Host-mediated gene engineering and microbiome-based technology optimization for sustainable agriculture and environment
Tóm tắt
Từ khóa
Tài liệu tham khảo
Adeniji AA, Babalola OO, Loots DT (2020) Metabolomic applications for understanding complex tripartite plant–microbes’ interactions: strategies and perspectives. Biotechnology Reports 25:00425
Al-Zyoud F (2014) Adoption range of integrated pest management (IPM) techniques by greenhouse vegetable growers in Jordan. Jordan J Agric Sci 10:504–525
Andrade GC, Freguglia RM, Furlani RP, Torres NH, Tornisielo VL (2011) Determination of pesticide residues in tomato using dispersive solid-phase extraction and gas chromatography/ion trap mass spectrometry. J Braz Chem Soc 22:1701–1708
APEDA RN (2014) Agricultural and Processed Food Products Export Development Authority.
Arias-Sanchez FI, Vessman B, Mitri S (2019) Artificially selecting microbial communities: if we can breed dogs, why not microbiomes? PLoS Biol 17:3000356
Arif I, Batool M, Schenk PM (2020) Plant microbiome engineering: expected benefits for improved crop growth and resilience. Trends Biotechnol 38(12):1385–1396
Bakker MG, Manter DK, Sheflin AM, Weir TL, Vivanco JM (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360:1–3
Balaneshinkordan S, Kotov A (2016) An empirical comparison of term association and knowledge graphs for query expansion. In Advances in Information Retrieval: 38th European Conference on IR Research, ECIR 2016, Padua, Italy, March 20–23, 2016. Proceedings 38. Springer International Publishing, pp 761–767
Bàrberi P (2015) Functional biodiversity in organic systems: the way forward. Sust Agric Res 4:37937
Barone P, Wu E, Lenderts B, Anand A, Gordon-Kamm W, Svitashev S, Kumar S (2020) Efficient gene targeting in maize using inducible CRISPR-Cas9 and marker-free donor template. Mol Plant 13(8):1219–1227
Bartoli M, Pelillo M, Siddiqi K, Zucker SW (2000) Attributed tree homomorphism using association graphs. In Proceedings 5th International Conference on Pattern Recognition. ICPR 2:133–136
Bashiardes S, Zilberman-Schapira G, Elinav E (2016) Use of metatranscriptomics in microbiome research. Bioinform Biol Insights 4610
Barrett CB, Christian P, Shiferaw BA (2017) The structural transformation of African agriculture and rural spaces: Introduction to a special section. Agric Econ 48(S1):5–10
Bhattacharyya A, Pablo CH, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV (2021) Rhizosphere plant-microbe interactions under water stress. In Advances in applied microbiology, vol 115. Academic Press, pp 65–113
Beckers B, Op De Beeck M, Weyens N, Van Acker R, Van Montagu M, Boerjan W, Vangronsveld J (2016) Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome. Proc Nat Acad Sci, USA 113:2312–2317
Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486
Birkhofer K, Bezemer TM, Bloem J, Bonkowski M, Christensen S, Dubois D, Ekelund F, Fließbach A, Gunst L, Hedlund K, Mäder P (2008) Long-term organic farming fosters below and above ground biota: implications for soil quality, biological control and productivity. Soil Biol Biochem 40:2297–2308
Birkhofer K, Arvidsson F, Ehlers D, Mader VL, Bengtsson J, Smith HG (2016) Organic farming affects the biological control of hemipteran pests and yields in spring barely independent of landscape complexity. Landsc Ecol 31:567–579
Blair PM, Land ML, Piatek MJ, Jacobson DA, Lu TS, Doktycz MJ, Pelletier DA (2018) Exploration of the biosynthetic potential of the Populus microbiome. mSystems 3:00045–18
Bona E, Massa N, Novello G, Boatti L, Cesaro P, Todeschini V, Magnelli V, Manfredi M, Marengo E, Mignone F et al (2019) Metaproteomic characterization of the Vitis vinifera rhizosphere. FEMS Microbiol Ecol 95:204
Bonvoisin T, Utyasheva L, Knipe D, Gunnel D, Eddleston M (2020) Suicide by pesticide poisoning in India: a review of pesticide regulations and their impact on suicide trends. BMC Public Health 20:251
