application of microbial genetics in agriculture
Vandenkoornhuyse P, Mahe S, Ineson P, Staddon P, Ostle N, Cliquet JB, Francez AJ, Fitter AH, Young JPW (2007) Active root inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. (3-0) Cr. This is not surprising, as the survival and activity of microbes in any soil system face a monumental task of competing with the myriad of microbes naturally adapted to that same soil. ISME J. It is now increasingly evident that plants employ fine-tuned mechanisms to shape the structure and function of their microbiome, with different genotypes of the same plant species growing in the same soil yet associating with distinct microbial communities (Berendsen et al., 2012). Biochem. In: Kalia V (eds) Microbial applications, vol. Therefore, designing a microbial consortium that carefully weighs and evaluates the relationship between inoculants and the resident microbiome would substantially improve the plant growth-promoting potential and resilience of agricultural biologicals to boost plant growth. Environ. Hydrobiologia 764:259–270. (2010). (2007). When the earliest plants extended their roots into primordial soils, they encountered a habitat already teeming with bacterial and fungal life (Bulgarelli et al., 2013; Kemen, 2014). doi: 10.1105/tpc.19.00385, Priyadharsini, P., and Muthukumar, T. (2016). Res. Front. Naito, M., Desirò, A., González, J. Plant beneficial microorganisms have been preserved and maintained for a long time in a series of ex situ repositories across the globe, for their potential applications in sustainable agriculture. Microbiol. 12:263. doi: 10.1038/nrmicro3218, Craven, K. D., and Ray, P. (2019). Critically analyze the primary literature doi: 10.1016/j.soilbio.2015.05.007. doi: 10.1016/j.crvi.2015.02.001, Fernandez, A. L., Sheaffer, C. C., Wyse, D. L., Staley, C., Gould, T. J., and Sadowsky, M. J. Can. Additionally, arbuscular mycorrhizae have been reported to increase the relative abundance of Firmicutes, Streptomycetes, Comamonadaceae, and Oxalobacteraceae inhabiting the mycorrhizosphere (Offre et al., 2007; Nuccio et al., 2013). 1:926. (1974). Can J Microbiol 47:793–800. Genetic engineering is used in the production of drugs, human gene therapy, and the development of improved plants (2). Biological fertilizer/ Biofertilizer. Sci Rep 6:28084. Rend. Soil Sci. Ecol. Environ. Since the early 1800s, the United States Department of Agriculture has recommended the use of certain rhizobacteria to improve nitrogen fertility in leguminous crops (Schneider, 1892). doi: 10.1371/journal.pgen.1004283, Bonfante, P., and Desirò, A. While these beneficial microorganisms can impart considerable benefits to plant growth and fitness, they are typically documented in simple, one-on-one studies, often conducted in sterile soils in greenhouse conditions. Surv. There is an urgent need to understand and explore new microbes, their biological activities, genetic makeup and further opportunities for utilizing them. doi: 10.1016/j.plaphy.2020.02.039, Yergeau, E., Bell, T. H., Champagne, J., Maynard, C., Tardif, S., Tremblay, J., et al. Sharma SK, Saini S, Verma A, Sharma PK, Lal R, Roy M, Singh UB, Saxena AK, Sharma AK (2017) National agriculturally important microbial culture collection in the global context of microbial culture collection centres. In any case, these intriguing fungi and their seemingly unlimited host range provide a novel symbiosis that could be used in a broad variety of cropping systems. Plant growth-promoting bacteria: mechanisms and applications. Bacteria from native soil in combination with arbuscular mycorrhizal fungi augment wheat yield and biofortification. Credit for graduation will not be allowed for more than one of the following: Gen 260, 313, 320 and Biol 313 and 313L. Fahrig L, Baudry J, Brotons L, Burel FG, Crist TO, Fuller RJ, Sirami C, Siriwardena GM, Martin JL (2011) Functional landscape heterogeneity and animal biodiversity in agricultural landscapes. Curr Opin Microbiol 11:442–446. doi: 10.1094/phyto-63-511. (1973), the authors have shown soil to become disease suppressive after mono-culturing wheat over time. Unfortunately, the agronomic utility of these fungi is hampered by the paucity of strains available, the large majority isolated from Australian orchids. Microbial Genomics Program Microorganisms dominate the planet in terms of total biomass, species diversity, and metabolic range and include pathogens and microbes that benefit higher organisms. various applications of bioinformatics in various fields and impact of bioinformatics in Medicine, Microbial Genome Application and Agriculture. Biochem. Kabaluk JT, Ericsson JD (2007) Seed treatment increases yield of field corn when applied for wireworm control. (Cross-listed with GEN). 