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]

Contents

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

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. Microbial consortia naturally formed on the roots of Arabidopsis thaliana.webp
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.

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

Microbialites

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

Rhizosphere microbial consortia Rhizosphere microbial consortia.webp
Rhizosphere microbial consortia 

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

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

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

Painting of a cross-section through an Escherichia coli bacterium, a chemoheterotrophic bacterium often used in synthetic microbial consortia. Escherichia-coli-bacterium(1).tif
Painting of a cross-section through an Escherichia coli bacterium, a chemoheterotrophic bacterium often used in 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

Notes

  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. CC-BY icon.svg 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.
  9. ↑ Shong, Jasmine; Jimenez Diaz, Manuel Rafael; Collins, Cynthia H. (2012). "Towards synthetic microbial consortia for bioprocessing". Current Opinion in Biotechnology. 23 (5): 798–802. doi:10.1016/j.copbio.2012.02.001. PMID   22387100.
  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.
  11. ↑ Cregut, Mickael; Bedas, M.; Durand, M.-J.; Thouand, G. (2013). "New insights into polyurethane biodegradation and realistic prospects for the development of a sustainable waste recycling process". Biotechnology Advances. 31 (8): 1634–1647. doi:10.1016/j.biotechadv.2013.08.011. PMID   23978675.
  12. ↑ Mikesková, H.; Novotný, Č.; Svobodová, K. (2012). "Interspecific interactions in mixed microbial cultures in a biodegradation perspective". Applied Microbiology and Biotechnology. 95 (4): 861–870. doi:10.1007/s00253-012-4234-6. PMID   22733114. S2CID   7420481.
  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. 1 2 3 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. 1 2 3 4 5 6 7 8 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. CC-BY icon.svg Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  24. 1 2 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. 1 2 3 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 . CC-BY icon.svg 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. 1 2 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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<span class="mw-page-title-main">Microbiome</span> Microbial community assemblage and activity

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.

Bioremediation of petroleum contaminated environments is a process in which the biological pathways within microorganisms or plants are used to degrade or sequester toxic hydrocarbons, heavy metals, and other volatile organic compounds found within fossil fuels. Oil spills happen frequently at varying degrees along with all aspects of the petroleum supply chain, presenting a complex array of issues for both environmental and public health. While traditional cleanup methods such as chemical or manual containment and removal often result in rapid results, bioremediation is less labor-intensive, expensive, and averts chemical or mechanical damage. The efficiency and effectiveness of bioremediation efforts are based on maintaining ideal conditions, such as pH, RED-OX potential, temperature, moisture, oxygen abundance, nutrient availability, soil composition, and pollutant structure, for the desired organism or biological pathway to facilitate reactions. Three main types of bioremediation used for petroleum spills include microbial remediation, phytoremediation, and mycoremediation. Bioremediation has been implemented in various notable oil spills including the 1989 Exxon Valdez incident where the application of fertilizer on affected shoreline increased rates of biodegradation.

<span class="mw-page-title-main">Synthetic microbial consortia</span>

Synthetic microbial consortia are multi-population systems that can contain a diverse range of microbial species, and are adjustable to serve a variety of industrial, ecological, and tautological interests. For synthetic biology, consortia take the ability to engineer novel cell behaviors to a population level.

<span class="mw-page-title-main">Plant microbiome</span>

The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".

<span class="mw-page-title-main">Plant holobiont</span>

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a holobiont. Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments.

<span class="mw-page-title-main">Plastic degradation by marine bacteria</span> Ability of bacteria to break down plastic polymers

Plastic degradation in marine bacteria describes when certain pelagic bacteria break down polymers and use them as a primary source of carbon for energy. Polymers such as polyethylene(PE), polypropylene (PP), and polyethylene terephthalate (PET) are incredibly useful for their durability and relatively low cost of production, however it is their persistence and difficulty to be properly disposed of that is leading to pollution of the environment and disruption of natural processes. It is estimated that each year there are 9-14 million metric tons of plastic that are entering the ocean due to inefficient solutions for their disposal. The biochemical pathways that allow for certain microbes to break down these polymers into less harmful byproducts has been a topic of study to develop a suitable anti-pollutant.

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