Babin, D.

Leoni, C.

Neal, A. L.

Sessitsch, A.

Smalla, K.

English

Rothamsted Repository

Patron:		Her	Majesty	The	Queen	 	 Rothamsted	Research	Harpenden,	Herts,	AL5	2JQ		Telephone:	+44	(0)1582	763133	Web:	http://www.rothamsted.ac.uk/			 			Rothamsted Research is a Company Limited by Guarantee Registered Office: as above.  Registered in England No. 2393175. Registered Charity No. 802038.  VAT No. 197 4201 51. Founded in 1843 by John Bennet Lawes.		Rothamsted Repository DownloadA - Papers appearing in refereed journalsBabin, D., Leoni, C., Neal, A. L., Sessitsch, A. and Smalla, K. 2021. Editorial to the Thematic Topic Towards a more sustainable agriculture through managing soil microbiomes. FEMS Microbiology Ecology. 97 (8), p. fiab094. https://doi.org/10.193/femsec/fiab094 The publisher's version can be accessed at:• https://doi.org/10.193/femsec/fiab094The output can be accessed at: https://repository.rothamsted.ac.uk/item/98593/editorial-to-the-thematic-topic-towards-a-more-sustainable-agriculture-through-managing-soil-microbiomes.© 14 July 2021, Please contact library@rothamsted.ac.uk for copyright queries.17/08/2021 09:50 repository.rothamsted.ac.uk library@rothamsted.ac.ukFEMS Microbiology Ecology, 97, 2021, fiab094https://doi.org/10.1093/femsec/fiab094EditorialEditorial to the Thematic Topic “Towards a more sustainableagriculture through managing soil microbiomes”Consistent with the concept of ecosystem sustainability—defined as ‘the ability of an ecosystem to maintain its poten-tial for self-regulation in the long term’ (Bender, Wagg and vander Heijden 2016)—sustainable agricultural production aims tomeet future food, feed and fibre demands with the given naturalresources and without adverse environmental impact or greaterland consumption. However, intensification of modern agricul-tural practices over recent decades with the ultimate aim ofhigher yields widely neglected environmental consequences—in particular with respect to soils. This resulted in a number ofnegative impacts such as reduced soil fertility and biodiversity,accumulation of plant pathogens, environmental contamina-tion with agrochemicals, or soil erosion jeopardizing soil health.Soil health is defined as the capacity of a soil to function as avital living system to maintain environmental quality, sustainbiological productivity and promote health of various organisms(Larkin 2015). In view of the limited arable land, we urgently needto restore soil health, i.e. with appropriate farming practices inorder to ensure agricultural productivity for future generations.Soil microorganisms are critical for soil-related ecosystem ser-vices. Harnessing their huge untapped and largely unexploredtaxonomic and functional diversity and gaining a better mech-anistic understanding of plant-microbe interactions under var-ious agricultural management practices can open up new waysto support an economically and environmentally-benign plantproduction (Bakker et al. 2012; Bender, Wagg and van der Heij-den 2016).This was the motivation for the Julius Kühn Institute(JKI, Germany) and the Instituto Nacional de InvestigaciónAgropecuaria (INIA, Uruguay) to organize an international work-shop from 14th to 16th November 2019 in Montevideo. SouthAmerica is one of the leading regions in the agricultural sec-tor worldwide and exhibits a tremendous record in agricul-tural research. The workshop was attended by fifty researchersfrom South American and European countries and served as aforum to inform each other about research projects, to exchangeideas and define future research needs. Twenty-eight speak-ers gave presentations across six sessions, covering aspectsas diverse as below/aboveground microbial-plant interactions,microbiome-based optimization of farming practices, soil qual-ity risk assessment, development of efficient plant probiotics,and microbiome-based plant breeding approaches. Participantstook