Effect of Long-Term Agricultural Management on the Soil Microbiota Influenced by the Time of Soil Sampling

Application of agrochemicals and mechanization enabled increasing agriculturalproductivity yet caused various environmental and soil health-related problems.Agricultural practices affect soil microorganisms, which are the key players of manyecosystem processes. However, less is known about whether this effect differs betweentime points. Therefore, soil was sampled in winter (without crop) and in summer (inthe presence of maize) from a long-term field experiment (LTE) in Bernburg (Germany)managed either under cultivator tillage (CT) or moldboard plow (MP) in combinationwith either intensive nitrogen (N)-fertilization and pesticides (Int) or extensive reducedN-fertilization without fungicides (Ext), respectively. High-throughput sequencing of 16SrRNA gene and fungal ITS2 amplicons showed that changes in the microbial communitycomposition were correlated to differences in soil chemical properties caused by tillagepractice. Microbial communities of soils sampled in winter differed only depending onthe tillage practice while, in summer, also a strong effect of the fertilization intensity wasobserved. A small proportion of microbial taxa was shared between soils from the twosampling times, suggesting the existence of a stable core microbiota at the LTE. Ingeneral, taxa associated with organic matter decomposition (such as Actinobacteria,Bacteroidetes, Rhizopus, and Exophiala) had a higher relative abundance under CT.Among the taxa with significant changes in relative abundances due to different long-termagricultural practices were putative pathogenic (e.g., Gibellulopsis and Gibberella) andbeneficial microbial genera (e.g., Chitinophagaceae, Ferruginibacter, and Minimedusa).In summary, this study suggests that the effects of long-term agricultural managementpractices on the soil microbiota are influenced by the soil sampling time, and this needsto be kept in mind in future studies for the interpretation of field data.Fil: Fernandez Gnecco, Gabriela Amancay. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Covacevich, Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Consolo, Verónica Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Behr, Jan H.. Leibniz Institute Of Vegetable And Ornamental Crops (; AlemaniaFil: Sommermann, Loreen. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Moradtalab, Narges. Department Of Nutritional Crop Physiology, Institute Of; AlemaniaFil: Maccario, Lorrie. Section Of Microbiology, Department Of Biology, Univers; AlemaniaFil: Sørensen, Søren J.. Section Of Microbiology, Department Of Biology, Univers; AlemaniaFil: Deubel, Annette. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Schellenberg, Ingo. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Geistlinger, Joerg. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Neumann, Günter. Department Of Nutritional Crop Physiology, Institute Of; AlemaniaFil: Grosch, Rita. Leibniz Institute Of Vegetable And Ornamental Crops (; AlemaniaFil: Smalla, Kornelia. Julius Kühn Institut Braunschweig; AlemaniaFil: Babin, Doreen. Julius Kühn Institut Braunschweig; Alemani

Impact of long-term agricultural management practices on therhizosphere microbiome and plant health

Increasing food and energy demands have resulted in a considerable intensification of farming practices, whichbrought about severe consequences for agricultural soils during last decades. In order to maintain soil quality andhealth for the future, the development of more extensive and sustainable farming strategies is urgently needed.The soil and rhizosphere microbiome play an integral role in virtually all soil processes and are intimately linkedto plant performance. Various studies indicated that agricultural management practices affect soil microbiomes.We therefore hypothesized that this external impact is conveyed by the microbial communities to the currentcrops at the time of their establishment. We used twelve differently managed soils from three long-term fieldtrials established in 1978 (Therwil, Switzerland), 1992 (Bernburg, Germany), and 2006 (Thyrow, Germany) toanalyze the impact of various management strategies (crop rotation, fertilization, tillage) on soil and its associatedrhizosphere microbiomes under consideration of plant productivity, plant health, and the ability of the soils tosuppress soil-borne phytopathogens. The model plant lettuce (Lactuca sativa L.) was cultivated for ten weeks undergrowth-chamber conditions in these soils. High-throughput sequencing of bacterial 16S rRNA genes or fungalITS fragments, respectively, PCR- amplified from total community DNA of rhizosphere and soil samples showedsignificant differences in microbial community compositions between soils that originated from the different fieldsites and long-term farming practices. Moreover, differences depending on long-term agricultural managementin plant productivity and health as measured by RT-qPCR of stress-related plant genes were observed. Localizedanalysis of rhizosphere soil solution was performed using non-invasive sampling techniques with sorption filtersplaced onto the surface of soil-grown roots along the root observation windows with subsequent HPLC-MSprofiling. Amino acids, sugars and antifungal organic acids such as benzoic acid detected in the rhizosphere soilsolutions confirmed variations in concentrations depending on the site and management practice indicating differ-ent stress potentials of farming practices for plants. Agricultural management also affected soil suppressiveness tothe soil-borne model pathogen Rhizoctonia solani.Under controlled growth chamber conditions, we could show the legacy of long-term agricultural managementpractices on the establishment and performance of a subsequent plant generation and its associated rhizospheremicrobiome

