Bioinformatic study of the soil microbiome under different cropping systems

[SPA] Esta tesis doctoral se presenta bajo la modalidad de compendio de publicaciones. Mantener la producción o, incluso aumentarla, es uno de los retos de esta época, ya que la población aumenta cada día. Sin embargo, la producción está disminuyendo por muchas razones, siendo una de ellas la degradación del suelo. Hay muchos factores que provocan esta degradación de los suelos como: la erosión, la pérdida de materia orgánica, el viento, el agua y, muy especialmente, las prácticas agrarias intensivas, que incluyen el uso de: pesticidas, herbicidas y fertilizantes químicos. Para evitar este daño al suelo, están surgiendo propuestas más sostenibles. Para estudiar la calidad del suelo generalmente se determinan algunos parámetros fisicoquímicos, químicos y biológicos, aunque las nuevas técnicas moleculares (como la secuenciación de última generación), están ganando fuerza para evaluar la calidad del suelo, debido al papel crucial que juegan los microorganismos en mantener la salud del suelo, participando en los ciclos bioquímicos (como el ciclo del nitrógeno) y, en consecuencia, en la producción agraria. Actualmente están surgiendo herramientas computacionales para analizar esos datos y sus relaciones, a través de técnicas estadísticas multivariantes conducidas dentro del campo de la bioinformática. De hecho, existen diversos recursos bioinformáticos para profundizar en el estudio de la estructura microbiana, su funcionalidad y las interconexiones entre la comunidad microbiana, así como las propiedades del suelo. Por lo tanto, el objetivo de esta tesis es evaluar la respuesta de los microorganismos del suelo a través del uso de herramientas bioinformáticas, su análisis estadístico y las relaciones de estos con los parámetros fisicoquímicos, físicos, químicos, biológicos y la producción de los cultivos bajo prácticas de cultivo sostenible. Los tres trabajos que han sido publicados son: a) Cambios en las comunidades bacterianas y fúngicas en sistemas de cultivo orgánico de largo plazo. Agriculture (https://doi.org/10.3390/agriculture11050445). b) Cambio en las interacciones y especializaciones en las comunidades bacterianas del suelo tras una aplicación a largo plazo de compost, que incrementó la presencia de genes del ciclo del nitrógeno en el suelo. Agronomy (https://doi.org/10.3390/agronomy12020316). c) Un año de cultivos asociados de melón:caupí mejora los nutrientes y cambia las comunidades microbianas del suelo. Agriculture, Ecosystems & Environment (https://doi.org/10.1016/j.agee.2022.107856) Las primeras dos publicaciones estudian el efecto de un experimento a largo plazo (10 años) donde dos cultivos orgánicos, uno con la adición de compost y té de compost y el otro con la adición de estiércol fresco, son comparados con el cultivo convencional. Para este propósito, las propiedades del suelo y las comunidades microbianas, determinadas a través de la secuenciación de los genes 16S e ITS, son estudiadas mediante el uso de técnicas estadísticas, tanto univariantes como multivariantes, y mediante el Análisis Discriminante Lineal por Efecto del Tamaño (LEfSe). Para profundizar en la funcionalidad, estructura y conexiones microbianas se aplican avanzados algoritmos bioinformáticos como la Investigación Filogenética de Comunidades por la Reconstrucción de Estados No observados (PICRUSt) y el Análisis de Redes Moleculares (MENA). Los resultados muestran como los dos sistemas sostenibles, en particular en el que se aplica el compost, produce un aumento del carbono orgánico total, nitrógeno total y algunos micronutrientes como boro o magnesio, comparado con el convencional. Con respecto a la comunidad microbiana, aunque la α-diversidad no detectó diferencias entre los sistemas de cultivo, la -diversidad y el algoritmo LEfSe son capaces de detectar cambios en las comunidades bacterianas y fúngicas, donde diferentes microorganismos se muestran asocidados a los diferentes cultivos realizados ejem. Haliangium, Wallemiales, Turicibacter, Pantoea o Pseudoalteromonas. La construcción de redes de coocurrencia y su posterior análisis, así como la predicción de una funcionalidad potencial, muestra como la incorporación de compost aumentó la modularidad, permitiendo que la comunidad hospedara un mayor número de nichos, lo que facilitaría la respuesta de la comunidad microbiana a cambios en factores externos. Además, la funcionalidad potencial revela como la aplicación de compost aumenta la fijación potencial de nitrógeno a través de los microorganismos, disminuyendo las emisiones de N2O y aumentando el secuestro potencial de carbono por parte de microorganismos autótrofos. La tercera publicación incluye el efecto, a corto plazo, de distintas distribuciones de cultivos asociados como melón (Cucumis melo) y caupí (Vigna unguiculata), en comparación con el monocultivo de melón y caupí, sobre las propiedades del suelo y la comunidad bacteriana obtenida a través de la amplificación del gen 16S rRNA. Los resultados obtenidos a través de los apropiados procedimientos estadísticos univariantes, multivariantes y el algoritmo LEfSe usando recursos computacionales, revelan como el sistema de cultivos asociados incrementa el nitrógeno total, el carbono orgánico total, el fósforo y la producción de melón en comparación con un sistema de monocultivo, pero también revela como el cultivo asociado cambia la población bacteriana y promueve el desarrollo de algunos microorganismos beneficiosos, como Pseudomonas, Bacillus, Sphingomonas y Strepmyces. [ENG] This doctoral dissertation has been presented in the form of thesis by publication. Maintaining crop yield, or even increasing, is