Braga ARC, de Rosso VV, Harayashiki CAY, Jimenez PC, Castro ÍB (2020) Global health risks from pesticide use in Brazil. Nature Food 1:312–314
Bulgarelli D, Rott M, Schlaeppi K, Loren V, van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95
Bulgarelli D, Schlaeppi K, Spaepen S, Van Themaat EV, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838
Bulgarelli D, Garrido-Other 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. Cell Host Microbe 17:392–403
Busby PE, Peay KG, Newcombe G (2016) Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity. New Phytol 209:1681–1692
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. PLoS Biol 15:2001793
Cai Y, Chen L, Zhang Y, Yuan S, Su Q, Sun S, Wu C, Yao W, Han T, Hou W (2020) Target base editing in soybean using a modified CRISPR/Cas9 system. Plant Biotechnol J 18:1996
Chihaoui SA, Trabelsi D, Jdey A, Mhadhbi H, Mhamdi R (2015) Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects the richness and structure of rhizosphere bacterial communities and enhances nodulation and growth. Arch Microbiol 197:805–813
Clouse KM, Wagner MR (2021) Plant genetics as a tool for manipulating crop microbiomes: Opportunities and challenges. Frontiers in Bioengineering and Biotechnology 9:567548
Coyte KZ, Schluter J, Foster KR (2015) The ecology of the microbiome: networks, competition, and stability. Science 350:663–666
Damalas CA, Koutroubas SD (2018) Current status and recent developments in biopesticide use. Agriculture 8:13
Danish S, Zafar-ul-Hye M (2019) Co-application of ACC-deaminase producing PGPR and timber-waste biochar improves pigments formation, growth, and yield of wheat under drought stress. Sci Rep 9:1–3
Date K, Gross GA, Khopkar S, Nagi R, Sambhoos K (2013) Data association and graph analytical processing of hard and soft intelligence data. In Proceedings of the 16th international conference on information fusion. IEEE, pp 404–411
del Carmen Orozco-Mosqueda M, del Carmen Rocha Granados M, Glick BR, Santoyo G (2018) Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res 208:25–31
Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci 106:16428–16433
Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11
Dubey A, Malla MA, Khan F, Chowdhary K, Yadav S, Kumar A, Sharma S, Khare PK, Khan ML (2019) Soil microbiome: a key player for conservation of soil health under changing climate. Biodivers Conserv 28:2405–2429
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci 112:911–920
Epelde L, Jauregi L, Urra J, Ibarretxe L, Romo J, Goikoetxea I, Garbisu C (2018) Characterization of composted organic amendments for agricultural use. Front Sustain Food Syst 2:44
FAO (2016) The FAO action plan on antimicrobial resistance 2016–2020. FAO, Roma
Food and Agriculture Organization of the United Nations (FAO) and World Health Organization (WHO), Global Situation of Pesticide Management in Agriculture and Public Health (2019).
Farrar K, Bryant D, Cope-Selby N (2014) Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. Plant Biotechnol J 12:1193–1206
Finkel OM, Castrillo G, Herrera Paredes S, Salas Gonzalez I, Dangl JL (2017) Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 38:155–163
Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y et al (2019) A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol 37:186–192
Frederiks C, Wesseler JH (2019) A comparison of the EU and US regulatory frameworks for the active substance registration of microbial biological control agents. Pest Manag Sci 75:87–103
Garrigou A, Laurent C, Berthet A, Colosio C, Jas N, Daubas-Letourneux V, Jackson Filho JM, Jouzel JN, Samuel O, Baldi I, Lebailly P, Galey L, Goutille F (2019) Judon N Critical review of the role of PPE in the prevention of risks related to agricultural pesticide use. Saf Sci 123:104527
Geiger F, Bengtsson J, Berendse F, Weisser WW, Emmerson M, Morales MB, Ceryngier P, Liira J, Tscharntke T, Winqvist C, Eggers S (2010) Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland. Basic Appl Ecol 11:97–105