time out to visit the long-term field trials managed by INIAat their Las Brujas experimental station. This Thematic Topicon ‘Sustainable Agriculture through Managing Soil Microbiomes’was compiled as a result of the workshop and includes nine-teen research articles, three minireviews, one current opinionand one perspective. The articles span a broad range of topics,including various crop plants, soil ecosystems, geographic loca-tions, and climatic conditions discussed by the attendees.A prerequisite of enhancing selected indigenous beneficialmicroorganisms for improved crop performance and soil healthis to understand the response of soil and plant-associatedmicrobiomes to various conventional and sustainable agricul-tural management practices. In addition, it is essential to iden-tify commonalities and site- or cultivar-dependent differencesin microbiomes. Simonin et al. (2020) identified the wheat rhi-zosphere core microbiome across various African and Euro-pean soils, conventional or organic cultivation and wheat geno-types. Management type (organic vs. conventional) in combina-tion with previous land use and plants’ stand age also shapedthe microbial community composition in shade coffee planta-tions with implications for long-term soil fertility as revealedby a study across nineteen individual farms in Nicaragua (Jur-burg, Shek and McGuire 2020). Garaycochea et al. (2020) investi-gated soil prokaryotic communities of five soils typical of theUruguayan Campos biome, one of the most fertile and bio-logically diverse natural grasslands in South America. Anothervulnerable habitat is the Amazon rainforest which is threat-ened by increasing deforestation. Pedrinho et al. (2020) com-bined metagenomic sequencing with quantitative real-time PCRto reveal that the effect of the conversion of rainforest to pas-ture on nitrogen-related microbial groups and functions can bereversed by reestablishment of forest growth. The rhizospheremicrobiota of rice was shown to be affected by water man-agement (lowland vs. upland) but independent of plant devel-opmental stage with consistent shifts in putative saprotrophs,pathogens and beneficials (Chialva et al. 2020). In commercialapple production, soils often show the problem of apple replantdisease (ARD) with unknown etiology and few ecological man-agement options. By growing a susceptible apple rootstock insplit-root set-ups, Balbı́n-Suárez et al. (2020) and Balbı́n-Suárezet al. (2021) revealed that ARD is a local, non-spreading soil phe-nomenon linked to microbial dysbiosis along the soil-root con-tinuum when compared to healthy soils.Neal et al. (2021) demonstrated that the source of phosphatefertilization (rock phosphate vs. triple superphosphate) exerteda minor role for phosphohydrolase gene abundance and diver-sity in the rhizosphere when compared to the crop type whichadds to the knowledge base of alternative phosphorus fertilizers.Received: 22 June 2021; Accepted: 22 June 2021C© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail:journals.permissions@oup.com12 EditorialGabbarini et al. (2021) studied the response dynamics of differ-ent biotic and abiotic parameters in soils under long-term con-ventional or no tillage practice to the switched management.Conservation practices (e.g. cover crops, crop rotation, reducedtillage, organic fertilization) were shown to have the potential torestore soil quality by recovering physical, chemical and biolog-ical parameters in degraded South American soils under long-term conventional soybean (Fernandez-Gnecco et al. 2021), com-mon bean (Abán et al. 2021), or intensive vegetable production(Cerecetto et al. 2021). Long-term farming practices can result ina soil biotic legacy modulating the rhizosphere microbiome andaffecting the performance of the model plant lettuce via alteredplant-microbial interactions in the rhizosphere (Babin et al.2021). For