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Microbial consortium

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A microbial consortium or microbial community, is two or more bacterial or microbial groups living symbiotically.[1][2] Consortiums can be endosymbiotic or ectosymbiotic, or occasionally may be both. The protist Mixotricha paradoxa, itself an endosymbiont of the Mastotermes darwiniensis termite, is always found as a consortium of at least one endosymbiotic coccus, multiple ectosymbiotic species of flagellate or ciliate bacteria, and at least one species of helical Treponema bacteria that forms the basis of Mixotricha protists' locomotion.[3]

The concept of a consortium was first introduced by Johannes Reinke in 1872,[4][5] and in 1877 the term symbiosis 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 and for their transition from algal communities in the sea to land.[6]

Overview

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Microbial consortia naturally formed
on the roots of Arabidopsis thaliana
Scanning electron microscopy pictures of root surfaces from natural A. thaliana populations showing the complex microbial networks formed on roots.
a) Overview of an A. thaliana root (primary root) with numerous root hairs. b) Biofilm-forming bacteria. c) Fungal or oomycete hyphae surrounding the root surface. d) Primary root densely covered by spores and protists. e, f) Protists, most likely belonging to the Bacillariophyceae class. g) Bacteria and bacterial filaments. h, i) Different bacterial individuals showing great varieties of shapes and morphological features.[7]

Microbes hold promising application potential to raise the efficiency of bioprocesses when dealing with substances that are resistant to decomposition.[8][9] A large number of microorganisms have been isolated based on their ability to degrade recalcitrant materials such as lignocellulose and polyurethanes.[10][11] In many cases of degradation efficiency, microbial consortia have been found superior when compared to single strains.[12] For example, novel thermophilic consortia of Brevibacillus spp. and Aneurinibacillus sp. have been isolated from the environment to enhance polymer degradation.[13]

Two approaches exist to obtain microbial consortia involving either (i) a synthetic assembly from scratch by combining several isolated strains,[14] or (ii) obtainment of complex microbial communities from environmental samples.[15] For the later, enrichment process is often used to get the desired microbial consortia.[16][17][18] 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.[19]

Relatively high diversity levels are still observed despite the use of enrichment steps when working from environmental samples,[18] likely due to the high functional redundancy observed in environmental microbial communities, being a key asset of their functional stability.[20][21] This intrinsic diversity may stand as a bottleneck in attempts to move forward to practical application due to (i) potential negative correlation with efficiency,[22] (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.[23]

Utilization of microbial consortia with less complexity, but equal efficiency, can lead to more controlled and optimized industrial processes.[24] 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.[25] 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 degradation based on different metabolic functional groups.[24] Additionally, artificial selection approaches (dilution, toxicity, and heat) have been also employed to obtain bacterial consortia.[26] Among them, dilution-to-extinction has already proven its efficiency for obtaining functional microbial consortia from seawater and rumen liquor .[27][28][29] 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.[30][23]

Examples

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Microbialites

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Microbialites are lithified microbial mats that grow in benthic freshwater and marine environments. Microbialites are the earliest known fossilised evidence of life, dating back 3.7 billion years.[citation needed] Today modern microbialites are scarce, and are formed mainly by Pseudomonadota (formerly Proteobacteria), cyanobacteria, sulphate-reducing bacteria, diatoms, and microalgae.[citation needed] These microorganisms produce adhesive compounds that cement sand and join other rocky materials to form mineral "microbial mats". The mats build layer by layer, growing gradually over time.[citation needed]

Rhizosphere

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Rhizosphere microbial consortia [31]

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. Beneficial mechanisms of plant growth stimulation include enhanced nutrient availability, phytohormone modulation, biocontrol, biotic and abiotic stress tolerance) exerted by different microbial players within the rhizosphere, such as plant-growth-promoting bacteria (PGPB) and fungi such as Trichoderma and Mycorrhizae.[31]

The diagram on the right illustrates that rhizosphere microorganisms like plant-growth-promoting bacteria (PGPB), arbuscular mycorrhizal fungi (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 spp. and Pseudomonas fluorescens), 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.[31]

Keratin degradation

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Workflow of enrichment and dilution-to-extinction cultures to select simplified microbial consortia (SMC) for keratin degradation.[23]

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 interactions.[23]

