consortia (commonly called co-cultures) are multi-population systems that can contain a diverse range of microbial species, and are adjustable to serve a variety of industrial and ecological interests. For

synthetic biology Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad ran ...

, consortia take the ability to engineer novel cell behaviors to a population level. Consortia are more common than not in nature, and generally prove to be more robust than monocultures. Just over 7,000 species of bacteria have been cultured and identified to date. Many of the estimated 1.2 million bacteria species that remain have yet to be cultured and identified, in part due to inabilities to be cultured axenically. When designing synthetic consortia, or editing naturally occurring consortia, synthetic biologists keep track of pH, temperature, initial metabolic profiles, incubation times, growth rate, and other pertinent variables.

Notes

{{microorganisms Microorganisms