Goold HD, Wright P, Hailstones D (2018) Emerging opportunities for synthetic biology in agriculture. Genes 9:341
Gu Y, Dong K, Geisen S, Yang W, Yan Y, Gu D, Liu N, Borisjuk N, Luo Y, Friman VP (2020) The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion. Plant Soil 452:105–117
Hamonts K, Trivedi P, Garg A, Janitz C, Grinyer J, Holford P, Botha FC, Anderson IC, Singh BK (2018) Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol 20:124–140
Harman GE, Howell CR, Viterbo A, Chet I, Lorito M (2004) Trichoderma species—opportunistic, avirulent plant symbionts. Nat Rev Microbiol 2:43–56
Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194
He F, Yang Y, Yang G, Yu L (2010) Studies on antibacterial activity and antibacterial mechanism of a novel polysaccharide from Streptomyces Virginia H03. Food Control 21:1257–1262
Hettich RL, Pan C, Chourey K, Giannone RJ (2013) Metaproteomics: harnessing the power of high-performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 85:4203–4214
Hill SB (2014) Considerations for enabling the ecological redesign of organic and conventional agriculture: a social ecology and psychosocial perspective. Organic Farming, Prototype for Sustainable Agricultures: Prototype for Sustainable Agricultures 401–422
Holmes I, Harris K, Quince C (2012) Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 7:30126
Hosseinkhani J, Chaprut S, Taherdoost H (2012) Criminal network mining by web structure and content mining. In 11th WSEAS International Conference on Information Security and Privacy (ISP'12), Prague, Czech Republic September, pp 24–26
Ichihashi Y, Date Y, Shino A, Shimizu T, Shibata A, Kumaishi K, Funahashi F, Wakayama K, Yamazaki K, Umezawa A et al (2020) Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield. Proc Nat Acad Sci, USA 117:14552–14560
Illukpitiya P, Khanal P (2016) Consumer perception of organic food and product marketing. Organic Farming for Sustainable Agriculture 315–324
Jacquet S, Miki T, Noble R, Peduzzi P, Wilhelm S (2010) Viruses in aquatic ecosystems: important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology. AIOL Journal 1:97–141
Jangir RP, Rathore MS, Bisnoi HR, Sundria MM (2008) National workshop on spices and aromatic plants. Agricultural Research Station 6–7.
Jayadevaprakash N, Mukhopadhyay S, Palakal M (2005) Generating association graphs of non-cooccurring text objects using transitive methods. In Proceedings of the 2005 ACM symposium on Applied computing 141–145.
Jochum MD, McWilliams KL, Pierson EA, Jo YK (2019) Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere. PLoS ONE 14:e0225933
Kalloo K (2003) Research and extension activities on organic agriculture in India. Organic farming in horticulture for sustainable production 29–30.
Kaminski TS, Scheler O, Garstecki P (2016) Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip 16:2168–2187
Kassam A, Friedrich T, Shaxson F et al (2009) The spread of conservation agriculture: justification, sustainability and uptake. Int J Agric Sustain 7:292–320
Kaur H, Pandey DK, Goutam U, Kumar V (2021) CRISPR/Cas9-mediated genome editing is revolutionizing the improvement of horticultural crops: Recent advances and future prospects. Sci Hortic 289:110476
Kemal RA, Islamaiah PWN, Sadah M, Lusiany T (2016) Synthetic biology for biocontrol: a mini-review. Proc 6th Int Confer Global Res Conserv 6:92–94
Khadse A, Rosset PM (2019) Zero budget natural farming in India–from inception to institutionalization. Agroecol Sustain Food Syst 43:848–871
Khadse A, Rosset PM, Morales H, Ferguson BG (2018) Taking agroecology to scale: the zero-budget natural farming peasant movement in Karnataka, India. J Peasant Stud 45(1):192–219
Kim D, Alptekin B, Budak H (2018) CRISPR/Cas9 genome editing in wheat. Functional & Integrative Genomics 18:31–41
Köhl J, Kolnaar R, Ravensberg WJ (2019) Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Front Plant Sci 845. https://doi.org/10.3389/fpls.2019.00845