instance, bacterial N-acyl homoserine lactones (AHLs)are a group of molecules that mediate inter-kingdom interac-tions. Shrestha & Schikora (2020) elucidated the mechanism ofplant priming via AHLs for enhanced resistance, yield and tol-erance towards (a)biotic stresses and its potential to reduce fer-tilizer and pesticide inputs. Evidence for the effect of the barleyrhizosphere microbiome on the plant defense response towardsBlumeria graminis was given by Bziuk et al. (2021) when compar-ing differently managed agricultural to potting soils.Besides molecular techniques, isolation of bacteria coupledwith functional screenings allows for phenotypic characteri-zation. Elsayed, Grosch and Smalla (2021) demonstrated usingcultivation-dependent techniques that the potato plant sphere,and to a lesser extent the soil type, affected the diversity andproportion of bacteria showing in vitro antagonistic activitytowards the soil-borne pathogen Ralstonia solanacearum. Anotherstudy described that long-term nitrogen fertilization in soilsunder maize monoculture resulted in fewer actinomycetes within vitro inhibitory capacities towards other actinomycetes com-pared to non-fertilized soils while crop residue incorporationshowed no effect (Gieske and Kinkel 2020).As an alternative to the management-dependent support ofthe indigenous microbiome, the external manipulation by inoc-ulation of soils or plants with beneficial microbial strains ormulti-species consortia holds great promise for an enhancedsustainable agriculture. Since plants interact with a multi-tude of microbes at their roots, Tsiknia et al. (2021) empha-sized the need for proceeding from pairwise interaction stud-ies to an understanding of multi-species relationships of theplant-microbiome-soil continuum, in this case with a specialfocus on legume roots. The work of Heijo et al. (2021) addedto the understanding of plant-endophyte interactions in agro-ecosystems by investigating the effect of diazotrophic bacterialendophyte inoculation on sweet sorghum performance depend-ing on nitrogen fertilization doses and the sorghum cultivar.Figueiredo dos Santos et al. (2021) showed that maize seed-borne bacteria are crucial for germination and developmentof maize seedlings. Combining in vitro functional screening forplant growth promotion with whole genome sequencing pro-vided new insights into the mechanisms of two tropical Bacillusinoculant strains on different maize genotypes (Vieira Vellosoet al. 2020). In view of the intensive rice and wheat cultivation inthe Indo-Gangetic Plains jeopardizing soil quality, Sarkar & Rak-shit (2020) promoted the application of microbial delivery sys-tems i.e. bioaugmentation to enable bioremediation of pollutedsites and/or bio-priming with bio-inoculants in order to stim-ulate plant growth and reduce the requirement for agrochemi-cal use. Microbiome-based approaches can also be important forimproving fruit/vegetable production as well as for the biologi-cal control of postharvest and storage pathogens (Kusstatscheret al. 2020). As a follow-up of the miCROPe 2019 symposium,Hohmann, Schlaeppi and Sessitsch (2020) summarized researchneeds for a successful implementation of microbe-assisted cul-tivation approaches with focus on the management of plantgenetics or of the microbiome via single or combined strain inoc-ulation.We strongly agree with the authors that microbiome-assistedagriculture offers a promising new toolkit. As a result of this The-matic Topic, FEMS Microbiology Ecology organized a webinar (https://www.youtube.com/watch?v=2YOqB-O3Jnc) with GabrieleBerg, Rodrigo Mendes and Doreen Babin on the current agri-cultural microbiome research. The high number of participantsof the webinar as well as of the numerous contributions tothis Thematic Topic showed the huge interest of the scientificcommunity. As a next step, mechanistic understandings underconsideration of various environmental