Long-term organic and mineral fertilization strategies shape the rhizosphere microbiota and performance of lettuce

International audienceBelowground plant-microbe interactions are crucial for plant development and health. Although previous studies have shown that soil microbial communities are influenced by fertilization strategies, less is known about the aboveground plant response to the rhizosphere microbiota assemblage shaped by agricultural management strategies. In our study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments situated in Therwil, Switzerland and Thyrow, Germany, each of which compared organic vs. mineral fertilization strategies. High-throughput sequencing of bacterial 16S rRNA genes amplified from total community DNA showed a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. Firmicutes were enriched irrespective of the field site in the rhizosphere of lettuce grown in organically fertilized soils. When cultivated in organically fertilized soils, a higher expression of several stress-related genes was observed by RT-qPCR analysis in lettuce leaves although plants were visibly free of disease symptoms. Another experiment showed that in presence of the soil-borne model pathogen Rhizoctonia solani AG1-IB, the plant productivity (dry biomass) decreased in soils from Thyrow with both long-term organic and mineral fertilization strategies. Moreover, we observed that the expression of genes like BGlu42 (β Glucosidase), OPT3 (Iron transporter) and MYB15 (Transcription factor) were significantly higher in the plants grown in organically fertilized soils in presence of R. solani. This could indicate an ISR response via iron-mobilizing phenolics, simulating root iron-deficiency response and changes in iron-homeostasis mechanisms in the rhizosphere, which can be expressed systemically throughout the plant. The ongoing analysis of the rhizosphere microbiome would reveal more information about the suggested mechanism. Taken together, besides effects of fertilization strategy and field site, results of our study under controlled conditions demonstrate the crucial role of the lettuce plant in driving the rhizosphere microbiota assemblage

Long-term organic and mineral fertilization strategies shape the rhizosphere microbiota and performance of lettuce

International audienceBelowground plant-microbe interactions are crucial for plant development and health. Although previous studies have shown that soil microbial communities are influenced by fertilization strategies, less is known about the aboveground plant response to the rhizosphere microbiota assemblage shaped by agricultural management strategies. In our study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments situated in Therwil, Switzerland and Thyrow, Germany, each of which compared organic vs. mineral fertilization strategies. High-throughput sequencing of bacterial 16S rRNA genes amplified from total community DNA showed a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. Firmicutes were enriched irrespective of the field site in the rhizosphere of lettuce grown in organically fertilized soils. When cultivated in organically fertilized soils, a higher expression of several stress-related genes was observed by RT-qPCR analysis in lettuce leaves although plants were visibly free of disease symptoms. Another experiment showed that in presence of the soil-borne model pathogen Rhizoctonia solani AG1-IB, the plant productivity (dry biomass) decreased in soils from Thyrow with both long-term organic and mineral fertilization strategies. Moreover, we observed that the expression of genes like BGlu42 (β Glucosidase), OPT3 (Iron transporter) and MYB15 (Transcription factor) were significantly higher in the plants grown in organically fertilized soils in presence of R. solani. This could indicate an ISR response via iron-mobilizing phenolics, simulating root iron-deficiency response and changes in iron-homeostasis mechanisms in the rhizosphere, which can be expressed systemically throughout the plant. The ongoing analysis of the rhizosphere microbiome would reveal more information about the suggested mechanism. Taken together, besides effects of fertilization strategy and field site, results of our study under controlled conditions demonstrate the crucial role of the lettuce plant in driving the rhizosphere microbiota assemblage