9:859. doi: 10.3389/fmicb.2018.00859, HoÈgberg, P., Nordgren, A., Buchmann, N., Taylor, A. F., Ekblad, A., HoÈgberg, M. N., et al. The study and comparison of entire genomes, including the complete set of genes and their nucleotide sequence and organization, is called genomics. doi: 10.1007/s11104-012-1361-x, Banerjee, S., Schlaeppi, K., and van der Heijden, M. G. (2018). Bamisile BS, Dash CK, Akutse KS, Keppanan R, Wang L (2018) Fungal endophytes: beyond herbivore management. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Environ. Am Phytopathol Soc 71:642–644. (2010). Mole. However, studies of natural populations suggest that groups of microbes with distinct function niches play pivotal roles in adhering and desorbing inorganic nutrients to physical surfaces, as well as breaking down organic residues and incorporating them into the soil (Lakshmanan et al., 2014; Finkel et al., 2017; Kumar and Dubey, 2020). doi: 10.1016/0038-0717(94)00205-f, Jeffries, P., and Rhodes, L. H. (1987). Whitton BA (2012) Ecology of Cyanobacteria II. The application of microbial genetics to understanding pathogenesis will be included. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Beyond positively affecting soil C and increasing the diversity of such beneficial fungi as arbuscular mycorrhiza, clover as a cover crop is often reported to suppress the relative abundance of pathogenic fungi (Benitez et al., 2016). Microbes Environ. The USA lags behind other agricultural nations in banning harmful pesticides. (2019). doi: 10.1111/1365-2435.12952, Timmusk, S., Behers, L., Muthoni, J., Muraya, A., and Aronsson, A.-C. (2017). 76, 226–239. The microorganisms are then grown on an industrial scale to synthesize products such as insulin, vaccines, and biodegradable polymers. Sci. 17, 478–486. The Minor in Plant, Animal and Microbial Biotechnology is available as an elective to students who are enrolled in Bachelor of Science degree programs with majors in animal science, biosystems engineering, fisheries and wildlife, food science, forestry, horticulture, and plant, soil and microbial sciences. Received: 29 October 2020; Accepted: 02 December 2020;Published: 21 December 2020. 15, 1870–1881. 74, 1–97. Freire JRJ, Kolling I (1986) World culture collections of, Gallegos-Robles MA, Morales-Loredo A, Alvarez-Ojeda G, Vega PA, Chew MY, Velarde S, Fratamico P (2008) Identification of. Microbiol. doi: 10.1007/s11557-014-0983-1, Offre, P., Pivato, B., Siblot, S., Gamalero, E., Corberand, T., Lemanceau, P., et al. Design of synthetic bacterial communities for predictable plant phenotypes. In addition to being the world’s largest agricultural producers and exporters, the EU, Brazil, United States, and China also are some of the world’s largest pesticide users – each using 827 million, 831 million, 1.2 billion, and 3.9 billion pounds of pesticides, respectively, in 2016 (Donley, 2019). This is demonstrated in the findings of Bazghaleh et al. (2018). Am. Chu Q, Sha Z, Nakamura T, Oka N, Osaki M, Watanabe T (2016) Differential responses of soybean and sorghum growth, nitrogen uptake, and microbial metabolism in the rhizosphere to cattle manure application: A rhizobox study. Similarly, a huge diversity of plant pathogens including bacteria and fungi have been isolated and preserved to be used as type specimens to breed disease-resistant crop varieties. 