one of the challenges of this time since every day the population increases. However, agricultural yield is declining for many reasons, being one of them, the soil degradation. There are many factors involve in this soil degradation such as erosion, loss of organic matter, the wind, the water, and most especially intensive farming practices which includes: pesticides, herbicides, and chemical fertilizers. To avoid this soil damage, many sustainable proposals have emerged. To study soil quality, generally the measurement of some physicochemical, chemical and biological parameters are used, although new molecular techniques (such a Next Generation Sequencing), are also gaining strength to asse soil quality due to the crucial role that microorganisms play in maintaining soil health participating in biochemical cycles (such N-cycle) and, in consequence, for crop production. Currently, there are a burgeoning development of computational tools to analyse such data, multidimensional by nature, and their interrelationships mainly through multivariate techniques conducted under the field of Bioinformatics. Indeed, specific bioinformatics resources are available to deep on the study of the microbial community structure, functionality and the interconnection between microbial community and soil properties. Therefore, the objective of this thesis is to evaluate the response of soil microorganisms, through the use of bioinformatic tools and its statistical analysis, and their relationship with soil physicochemical, physical, chemical, biological parameters and crop yield when sustainable crop systems are assayed. Three papers have been published: a) Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems. Agriculture (https://doi.org/10.3390/agriculture11050445). b) Long-Term Compost Amendment Changes Interactions and Specialization in the Soil Bacterial Community, Increasing the Presence of Beneficial N-Cycling Genes in the Soil. Agronomy (https://doi.org/10.3390/agronomy12020316). c) A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community. Agriculture, Ecosystems & Environment (https://doi.org/10.1016/j.agee.2022.107856) The first two publications study the effect of a long-term experiment (10 years) where two sustainable cropping systems with the application of compost and compost tea in one hand; and fresh manure in the other are compared with a conventional cropping system. For this purpose, soil properties and microbial communities which are determined by sequencing of 16S rRNA and ITS genes, are studied by using univariate and multivariate statistical methodologies, and Linear discriminant analysis Effect Size analysis (LEfSe). To deepen on functional microbial structure and microbial connections, advanced bioinformatics algorithms are applied through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Molecular Ecological Network Analysis (MENA). Results show that both sustainable cropping systems, in particular the one with compost, produces an increase on total organic carbon, total nitrogen and some micronutrients such as boron or magnesium compared to the conventional one. Regarding to microbial community, although α-diversity do not detected differences between different cropping system, β-diversity and LEfSe algorithm are able to detect changes in bacterial and fungal communities, where different microorganisms are associated with the different cultivation systems carried out e.g., Haliangium, Wallemiales, Turicibacter, Pantoea or Pseudoalteromonas. The co-occurrence network construction and the prediction of potential functionality show that the incorporation of compost increases the modularity, allowing the community to host greater number of niches that would facilitate the response of microbial community to environmental factors. In addition, potential functionality reveal how compost application increases bacterial nitrogen-fixing potential, decreasing N2O emissions and increasing the carbon-sequestration potential by autotrophic microorganisms. The third publication includes the effect of different intercropping patterns (melon (Cucumis melo)/cowpea (Vigna unguiculata) a legume able to for nodules and fixing atmospheric nitrogen), in comparison to melon and cowpea monoculture on soil properties and bacterial community by sequencing of 16S rRNA gene. Results through suitable univariate and multivariate statistical procedures and LEfSe analysis, reveal how intercropping system increases total nitrogen, total organic carbon, phosphorous and crop yield compared with melon monocrop systems, but it also reveals how the intercropping system changes the bacterial community and promotes the growth of some beneficial microorganisms such as Pseudomonas, Bacillus, Sphingomonas and Streptomyces.Esta tesis doctoral se presenta bajo la modalidad de compendio de publicaciones, con tres artículos: 1. Cambios en las comunidades bacterianas y fúngicas en sistemas de cultivo orgánico de largo plazo. Agriculture (https://doi.org/10.3390/agriculture11050445). 2. Cambio en las interacciones y especializaciones en las comunidades bacterianas del suelo tras una aplicación a largo plazo de compost, que incrementó la presencia de genes del ciclo del nitrógeno en el suelo. Agronomy (https://doi.org/10.3390/agronomy12020316). 3. Un año de cultivos asociados de melón:caupí mejora los nutrientes y cambia las comunidades microbianas del suelo. Agriculture, Ecosystems & Environment (https://doi.org/10.1016/j.agee.2022.107856)Escuela Internacional de Doctorado de la Universidad Politécnica de CartagenaUniversidad Politécnica de CartagenaPrograma de Doctorado en Técnicas Avanzadas en Investigación y Desarrollo Agrario y Alimentario (TAIDA