Kour D, Rana KL, Kaur T, Singh B, Chauhan VS, Kumar A, Gupta VK (2019) Extremophiles for hydrolytic enzymes productions: biodiversity and potential biotechnological applications. Bioprocessing for biomolecules production, pp 321–372
Kumar R, Kumar S, Yashavanth BS, Meena PC (2019) Natural Farming practices in India: Its adoption and impact on crop yield and farmers’ income. Indian J Agric Econ 74:420–432
Lakshmanan V, Selvaraj G, Bais HP (2014) Functional soil microbiome: belowground solutions to an aboveground problem. Plant Physiol 166:689–700
Lampel J, Scarbrough H, Macmillan S (2008) Managing through projects in knowledge-based environments: special issue introduction by the guest editors. Long Range Plan 41:7–16. https://doi.org/10.1016/j.lrp.2007.11.007
Lay CY, Bell TH, Hamel C, Harker KN, Mohr R, Greer CW, Yergeau E, St- Arnaud M (2018a) Canola root-associated microbiomes in the Canadian prairies. Front Microbiol 9:1188
Lay CY, Bell TH, Hamel C, Harker KN, Mohr R, Greer CW, Yergeau E, St-Arnaud M (2018b) Canola root-associated microbiomes in the Canadian prairies. Front Microbiol 9:1188
Leahy J, Mendelsohn M, Kough J, Jones R, Berckes N (2014) Biopesticide oversight and registration at the US Environmental Protection Agency. Biopesticides: state of the art and future opportunities, pp 3–18
Leifeld J, Angers DA, Chenu C, Fuhrer J, Kätterer T, Powlson DS (2013) Organic farming gives no climate change benefit through soil carbon sequestration. Proc Natl Acad Sci 110:984–984
Leithold G, Hülsbergen KJ, Brock C (2015) Organic matter returns to soils must be higher under organic compared to conventional farming. J Plant Nutr Soil Sci 178:4–12
Leonard SP, Powell JE, Perutka J, Geng P, Heckmann LC, Horak RD, Davies BW, Ellington AD, Barrick JE, Moran NA (2020) Engineered symbionts activate honey bee immunity and limit pathogens. Science 367:573–576
Letourneau DK, Bothwell SG (2008) Comparison of organic and conventional farms: challenging ecologists to make biodiversity functional. Front Ecol Environ 6:430–438
Levy A, Conway JM, Dangl JL, Woyke T (2018) Elucidating bacterial gene functions in the plant microbiome. Cell Host Microbe 24:475–485
Li C, Brant E, Budak H, Zhang B (2021) CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 22(4):253–284. https://doi.org/10.1631/jzus.B2100009
Li Z, Jing XY, Zhu X (2018) Progress on approaches to software defect prediction. IET Softw 12(3):161–175
Liu F, Hewezi T, Lebeis SL, Pantalone V, Grewal PS, Staton ME (2019a) Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly. BMC Microbiol 19:1–19
Liu H, Khan MY, Carvalhais LC, Delgado-Baquerizo M, Yan L, Crawford M, Schenk PM (2019b) Soil amendments with ethylene precursor alleviate negative impacts of salinity on soil microbial properties and productivity. Sci Rep 9:1–13
Lu Y, Tian Y, Shen R, Yao Q, Wang M, Chen M, Dong J, Zhang T, Li F, Lei M, Zhu JK (2020) Targeted, efficient sequence insertion and replacement in rice. Nat Biotechnol 38(12):1402–1407
Lucas JA, García-Villaraco A, Ramos B, García-Cristobal J, Algar E, Gutierrez-Manero J (2013) Structural and functional study in the rhizosphere of Oryza sativa L. plants growing under biotic and abiotic stress. J Appl Microbiol 115:218–235
Luo Y, Uzuner Ö, Szolovits P (2017) Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations. Brief Bioinform 18:160–178
Ma Y, Rajkumar M, Oliveira RS, Zhang C, Freitas H (2019) Potential of plant beneficial bacteria and arbuscular mycorrhizal fungi in phytoremediation of metal-contaminated saline soils. J Hazard Mater 379:120813
Macdonald C, Singh B (2014) Harnessing plant-microbe interactions for enhancing farm productivity. Bioengineered 5(1):5–9
Maher MF, Nasti RA, Vollbrecht M, Starker CG, Clark MD, Voytas DF (2020) Plant gene editing through de novo induction of meristems. Nat Biotechnol 38(1):84–89