conditions should bebrought into focus to improve efficiencies and stability of biolog-ical solutions. Application of new analytical methods and multi-disciplinary approaches is essential. We should aim at develop-ing models to predict the response and functioning of the soil-microbiome-plant system and to fine-tune measures in a tar-geted way. Finally, we strongly encourage scientists to dissem-inate their knowledge to stakeholders, policy makers, and thepublic to promote the acceptance of microbial solutions.ACKNOWLEDGEMENTSWe are grateful to all workshop participants, authors, reviewersand regular FEMS Microbiology Ecology editors who contributedto this Thematic Topic.FundingThe workshop was co-organized and financed by Julius KühnInstitute (JKI, Germany) and the Instituto Nacional de Investi-gación Agropecuaria (INIA, Uruguay), with additional supportfrom Centro de Energia Nuclear na Agricultura—Universidadede São Paulo (CENA-USP, Brazil). Doreen Babin was supportedfinancially by the German Federal Ministry of Education andResearch (BMBF, Germany) in the framework of the projectDiControl (http://dicontrol.igzev.de/; grant number 031B0514C)as part of the BonaRes initiative ‘Soil as a sustainable resourcefor the bioeconomy’ (https://www.bonares.de/). Andrew Neal issupported by the United Kingdom’s Biotechnology and Biolog-ical Science Research Council (BBSRC)-funded Soil to Nutritionstrategic program (BBS/E/C/000I0310).Conflicts of interest. None declared.REFERENCESAbán CL, Verdenelli R, Gil SV et al. Service crops improve adegraded monoculture system by changing common beanrhizospheric soil microbiota and reducing soil-borne fungaldiseases. FEMS Microbiol Ecol 2021;97:fiaa258.Babin D, Sommermann L, Chowdhury SP et al. Distinct rhi-zomicrobiota assemblages and plant performance in lettucegrown in soils with different agricultural management his-tories. FEMS Microbiol Ecol 2021;97:fiab027.Bakker MG, Manter DK, Sheflin AM et al. Harnessing the rhizo-sphere microbiome through plant breeding and agriculturalmanagement. Plant Soil 2012;360:1–13.Balbı́n-Suárez A, Jacquiod S, Rohr A-D et al. Root exposure toapple replant disease soil triggers local defense responseEditorial 3and rhizoplane microbiome dysbiosis. FEMS Microbiol Ecol2021;97:fiab031.Balbı́n-Suárez A, Lucas M, Vetterlein D et al. Exploring micro-bial determinants of apple replant disease (ARD): a micro-habitat approach under split-root design. FEMS Microbiol Ecol2020;96:fiaa211.Bender SF, Wagg C, van der Heijden MGA. An Underground Rev-olution: biodiversity and Soil Ecological Engineering for Agri-cultural Sustainability. Trends Ecol Evol 2016;31:440–452.Bziuk N, Maccario L, Douchkov D et al. Tillage shapes the soiland rhizosphere microbiome of barley-but not its suscepti-bility towards Blumeria graminis f. sp. hordei. FEMS MicrobiolEcol 2021;97:fiab018.Cerecetto V, Smalla K, Nesme J et al. Reduced tillage, cover cropsand organic amendments affect soil microbiota and improvesoil health in Uruguayan vegetable farming systems. FEMSMicrobiol Ecol 2021;97:fiab023.Chialva M, Ghignone S, Cozzi P et al. Water management andphenology influence the root-associated rice field micro-biota. FEMS Microbiol Ecol 2020;96:fiaa146.Elsayed TR, Grosch R, Smalla K. Potato plant spheres andto a lesser extent the soil type influence the proportionand diversity of bacterial isolates with in vitro antagonis-tic activity towards Ralstonia solanacearum. FEMS Microbiol Ecol2021;97:fiab038.Fernandez-Gnecco G, Smalla K, Maccario L et al. Microbial com-munity analysis of soils under different soybean croppingregimes in the Argentinean south-eastern Humid Pampas.FEMS Microbiol Ecol 2021;97:fiab007.Figueiredo Dos Santos L, Fernandes Souta J, De Paula SoaresC et al. Insights into the structure and role of seed-bornebacteriome during maize germination. FEMS Microbiol Ecol2021;97:fiab024.Gabbarini LA, Figuerola