3, 137–141. Understanding and exploiting plant beneficial microbes. Engin. Hereditary processes in microorganisms are analogous to those in multicellular organisms. PLoS Biol e2001793:15. Now, plant-associated fungal and bacterial stains from various plant species are being isolated, which will provide in the near future an inestimable resource for assembling taxonomically defined microbial communities with increasing complexity. Upadhyay SK, Singh DP, Saikia R (2009) Genetic diversity of plant growth promoting rhizobacteria isolated from rhizospheric soil of wheat under saline condition. (2020). Rev. Soil is a vastly heterogeneous growth medium, providing a wide spectrum of ecological niches for microorganisms that enable diverse strains to coexist and form complex microbial communities. Beneficial features of plant growth-promoting rhizobacteria for improving plant growth and health in challenging conditions: A methodical review. Fungal Ecol 2(4):149–159. (2019). The importance of the microbiome of the plant holobiont. doi: 10.1890/13-0616.1. Environ. 27, 591–598. Who lives in a fungus? Dimkpa C, Weinand T, Asch F (2009) Plant-rhizobacteria interactions alleviate abiotic stress conditions. PLoS biology 16:e2003962. 74, 1181–1192. Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Microbiol. The next-generation sequencing technologies have exhibited that only a small portion of microorganisms could be cultivated until now. Chithrashree, Udayashankar AC, Chandra Nayaka S, Reddy MS, Srinivas C (2011) Plant growth-promoting rhizobacteria mediate induced systemic resistance in rice against bacterial leaf blight caused by. Jetiyanon J, Kloepper JW (2002) Mixtures of plant growth-promoting rhizobacteria for induction of systemic resistance against multiple plant diseases. Deploying microbes to improve agriculture productivity is an extremely attractive approach that is non-transgenic and can be viewed collectively as the extended plant genome. Plant Stress Tolerance 163, 69–84. Tran H, Kruijt M, Raaijmakers JM (2008) Diversity and activity of biosurfactant-producing. Synthetic biology approaches to engineering the nitrogen symbiosis in cereals. For example, an âinsect protectionâ gene (Bt) has been inserted into several crops - corn, cotton, and potatoes - to give farmers new tools for integrated pest management. Soil Biol. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Unfortunately, only a few agroecosystem experiments exist that compare organic and conventional management strategies over an extended period for evaluation of impact on soil health and restoration (Raupp et al., 2006; Khatoon et al., 2020). Topics in Biodiversity and Conservation, vol 16. Bull. doi: 10.1016/j.soilbio.2014.04.014, Yadav, R., Ror, P., Rathore, P., and Ramakrishna, W. (2020). (2016). Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL (2017) Research priorities for harnessing plant microbiomes in sustainable agriculture. Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Appl. Microb Cell Factories 13:66. Donley, N. (2019). Rekadwad BN, Khobragade CN (2017) Microbial biofilm: role in crop productivity. Managing and manipulating the rhizosphere microbiome for plant health: a systems approach. Manipulation of rhizosphere bacterial communities to induce suppressive soils. (2017). Newton AC, Fitt BDL, Atkins SD, Walters DR, Daniell TJ (2010) Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions. Biol. Rev. Rev. Proc Natl Acad Sci U S A 99:15681–15686. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. Biol. Res. Soil organic matter turnover is thus considered a net positive, as it liberates the nutrients locked up in organic matter. 129, 17–28. Plant Pathol. Crit Rev Biotechnol 37:229–237. (2011). Microbiol. Pollut. doi: 10.4141/cjss2013-005, Luo, Y., Wang, F., Zhou, M., and Sheng, H. M. (2019). Table 1. 12: Modern Applications of Microbial Genetics Last updated Aug 14, 2020; Save as PDF 11.7: Gene Regulation- Operon Theory; 12.1: Microbes and the Tools of Genetic Engineering Despite the obvious importance of beneficial microorganisms for plant growth and fitness, and the impact of plant genotype on shaping their microbiome composition, plant germplasm is typically screened in the absence of microbes, and the selection of best breeding lines made solely based on the interaction between plant genotype and performance under various abiotic factors. United states: WH Freeman and Company. They proposed that this bacterial population shift led to the induction of enzymatic activities associated with fungal cell-wall degradation, as well as secondary metabolite biosynthesis, all aimed at accelerating and augmenting the plant defense response(s). More specifically, soil bacterial communities were primarily found to be structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage (Hartman et al., 2018). Analysis of microbial genomes has contributed to the development of new antibiotics, diagnostic tools, vaccines, medical treatments, and environmental cleanup techniques. Michael Fry, in Landmark Experiments in Molecular Biology, 2016. Nat Rev Microbiol 6:431–440. Mol Plant-Microbe Interact 19:827–837. Netherlands J. Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: Implications for soil quality. Scientists are trying to design microbes that will perform reliably and target specific plant/microbe interactions. doi: 10.1094/pbiomes-09-16-0008-r, Yuan, Z. L., Druzhinina, I. S., Labbé, J., Redman, R. S., Qin, Y., Rodriguez, R., et al. 3, 1445–1454. A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome. For this reason, amending the soil with such organic fertilizers as compost or manure contributes to higher microbial diversity and biomass compared to mineral-fertilized soils, which in turn positively impacts soil health (Schmid et al., 2018; Banerjee et al., 2019). Studium Press Pvt. Suppression of other soil microorganisms by mycelium of arbuscular mycorrhizal fungi in root-free soil. Mycorrhiza 28, 403–409. Ray, P., and Craven, K. D. (2016). Sci. Biochem. A., and Tarkka, M. (2007). Bashan Y, Holguin G (1998) Proposal for the division of plant growth-promoting rhizobacteria into two classifications: biocontrol-PGPB (plant growth-promoting bacteria) and PGPB. More recently, a comparative metatranscriptome analysis of wheat rhizosphere microbiome grown in fields suppressive and non-suppressive to the plant pathogen R. solani AG8 clearly revealed distinct dominant taxa in these two soil types. Biochem. PLoS One 9(8):e103891, Lopez DC, Sword GA (2015) The endophytic fungal entomopathogens Beauveria bassiana and Purpureocillium lilacinum enhance the growth of cultivated cotton (Gossypium hirsutum) and negatively affect survival of the cotton bollworm (Helicoverpa zea). doi: 10.1111/gcbb.12289, Kemen, E. (2014). Exploiting plant-microbe partnerships to improve biomass production and remediation. Rhizosphere 3:222–229. Caleza V, Castillo S, Gomis MD, Kamah S, López R, Garcia-Seco D, Varma A, Akdi K (2017) Conservation strategies of new fungi samples in culture collections: Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fiererb N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. List of recent publications in plant and soil microbiome focusing on plant fitness and productivity. Ecol. Particulate organic matter and soil mineral nitrogen concentrations are good predictors of the soil nitrogen supply to canola following legume and non-legume crops in western Canada. (2008). Thus, although culture-independent methods have contributed tremendously to our understanding of plant-associated fungal and bacterial community structures, the study of microbiome functions remains challenging because of the inherent noise of plant-associated microbial communities. Further, different types of soil C selectively manipulate soil microbial community composition, resulting in changes in such belowground ecosystem functions as decomposition and nutrient transfer and creating feedbacks that may affect overall plant growth and productivity (Orwin et al., 2006). Stewart EJ (2012) Growing unculturable bacteria. Sci. doi: 10.1007/s11356-014-3231-y. J. Environ. Therefore the genetic improvement of microbial strains involved in food processing may represent a viable solution for globalization of the food and agriculture markets. MBio 7, e1790–e1716. Example: Green … Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia, Egypt. Symbiosis 68, 73–78. 13, 445–470. Plant Soil 308:161. Microbiol. 1.2.1 Fundamental Tenets of Molecular Biology. Microbial herbicides for weed management: prospects, progress and constraints. Genetic engineering is used in the production of drugs, human gene therapy, and the development of improved plants (2). We propose that the manipulation of the plant microbiome holds tremendous potential for agricultural improvement (Table 1). Again, defining nutrient fluxes with techniques like Stable Isotope Labeling (SIP) holds great potential to define and construct resilient, functioning and beneficial microbiomes that can contribute to future holistic agriculture. doi: 10.1046/j.1469-8137.2002.00397.x, Brundrett, M. C., and Tedersoo, L. (2018). doi: 10.1038/ismej.2014.210, Hayat, R., Ali, S., Amara, U., Khalid, R., and Ahmed, I. Microbiol. Biol Control 116:36–45. Use of mycorrhizae in agriculture. 