Malabarba J, Chevreau E, Dousset N, Veillet F, Moizan J, Vergne E (2021) New strategies to overcome present CRISPR/Cas9 limitations in apple and pear: efficient dechimerization and base editing. Int J Mol Sci 22:319
Marasco R, Rolli E, Fusi M, Michoud G, Daffonchio D (2018) Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Microbiome 6:1–17
Mendes R, Kruijt M, De Bruijn I, Dekkers E, Van Der Voort M, Schneider JH, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100
Mendes LW, de Chaves MG, Fonseca MC, Mendes R, Raaijmakers JM, Tsai SM (2019) Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome. Front Microbiol 10:2252
Mendes LW, Mendes R, Raaijmakers JM, Tsai SM (2018) Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. The ISME Journal 12(12):3038–3042
Merker L, Schindele P, Huang TK, Wolter F, Puchta H (2020) Enhancing in planta gene targeting efficiencies in Arabidopsis using temperature-tolerant CRISPR/LbCas12a. Plant Biotechnol J 18(12):2382–2384
Mitter B, Pfaffenbichler N, Flavell R, Compant S, Antonielli L, Petric A, Sessitsch A (2017) A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds. Front Microbiol 8:11
Morella NM, Weng FC, Joubert PM, Metcalf CJE, Lindow S, Koskella B (2020) Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc Nat Acad Sci, USA 117:1148–1159
Mulet JM (2014) Should we recommend organic crop foods on the basis of health benefits? Letter to the editor regarding the article by Barańskiet al. Br J Nutr 112:1745–1747
Munster D (2019) Affect beyond the human: Indian agriculture in a multispecies world. In Engaging transculturality. Routledge, pp 398–412
Nicholson JK, Holmes E, Wilson ID (2005) Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3:431–438
Niggli U (2015) Sustainability of organic food production: challenges and innovations. Proc Nutr Soc 74:83–88
Ofek-Lalzar M, Sela N, Goldman-Voronov M, Green SJ, Hadar Y, Minz D (2014) Niche and host-associated functional signatures of the root surface microbiome. Nat Commun 5:4950
Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, ... Yang B (2019) Broadspectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 37(11):1344–1350
Palekar S (2010) The philosophy of spiritual farming: zero budget natural farming–part 1, 5th revised renewal edn. Amravati: Zero Budget Natural Farming Research. Development and Extension Movement
Panke-Buisse K, Lee S, Kao-Kniffin J (2017) Cultivated sub-populations of soil microbiomes retain early flowering plant trait. Microb Ecol 73:394–403
Panneerselvam P, Halberg N, Vaarst M, Hermansen JE (2012) Indian farmers’ experience with and perceptions of organic farming. Renew Agric Food Syst 27:157–169
Pascale A, Proietti S, Pantelides IS, Stringlis IA (2020) Modulation of the root microbiome by plant molecules: the basis for targeted disease suppression and plant growth promotion. Front Plant Sci 10:1741
Peshin R, Dhawan AK (2009) Integrated pest management: volume 1: innovation-development process. Springer, Science & Business Media.
Peshin R, Zhang W (2014) Integrated pest management and pesticide use. Springer, Netherlands, pp 1–46
Pineda A, Kaplan I, Hannula SE, Ghanem W, Bezemer TM (2020) Conditioning the soil microbiome through plant–soil feedbacks suppress an aboveground insect pest. New Phytol 226:595–608
Ponisio LC, M’Gonigle LK, Mace KC, Palomino J, De Valpine P, Kremen C (2015) Diversification practices reduce organic to conventional yield gap. Proc Royal Soc B Biol Sci 282:20141396
Postma-Blaauw MB, De Goede RG, Bloem J, Faber JH, Brussaard L (2012) Agricultural intensification and de-intensification differentially affect taxonomic diversity of predatory mites, earthworms, enchytraeids, nematodes and bacteria. Appl Soil Ecol 57:39–49
Pretty J, Benton TG, Bharucha ZP, Dicks LV, Flora CB, Godfray HCJ, Goulson D, Hartley S, Lampkin N, Morris C et al (2018) Global assessment of agricultural system redesign for sustainable intensification. Nat Sustain 1(8):441–446