Long-term organic and mineral fertilization strategies shape the rhizosphere microbiota and performance of lettuce

International audienceBelowground plant-microbe interactions are crucial for plant development and health. Although previous studies have shown that soil microbial communities are influenced by fertilization strategies, less is known about the aboveground plant response to the rhizosphere microbiota assemblage shaped by agricultural management strategies. In our study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments situated in Therwil, Switzerland and Thyrow, Germany, each of which compared organic vs. mineral fertilization strategies. High-throughput sequencing of bacterial 16S rRNA genes amplified from total community DNA showed a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. Firmicutes were enriched irrespective of the field site in the rhizosphere of lettuce grown in organically fertilized soils. When cultivated in organically fertilized soils, a higher expression of several stress-related genes was observed by RT-qPCR analysis in lettuce leaves although plants were visibly free of disease symptoms. Another experiment showed that in presence of the soil-borne model pathogen Rhizoctonia solani AG1-IB, the plant productivity (dry biomass) decreased in soils from Thyrow with both long-term organic and mineral fertilization strategies. Moreover, we observed that the expression of genes like BGlu42 (β Glucosidase), OPT3 (Iron transporter) and MYB15 (Transcription factor) were significantly higher in the plants grown in organically fertilized soils in presence of R. solani. This could indicate an ISR response via iron-mobilizing phenolics, simulating root iron-deficiency response and changes in iron-homeostasis mechanisms in the rhizosphere, which can be expressed systemically throughout the plant. The ongoing analysis of the rhizosphere microbiome would reveal more information about the suggested mechanism. Taken together, besides effects of fertilization strategy and field site, results of our study under controlled conditions demonstrate the crucial role of the lettuce plant in driving the rhizosphere microbiota assemblage

Fungal community diversity indices according to Simpson and Shannon.

<p>Fungal community diversity indices according to Simpson and Shannon.</p

PermANOVA analysis of ITS1 and ITS2 data based on Bray-Curtis dissimilarities (10,000 permutations).

<p>PermANOVA analysis of ITS1 and ITS2 data based on Bray-Curtis dissimilarities (10,000 permutations).</p

Fungal OTU richness according to agricultural management practice.

<p>Median values for the numbers of OTUs in the 4 replicates per treatment were calculated for the pre-crop maize (WW1), pre-crop rapeseed (WW2), regarding mould-board plough (MP) <i>vs</i>. conservation tillage cultivator (CT), extensive (ext) and intensive (int) N fertilization.</p

Schematic diagram of the long-term field trial.

<p>Experimental design: strip-split-plot design with five fields of crop rotation as main plots (lower panel, rotation cycle from right to left). Management practice (upper panel) for each main plot: tillage MP (left half) and CT (right half) as sub-plots and N-fertilization (int/ext) as sub-sub-plots in four replicates.</p

Venn diagrams depicting the numbers and percentages of fungal genera in differently managed soils.

<p>For the two winter wheat fields WW1 pre-crop maize (left) and WW2 pre-crop rapeseed (right), absolute numbers and percentages are given. Soil samples were investigated from mould-board plough intensive (MP_int), mould-board plough extensive (MP_ext), conservation tillage intensive (CT_int) and CT extensive variants (CT_ext) in four replicates. Two threshold values were applied (minimum relative abundance 0.01% and reproducibility with minimum presence in two out of four replicates). Genera are listed in descending order of relative abundance (*genera including plant beneficial or ^<b>#</b>plant pathogenic species). Unique genera in distinct soil treatments are shown below the respective figure panels. Genera in bold appeared in both pre-crops.</p