Keratins are recalcitrant fibrous materials with cross-linked components, representing the most abundant proteins in epithelial cells.[32] They are estimated to have considerable economic value after biodegradation.[33] An efficient keratinolytic microbial consortium (KMCG6) was previously enriched from an environmental sample through cultivation in keratin medium.[18] Despite reducing the microbial diversity during the enrichment process, KMCG6 still included several OTUs scattered amongst seven bacterial genera.[23]

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.[23] 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 assays 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.[23]

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.[23]

Human health

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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 evidence suggesting the species found may be enteric in origin.[34][35] 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.[36]

Synthetic microbial consortia

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Painting of a cross-section through an Escherichia coli bacterium, a chemoheterotrophic bacterium often used in synthetic microbial consortia.
Main article: 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, 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.[37] 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.[38] 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.[37]

See also

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Notes

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  1. ^ Madigan, M; Bender, K; Buckley, D; Sattley, W; Stahl, D (2019). Brock biology of microorganisms (Fifteenth, Global ed.). New York, NY: Pearson. p. 173. ISBN 9781292235103.
  2. ^ Mark, Martin (2009-04-27). "Happy Together… Life of the Bacterial Consortium Chlorochromatium aggregatum". Small Things Considered - The Microbe Blog. American Society for Microbiology. Archived from the original on 2009-05-01. Retrieved 2012-01-11. Consortia are assemblages of different species of microbes in physical (and sometimes intricate biochemical) contact with one another, and are implicated in biological processes ranging from sewage treatment to marine nitrogen cycling to metabolic processes within the rumen.
  3. ^ Thompson, William Irwin (1991). Gaia 2 : emergence : the new science of becoming. Hudson, NY: Lindisfarne Press. pp. 51–58. ISBN 9780940262409.
  4. ^ Reinke, Johannes 1872. Ueber die anatomischen Verhältnisse einiger Arten von Gunnera L. Nachrichten von der Königl. Gesellschaft der Wissenschaften und der Georg-Augusts-Universität zu Göttingen 9: 100–108.
  5. ^ Kull, Kalevi 2010. Ecosystems are made of semiosic bonds: Consortia, umwelten, biophony and ecological codes. Biosemiotics 3(3): 347–357.
  6. ^ Delaux, Pierre-Marc; Radhakrishnan, Guru V.; Jayaraman, Dhileepkumar; Cheema, Jitender; Malbreil, Mathilde; Volkening, Jeremy D.; Sekimoto, Hiroyuki; Nishiyama, Tomoaki; Melkonian, Michael (2015-10-27). "Algal ancestor of land plants was preadapted for symbiosis". Proceedings of the National Academy of Sciences of the United States of America. 112 (43): 13390–13395. Bibcode:2015PNAS..11213390D. doi:10.1073/pnas.1515426112. PMC 4629359. PMID 26438870.
  7. ^ Hassani, M.A., Durán, P. and Hacquard, S. (2018) "Microbial interactions within the plant holobiont". Microbiome, 6(1): 58. doi:10.1186/s40168-018-0445-0. Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  8. ^ Subashchandrabose, Suresh R.; Ramakrishnan, Balasubramanian; Megharaj, Mallavarapu; Venkateswarlu, Kadiyala; Naidu, Ravi (2011). "Consortia of cyanobacteria/Microalgae and bacteria: Biotechnological potential". Biotechnology Advances. 29 (6): 896–907. doi:10.1016/j.biotechadv.2011.07.009. PMID 21801829.