Qin L, Li J, Wang Q, Xu Z, Sun L, Alariqi M, Manghwar H, Wang G, Li B, Ding X, Rui H (2020) High-efficient and precise base editing of C• G to T• A in the allotetraploid cotton (Gossypium hirsu-tum) genome using a modified CRISPR/Cas9 system. Plant Biotechnol J 18:45–56. https://doi.org/10.1111/pbi.13168.25
Rani L, Thapa K, Kanojia N, Sharma N, Singh S, Grewal AS, ... Kaushal J (2021) An extensive review on the consequences of chemical pesticides on human health and environment. J Clean Prod 283:124657. https://doi.org/10.1016/j.jclepro.2020.124657
Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, Vazquez MP (2016) Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Sci Rep 6:1–12
Ratnadass A (2020) Crop protection for agricultural intensification systems in Sub-Saharan Africa. Sustain Agric Rev 39:1–34. https://doi.org/10.1007/978-3-030-38881-2_1
Ratnadass A, Barzman M (2014) Ecological intensification for crop protection. Sustain Agric Rev 14:53–81. https://doi.org/10.1007/978-3-319-06016-3_3
Ratnadass A, Fernandes P, Avelino J, Habib R (2012) Plant species diversity for sustainable management of crop pests and diseases in agroecosystems: a review. Agron Sustain Dev 32:273–303. https://doi.org/10.1007/s13593-011-0022-4
Reddy BS (2010) Organic farming: status, issues and prospects–a review. Agric Econ Res Rev 23:343–358
Reddy PP (2017) Agro-ecological approaches to pest management for sustainable agriculture. Springer, Singapore, pp 29–41
Redlich S, Martin EA, Steffan-Dewenter I (2018) Landscape-level crop diversity benefits biological pest control. J Appl Ecol 55:2419–2428. https://doi.org/10.1111/1365-2664.13126
Reganold JP, Wachter JM (2016) Organic agriculture in the twenty-first century. Nat Plants 2:1–8
Roman-Reyna V, Pinili D, Borjaa FN, Quibod I, Groen SC, Mulyaningsih ES, Rachmat A, Slamet-Loedin IH, Alexandrov N, Mauleon R et al (2019) The rice leaf microbiome has a conserved community structure controlled by complex host–microbe interactions. Cell Host Microbe 19:00340. https://doi.org/10.2139/ssrn.3382544
Rothschild N, Novotný Č, Šašek V, Dosoretz CG (2002) Ligninolytic enzymes of the fungus Irpex lacteus (Polyporus tulipiferae): isolation and characterization of lignin peroxidase. Enzyme Microb Technol 31:627–633
Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ane JM et al (2020) Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 5:314–330
Schäffer A, Filser J, Frische T, Gessner M, Köck W, Kratz W, ... Scheringer M (2018) The Silent Spring: On the need for sustainable plant protection. Deutsche Akademie der Naturforscher Leopoldina eV-Nationale Akademie der Wissenschaften (German National Academy of Sciences) Leopoldin
Scheller E, Joergensen RG (2008) Decomposition of wheat straw differing in nitrogen content in soils under conventional and organic farming management. J Plant Nutr Soil Sci 171:886–892
Schwartz MW, Hoeksema JD, Gehring CA, Johnson NC, Klironomos JN, Abbott LK, Pringle A (2006) The promise and the potential consequences of the global transport of mycorrhizal fungal inoculum. Ecological Letters 9:501–515
Servadio JL, Convertino M (2018) Optimal information networks: application for data-driven integrated health in populations. Sci Adv 4:1701088
Setala H, Bardgett RD, Birkhofer K, Brady M, Byrne L, De Ruiter PC, Van der Putten WH (2014) Urban and agricultural soils: conflicts and trade-offs in the optimization of ecosystem services. Urban Ecosyst 17:239–253
Shepherd M, Pearce B, Cormack B, Philipps L, Cuttle S, Bhogal A, Unwin R (2003) An assessment of the environmental impacts of organic farming. A review for DEFRA-funded Project OF0405
Sheth RU, Cabral V, Chen SP, Wang HH (2016) Manipulating bacterial communities by in situ microbiome engineering. Trends Genet 32:189–200
Sime-Ngando T (2014) Environmental bacteriophages: viruses of microbes in aquatic ecosystems. Front Microbiol 5:355