E, Frene JP et al. Impacts of switchingtillage to no-tillage and vice versa on soil structure, enzymeactivities and prokaryotic community profiles in Argen-tinean semi-arid soils. FEMS Microbiol Ecol 2021;97:fiab025.Garaycochea S, Romero H, Beyhaut E et al. Soil structure, nutri-ent status and water holding capacity shape Uruguayangrassland prokaryotic communities. FEMS Microbiol Ecol2020;96:fiaa207.Gieske MF, Kinkel LL. Long-term nitrogen addition in maizemonocultures reduces in vitro inhibition of actinomycetestandards by soil-borne actinomycetes. FEMS Microbiol Ecol2020;96:fiaa181.Heijo G, Taulé C, Mareque C et al. Interaction among endo-phytic bacteria, sweet sorghum (Sorghum bicolor) cultivarsand chemical nitrogen fertilization. FEMS Microbiol Ecol2021;97:fiaa245.Hohmann P, Schlaeppi K, Sessitsch A. miCROPe 2019 - emerg-ing research priorities towards microbe-assisted crop pro-duction. FEMS Microbiol Ecol 2020;96:fiaa177.Jurburg SD, Shek KL, McGuire K. Soil microbial compositionvaries in response to coffee agroecosystem management.FEMS Microbiol Ecol 2020;96:fiaa164.Kusstatscher P, Cernava T, Abdelfattah A et al. Microbiomeapproaches provide the key to biologically control posthar-vest pathogens and storability of fruits and vegetables. FEMSMicrobiol Ecol 2020;96:fiaa119.Larkin RP. Soil health paradigms and implications for diseasemanagement. Annu Rev Phytopathol 2015;53:199–221.Neal AL, McLaren T, Lourenço Campolino M et al. Crop typeexerts greater influence upon rhizosphere phosphohydro-lase gene abundance and phylogenetic diversity than phos-phorus fertilization. FEMS Microbiol Ecol 2021;97:fiab033.Pedrinho A, Mendes LW, Merloti LF et al. The natural recovery ofsoil microbial community and nitrogen functions after pas-ture abandonment in the Amazon region. FEMS Microbiol Ecol2020;96:fiaa149.Sarkar D, Rakshit A. Safeguarding the fragile rice-wheatecosystem of the Indo-Gangetic Plains through bio-primingand bioaugmentation interventions. FEMS Microbiol Ecol2020;96:fiaa221.Shrestha A, Schikora A. AHL-priming for enhanced resistanceas a tool in sustainable agriculture. FEMS Microbiol Ecol2020;96:fiaa226.Simonin M, Dasilva C, Terzi V et al. Influence of plant genotypeand soil on the wheat rhizosphere microbiome: evidences fora core microbiome across eight African and European soils.FEMS Microbiol Ecol 2020;96:fiaa067.Tsiknia M, Tsikou D, Papadopoulou KK et al. Multi-species rela-tionships in legume roots: from pairwise legume-symbiontinteractions to the plant - microbiome - soil continuum.FEMS Microbiol Ecol 2021;97:fiaa222.Vieira Velloso CC, Oliveira CA de, Gomes EA et al. Genome-guidedinsights of tropical Bacillus strains efficient in maize growthpromotion. FEMS Microbiol Ecol 2020;96:fiaa157.Doreen BabinJulius Kühn Institute (JKI) - Federal Research Centre for CultivatedPlants, Institute for Epidemiology and Pathogen Diagnostics,Messeweg 11–12, 38104 Braunschweig, GermanyCarolina LeoniInstituto Nacional de Investigación Agropecuaria (INIA), Programa deProducción y Sustentabilidad Ambiental, Estación Experimental INIALas Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones,UruguayAndrew L. NealDepartment of Sustainable Agricultural Sciences, RothamstedResearch, North Wyke, Devon EX20 2SB, United KingdomAngela SessitschAIT Austrian Institute of Technology, Center for Health andBioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln,AustriaKornelia SmallaJulius Kühn Institute (JKI) - Federal Research Centre for CultivatedPlants, Institute for Epidemiology and Pathogen Diagnostics,Messeweg 11–12, 38104 Braunschweig, Germany

Editorial to the Thematic Topic Towards a more sustainable agriculture through managing soil microbiomes

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Editorial to the Thematic Topic Towards a more sustainable agriculture through managing soil microbiomes

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