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  10. ^ Brown, Margaret E.; Chang, Michelle CY (2014). "Exploring bacterial lignin degradation". Current Opinion in Chemical Biology. 19: 1–7. doi:10.1016/j.cbpa.2013.11.015. PMID 24780273.
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  13. ^ Skariyachan, Sinosh; Patil, Amulya A.; Shankar, Apoorva; Manjunath, Meghna; Bachappanavar, Nikhil; Kiran, S. (2018). "Enhanced polymer degradation of polyethylene and polypropylene by novel thermophilic consortia of Brevibacillus SPS. And Aneurinibacillus sp. Screened from waste management landfills and sewage treatment plants". Polymer Degradation and Stability. 149: 52–68. doi:10.1016/j.polymdegradstab.2018.01.018.
  14. ^ Skariyachan, Sinosh; Patil, Amulya A.; Shankar, Apoorva; Manjunath, Meghna; Bachappanavar, Nikhil; Kiran, S. (2018). "Enhanced polymer degradation of polyethylene and polypropylene by novel thermophilic consortia of Brevibacillus SPS. And Aneurinibacillus sp. Screened from waste management landfills and sewage treatment plants". Polymer Degradation and Stability. 149: 52–68. doi:10.1016/j.polymdegradstab.2018.01.018.
  15. ^ Skariyachan, Sinosh; Setlur, Anagha Shamsundar; Naik, Sujay Yashwant; Naik, Ashwini Amaresh; Usharani, Makam; Vasist, Kiran S. (2017). "Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions". Environmental Science and Pollution Research. 24 (9): 8443–8457. doi:10.1007/s11356-017-8537-0. PMID 28188552. S2CID 9776975.
  16. ^ Luo, Fei; Devine, Cheryl E.; Edwards, Elizabeth A. (2016). "Cultivating microbial dark matter in benzene-degrading methanogenic consortia". Environmental Microbiology. 18 (9): 2923–2936. doi:10.1111/1462-2920.13121. PMID 26549712.
  17. ^ Burniol-Figols, Anna; Varrone, Cristiano; Le, Simone Balzer; Daugaard, Anders Egede; Skiadas, Ioannis V.; Gavala, Hariklia N. (2018). "Combined polyhydroxyalkanoates (PHA) and 1,3-propanediol production from crude glycerol: Selective conversion of volatile fatty acids into PHA by mixed microbial consortia". Water Research. 136: 180–191. doi:10.1016/j.watres.2018.02.029. PMID 29505919.
  18. ^ a b c Kang, Dingrong; Herschend, Jakob; Al-Soud, Waleed Abu; Mortensen, Martin Steen; Gonzalo, Milena; Jacquiod, Samuel; Sørensen, Søren J. (2018). "Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity". Bioresource Technology. 270: 303–310. doi:10.1016/j.biortech.2018.09.006. PMID 30236907.
  19. ^ Lazuka, Adèle; Auer, Lucas; o'Donohue, Michael; Hernandez-Raquet, Guillermina (2018). "Anaerobic lignocellulolytic microbial consortium derived from termite gut: Enrichment, lignocellulose degradation and community dynamics". Biotechnology for Biofuels. 11: 284. doi:10.1186/s13068-018-1282-x. PMC 6191919. PMID 30356893.
  20. ^ Shade, Ashley; Peter, Hannes; Allison, Steven D.; Baho, Didier L.; Berga, Mercè; Bürgmann, Helmut; Huber, David H.; Langenheder, Silke; Lennon, Jay T.; Martiny, Jennifer B. H.; Matulich, Kristin L.; Schmidt, Thomas M.; Handelsman, Jo (2012). "Fundamentals of Microbial Community Resistance and Resilience". Frontiers in Microbiology. 3: 417. doi:10.3389/fmicb.2012.00417. PMC 3525951. PMID 23267351.
  21. ^ Awasthi, Ashutosh; Singh, Mangal; Soni, Sumit K.; Singh, Rakshapal; Kalra, Alok (2014). "Biodiversity acts as insurance of productivity of bacterial communities under abiotic perturbations". The ISME Journal. 8 (12): 2445–2452. doi:10.1038/ismej.2014.91. PMC 4260711. PMID 24926862.
  22. ^ Banerjee, Samiran; Kirkby, Clive A.; Schmutter, Dione; Bissett, Andrew; Kirkegaard, John A.; Richardson, Alan E. (2016). "Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil". Soil Biology and Biochemistry. 97: 188–198. doi:10.1016/j.soilbio.2016.03.017.