Skinner C, Gattinger A, Muller A, Mäder P, Flieβbach A, Stolze M, Niggli U (2014) Greenhouse gas fluxes from agricultural soils under organic and non-organic management—a global meta-analysis. Sci Total Environ 468:553–563
Spence C, Bais H (2013) Probiotics for plants: rhizospheric microbiome and plant fitness. Mol Microb Ecol Rhizosphere 1:713–721
Syed-Ab-Rahman SF, Xiao Y, Carvalhais LC, Ferguson BJ, Schenk PM (2019) Suppression of Phytophthora capsici infection and promotion of tomato growth by soil bacteria. Rhizosphere 9:72–75
Tallapragada P, Seshachla U (2020) Seed microbiome and its implication in plant growth promotion and health. In The plant microbiome in sustainable agriculture, pp 47–64
Taye ZM, Helgason BL, Bell JK, Norris CE, Vail S, Robinson SJ, Parkin IA, Arcand M, Mamet S, Links MG et al (2020) Core and differentially abundant bacterial taxa in the rhizosphere of field grown Brassica napus genotypes: implications for canola breeding. Front Microbiol 10:3007
Thakur N (2017a) Increased soil-microbial-eco-physiological interactions and microbial food safety in tomato under organic strategies. Probiotics and plant health, pp 215–232
Thakur N (2017b) Increased soil-microbial-eco-physiological interactions and microbial food safety in tomato under organic strategies. In: Kumar, V. Kumar, M. Sharma, S. Prasad, R. (eds) Probiotics and Plant Health. Springer, Singapore. https://doi.org/10.1007/978-981-10-3473-2_9
Thakur N (2017c) Organic farming, food quality, and human health: a trisection of sustainability and a move from pesticides to eco-friendly biofertilizers. Probiotics in agroecosystem, pp 491–515
Thakur N (2017d). Integrated approach for the management of differential patterns of diseases and pest incidence in lychee. In: Kumar, M. Kumar, V. Bhalla-Sarin, N. Varma, A. (eds) Lychee Disease Management. Springer, Singapore. https://doi.org/10.1007/978-981-10-4247-8_16
Thakur N (2017e) Organic farming, food quality, and human health: a trisection of sustainability and a move from pesticides to eco-friendly biofertilizers. In: V Kumar, Kumar M, Sharma S, Prasad R (eds) Probiotics in Agroecosystem. Springer, Singapore. https://doi.org/10.1007/978-981-10-4059-7_26
Thakur N (2022) Physicochemical analysis and studies on soil profile of Prunus Armeniaca collected from mid-hill of Himachal Pradesh. Natl Acad Sci Lett 45:541–548
Thakur N, Nigam M, Tewary R, Rajvanshi K, Kumar M, Shukla SK, Mahmoud G-E, Gupta S (2022) Drivers for the behavioural receptiveness and non-receptiveness of farmers towards organic cultivation system. J King Saud Univ - Sci 34(5):1018–3647
Thakur N, Sharma P, Govender PP, Shukla SK (2022) Analysis and extraction of curcumin at mid and late phase harvested Curcuma Longa samples collected from Western Himalayan regions. Chemistry Africa 5:1733–1742
Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS (2020) Influence of plant fraction, soil, and plant species on microbiota: a multi-kingdom comparison. Mol Bio 11:02785–02819
Tkacz A, Pini F, Turner TR, Bestion E, Simmonds J, Howell P, Greenland A, Cheema J, Emms DM, Uauy C et al (2020) Agricultural selection of wheat has been shaped by plant–microbe interactions. Front Microbiol 11:132
Tonfack LB, Bernadac A, Youmbi E, Mbouapouognigni VP, Ngueguim M, Akoa A (2009) Impact of organic and inorganic fertilizers on tomato vigor, yield and fruit composition under tropical andosol soil conditions. Fruits 64:167–177
Treseder KK, Balser TC, Bradford MA, Brodie EL, Dubinsky EA, Eviner VT, Waldrop MP (2012) Integrating microbial ecology into ecosystem models: challenges and priorities. Biogeochemistry 109:7–18
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK (2020) Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol 18:607–621
Tshikantwa TS, Ullah MW, He F, Yang G (2018) Current trends and potential applications of microbial interactions for human welfare. Front Microbiol 9:1156
Tuck SL, Winqvist C, Mota F, Ahnström J, Turnbull LA, Bengtsson J (2014) Land-use intensity and the effects of organic farming on biodiversity: a hierarchical meta-analysis. J Appl Ecol 51:746–755