206, 1196–1206. (2014). Plant Cell 32, 486–507. 1. Microb Ecol 73:162. Int J Syst Evol Microbiol 55:11–26. 95:fiz138. Part of Springer Nature. 8, 922–933. J. 81, 2368–2377. Cell Host Microbe 22, 142–155. (2016). Rahi P (2017) Phytomicrobiome: a reservoir for sustainable agriculture. (2019). In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than … J. Contrarily, in a 2-year field study, cover crops reportedly increased overall phylogenetic diversity of fungi but did not change the relative abundance of saprophytes, symbionts or pathogens, implying that cover cropping does not always appear to contribute to functional changes in the fungal community (Schmidt et al., 2019). bescii: The first native strain from North America. doi: 10.1126/science.aaw9285, Castrillo, G., Teixeira, P. J. P. L., Paredes, S. H., Law, T. F., de Lorenzo, L., Feltcher, M. E., et al. Current status of the application of traditional and new biotechnologies in food processing in developing countries . Comparative metatranscriptomics of wheat rhizosphere microbiomes in disease suppressive and non-suppressive soils for Rhizoctonia solani AG8. doi: 10.1111/1462-2920.12081, Oberwinkler, F., Riess, K., Bauer, R., and Garnica, S. (2014). Can genetic engineering deliver a natural microbial fertilizer for crops? 220, 957–962. Proc Natl Acad Sci U S A 108:4516–4522. A., Fanega-Sleziak, N., Papageorgiou, S., Tsalakou, A., Pantelides, I. S., et al. Discreet heterotrophs: green plants that receive fungal carbon through Paris−type arbuscular mycorrhiza. (2017). New Phytol 210:1022–1032. Biochem Eng 103:158–169. Plant Sci. Baker, K., and Cook, R. J. This is simply because each strain in the multi-strain consortium can compete effectively with the indigenous rhizosphere population and enhance plant growth with its partners. In 1904, the German agronomist and plant physiologist Lorenz Hiltner coined the term rhizosphere (Hartmann et al., 2008) to describe the area around a plant root inhabited by a unique population of microorganisms. Appl. Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment. A thermal cycler (left) is used during a polymerase chain reaction (PCR). Res. doi: 10.1007/978-3-319-44530-4_19, Barelli, L., Waller, A. S., Behie, S. W., and Bidochka, M. J. Tot. Nat India. Mar Drugs 9:1664–1681. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. In another study, soil microbial communities of corn and switchgrass in mono-cropping systems when compared with mixed prairie grasses demonstrated that bacterial and fungal biomass, especially arbuscular mycorrhizal fungi, were higher in plots with mixed prairie grasses (Jesus et al., 2016). Front. New Phytol 196:341–344. As an example, Lekberg and Helgason (2018) conducted a literature survey of research papers published on mycorrhizal functioning spanning a 30-year period (1987–2017). Teplitski M, Warriner K, Bartz J, Schneider KR (2011) Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety. Cover crops are typically unharvested crops planted between cash crops that augment C provisioning to the soil system not only via unharvested residues, but also as root exudates that can support many rhizosphere microbes during the active growing season of the cover crop. The advent of powerful new methodologies in microbial genetics, molecular biology and biotechnology has only quickened the pace of developments. Microb Biotechnol 10:50–53. Such disease-suppressive soils have been described for various soil-borne pathogens, including fungi, bacteria, oomycetes, and nematodes (Mazzola, 2007; Kwak et al., 2018). (2017), who showed that long-term application of high doses of inorganic nitrogenous fertilizers severely reduces relative abundance, diversity and structure of diazotrophs, which play a key role in converting atmospheric N2 to plant-available ammonium. Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Since that time, a great deal of research has been conducted on this relationship between legumes and these bacteria, now termed rhizobia, that inhabit unique structures, the nodules, that form on the roots. An example of how they may accomplish this is studying natural selection or drift of microbes. Microorganisms have significant impacts on U.S. agriculture, natural resources, and food safety. Long-term chemical fertilization has been shown to dramatically decrease the soil pH, which leads to a decrease in bacterial diversity and other changes in microbial community structure (Sun et al., 2015). B., Bonfante, P., et al. Agron J 99(5):1377. doi: 10.1007/s00572-018-0865-5. Ecol. 16, 567–576. Such findings certainly reveal a role for native microbiota in protecting plants from phytopathogens, and pave a way forward for the development of probiotics to ameliorate plant diseases akin to human health (Kwak et al., 2018). Proc. Ecol. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Ecological consequences of carbon substrate identity and diversity in a laboratory study. Opin. Biocontrol Sci Tech 27:28–41. Biochimie. (2019). 23, 606–617. Microbiol. Acad. Environ Pollut 102:6697–6704. 6, 7633–7644. Microbe-microbe interactions determine oomycete and fungal host colonization. 6. Ruth D, Sven R, Hans H, Christel V, Joost J, Kristien B, Maarten F, Serge B, Christophe H, Ivo L, Drik EDV, Jos V, Jan V, Jan M (2006) Quorum signal molecules as biosurfactants affecting swarming in. Front. Despite these limited applications, much remains to be learned regarding both the functional and taxonomic diversity of these symbiotic bacteria and their host plants, the role they play in the global nitrogen cycle, and ultimately, how they can best be harnessed for improving plant productivity. doi: 10.1093/femsec/fiz138, Turrini, A., Avio, L., Giovannetti, M., and Agnolucci, M. (2018). Environ. J Appl Microbiol 122:1057–1070. A thermal cycler (left) is used during a polymerase chain reaction (PCR). Such studies typically take place in a controlled, artificial condition, such as a defined growth medium in a greenhouse, where competition from a native rhizosphere community is relatively low or non-existent. Johnston-Monje D, Raizada MN (2011) Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology. Biochem. Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils. doi: 10.2489/jswc.72.4.361, Frey-Klett, P., Garbaye, J. US Patent App. B., Tao, G., Morton, J. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. biodegradable plastics, vegetable oil, biofuels), and environmental uses. Comp. The soil microbial community often assists plants by weathering minerals from rock surfaces and degrading recalcitrant soil organic matter whereby soil microbes break down soluble and insoluble organic matter and convert it into inorganic, plant-available forms. Figure 1. 9, 1177–1194. Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture. Nat. Singh, S. (2016). Similarly, the extraradical hyphae of arbuscular mycorrhiza provide a direct pathway for the translocation of photosynthetically derived carbon to the soil, leading to the development of nutrient-rich niches for other soil microorganisms, particularly bacteria. Augment. Souza, R. D., Ambrosini, A., and Passaglia, L. M. (2015). Analysis of microbial genomes has contributed to the development of new antibiotics, diagnostic tools, vaccines, medical treatments, and environmental cleanup techniques. A study aimed at comparing the soil microbiome in conventional and organic farming systems in central Europe revealed no major differences among the main phyla of bacteria between the two farming styles (Armalytë et al., 2019), whereas another study that investigated the effects of 12 years of organic farming on soil microbiomes in northern China reported shifting of the community composition of dominant phyla and significant alterations of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling when compared to conventional farming systems (Ding et al., 2019). Not surprisingly, recent culture-independent analyses thus have paved the way for developing SynComs more often (Bodenhausen et al., 2014; Armanhi et al., 2018; Carlström et al., 2019). 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