  23. ^ a b c d e f g h Kang, Dingrong; Jacquiod, Samuel; Herschend, Jakob; Wei, Shaodong; Nesme, Joseph; Sørensen, Søren J. (2020). "Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures". Frontiers in Microbiology. 10: 3010. doi:10.3389/fmicb.2019.03010. PMC 6968696. PMID 31998278. Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  24. ^ a b Puentes-Téllez, Pilar Eliana; Falcao Salles, Joana (2018). "Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation". Microbial Ecology. 76 (2): 419–429. doi:10.1007/s00248-017-1141-5. PMC 6061470. PMID 29392382.
  25. ^ Jung, Jaejoon; Philippot, Laurent; Park, Woojun (2016). "Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms". Scientific Reports. 6: 23012. Bibcode:2016NatSR...623012J. doi:10.1038/srep23012. PMC 4789748. PMID 26972977.
  26. ^ Lee, Duu-Jong; Show, Kuan-Yeow; Wang, Aijie (2013). "Unconventional approaches to isolation and enrichment of functional microbial consortium – A review". Bioresource Technology. 136: 697–706. doi:10.1016/j.biortech.2013.02.075. PMID 23566469.
  27. ^ Ho, Kuo-Ling; Lee, Duu-Jong; Su, Ay; Chang, Jo-Shu (2012). "Biohydrogen from lignocellulosic feedstock via one-step process". International Journal of Hydrogen Energy. 37 (20): 15569–15574. doi:10.1016/j.ijhydene.2012.01.137.
  28. ^ Hoefman, Sven; Van Der Ha, David; De Vos, Paul; Boon, Nico; Heylen, Kim (2012). "Miniaturized extinction culturing is the preferred strategy for rapid isolation of fast-growing methane-oxidizing bacteria". Microbial Biotechnology. 5 (3): 368–378. doi:10.1111/j.1751-7915.2011.00314.x. PMC 3821679. PMID 22070783.
  29. ^ Sosa, Oscar A.; Gifford, Scott M.; Repeta, Daniel J.; Delong, Edward F. (2015). "High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures". The ISME Journal. 9 (12): 2725–2739. doi:10.1038/ismej.2015.68. PMC 4817625. PMID 25978545.
  30. ^ Roger, Fabian; Bertilsson, Stefan; Langenheder, Silke; Osman, Omneya Ahmed; Gamfeldt, Lars (2016). "Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality". Ecology. 97 (10): 2716–2728. doi:10.1002/ecy.1518. PMID 27859115.
  31. ^ a b c Santoyo, Gustavo; Guzmán-Guzmán, Paulina; Parra-Cota, Fannie Isela; Santos-Villalobos, Sergio de los; Orozco-Mosqueda, Ma. del Carmen; Glick, Bernard R. (2021). "Plant Growth Stimulation by Microbial Consortia". Agronomy. 11 (2): 219. doi:10.3390/agronomy11020219. Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  32. ^ Coulombe, Pierre A.; Omary, M.Bishr (2002). "'Hard' and 'soft' principles defining the structure, function and regulation of keratin intermediate filaments". Current Opinion in Cell Biology. 14 (1): 110–122. doi:10.1016/s0955-0674(01)00301-5. PMID 11792552.
  33. ^ Korniłłowicz-Kowalska, Teresa; Bohacz, Justyna (2011). "Biodegradation of keratin waste: Theory and practical aspects". Waste Management. 31 (8): 1689–1701. doi:10.1016/j.wasman.2011.03.024. PMID 21550224.
  34. ^ Pennisi, Elizabeth (7 May 2020). "Meet the 'psychobiome': the gut bacteria that may alter how you think, feel, and act". Science Magazine. Retrieved 12 December 2020.
  35. ^ Rettner, Rachel (15 November 2018). "Bacteria May Live (Harmlessly) in Your Brain". livescience.com. Live Science. Retrieved 12 December 2020.
  36. ^ Roberts, R. C.; Farmer, C. B.; Walker, C. K. (6 November 2018). "The human brain microbiome; there are bacteria in our brains!". Psychiatry and Behavioral Neurobio., Univ. Of Alabama, Birmingham, Birmingham, AL. 2018 Neuroscience Meeting Planner. (Program No. 594.08). Retrieved 12 December 2020.
  37. ^ a b Hays, Stephanie G.; Ducat, Daniel C. (14 February 2014). "Engineering cyanobacteria as photosynthetic feedstock factories". Photosynthesis Research. 123 (3): 285–295. doi:10.1007/s11120-014-9980-0. PMC 5851442. PMID 24526260.
  38. ^ Stewart, Eric J. (2012-08-15). "Growing Unculturable Bacteria". Journal of Bacteriology. 194 (16): 4151–4160. doi:10.1128/JB.00345-12. PMC 3416243. PMID 22661685.
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