Uniyal AP, Mansotra K, Yadav SK, Kumar V (2019) An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech 9(6):223
Veillet F, Perrot L, Chauvin L, Kermarrec MP, Guyon-Debast A, Chauvin JE, Nogué F, Mazier M (2019) Transgene-free genome editing in tomato and potato plants using agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Int J Mol Sci 20:402
Verheijen LM, Aerts R, Brovkin V, Cavender-Bares J, Cornelissen JH, Kattge J, Van Bodegom PM (2015) Inclusion of ecologically based trait variation in plant functional types reduces the projected land carbon sink in an earth system model. Glob Chang Biol 21:3074–3086
Via Campesina L (2016) Zero budget natural farming in India. Family Farming Knowledge Platform of Fao
Vyas P, Kumar D, Dubey A, Kumar A (2018) Screening and characterization of Achromobacter xylosoxidans isolated from the rhizosphere of Jatropha curcas L. (energy crop) for plant-growth-promoting traits. J Adv Res Biotechnol 3:1–8
Walker G, Osbahr H, Cardey S (2021) Thematic collages in participatory photography: a process for understanding the adoption of zero budget natural farming in India. Int J Qual Methods 20:1–13
Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, Gonzalez-Pena A, Peiffer J, Koren O, Shi Q et al (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Pro Nat Acad Sci, USA 115:7368–7373
Waltz E (2018) With a free pass, CRISPR-edited plants reach market in record time. Nat Biotechnol 36(1):6–7
Wille L, Messmer MM, Studer B, Hohmann P (2019) Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. Plant, Cell Environ 42:20–40
Williams PA, Sikutshwa L, Shackleton S (2020) Acknowledging indigenous and local knowledge to facilitate collaboration in landscape approaches—lessons from a systematic review. Land 9(9):331
Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M (2017) Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu Rev Virol 4:201–219
Wintermans PC, Bakker PA, Pieterse CM (2016) Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria. Plant Mol Biol 90:623–634
Xing Z, Li L, Wang W (2021) Evaluation for education of the sustainable development of engineering college students base on NLP method. In 2021 2nd International Conference on Information Science and Education (ICISE-IE). IEEE, pp 705–709
Xu J, Zhang Y, Zhang P, Trivedi P, Riera N, Wang Y, Liu X, Fan G, Tang J, Coletta-Filho HD et al (2018) The structure and function of the global citrus rhizosphere microbiome. Nat Commun 9:4894
Xu Z, Xu X, Gong Q, Li Z, Li Y, Wang S, Yang Y, Ma W, Liu L, Zhu B, Zou L, Chen G (2019) Engineering broad-spectrum bacterial blight resistance by simultaneously disrupting variable TALE-binding elements of multiple susceptibility genes in rice. Mol Plant 12(11):1434–1446
Yanar D, Naif G, Yusuf Y, Mine A, Perihan C (2011) Effect of different organic fertilizers on yield and fruit quality of indeterminate tomato. Sci Rese Essays 6:3623–3628
Yang X, Guo W, Li F, Sunter G, Zhou X (2019) Geminivirus-associated betasatellites: exploiting chinks in the antiviral arsenal of plants. Trends Plant Sci 24(6):519–529
Yi HY, Chowdhury M, Huang YD, Yu XQ (2014) Insect antimicrobial peptides and their applications. Appl Microbiol Biotechnol 98:5807–5822
Yu QH, Wang B, Li N, Tang Y, Yang S, Yang T, Xu J, Guo C, Yan P, Wang Q, Asmutola P (2017) CRISPR/Cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Sci Rep 7(1):11874. https://doi.org/10.1038/s41598-017-12262-1
Zaidi SSEA, Mahas A, Vanderschuren H, Mahfouz MM (2020) Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biol 21(1):1–19
Zeng Q, Sukumaran J, Wu S, Rodrigo A (2015) Neutral models of microbiome evolution. PLoS Comput Biol 11:1004365
Zhang D, Zhang Z, Unver T, Zhang B (2021) CRISPR/Cas: a powerful tool for gene function study and crop improvement. J Adv Res 21(29):207–221. https://doi.org/10.1016/j.jare.2020.10.003