Impact of different crop rotation sequences and management practices on soil bacterial diversity in Northern Netherlands

[SPA] La identificación de la estructura y diversidad bacteriana edáfica proporciona una visión enorme de la calidad del suelo debido a las intensas relaciones bioquímicas entre el microbioma del suelo y las plantas que interactúan. El objetivo de este estudio fue evaluar cómo diferentes sistemas de cultivo diversificados bajo dos diferentes tipos de manejo (convencional y biodinámico) afectan a la diversidad bacteriana del suelo. La comunidad bacteriana del suelo se identificó a través de la secuenciación de próxima generación de genes de codificación del RNAr 16S bacteriano. Los resultados mostraron que diferentes secuencias de rotaciones de cultivos, el periodo de implementación de las rotaciones y la práctica de manejo tienen una fuerte influencia en la biomasa microbiana, la biodiversidad bacteriana y la abundancia de diferentes filos bacterianos. [ENG] Identification of soil bacterial community structure and diversity provides a huge insight into soil quality due to the intense biochemical relationships between soil microbiome and interacting plants. The aim of this study was to assess how different diversified cropping systems under two different management (conventional and biodynamic) can affect soil bacterial diversity. Soil bacterial community was identified through next-generation sequencing of 16S rRNA coding genes of soil bacteria. The findings showed that different sequences of crop rotations, period of implementation of rotations and management practice had a strong influence on soil microbial biomass, bacterial biodiversity and the abundance of different bacterial phyla, without a specific trend regulated by these factors.This work was supported by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003]

Study of soil microbiota though ʻomicsʼ techniques and its bioinformatics and biostatistical analysis in samples of horticultural crop diversification

[SPA] La utilización de la agricultura intensiva ha dado lugar a la degradación del suelo, que ha provocado la reducción de la diversidad y el aumento de riesgos económicos para los granjeros. Por ello, necesitamos un sistema que nos permita mantener nuestro estilo de vida sin dañar el ambiente, como la diversificación de cultivos, basada en el crecimiento de dos o más cultivos en proximidad o la rotación de los cultivos. Su principal beneficio es un aumento de la diversidad y estabilidad del suelo, de la sostenibilidad del ambiente y beneficio económico. El suelo está formado por elementos naturales abióticos y bióticos estrechamente relacionados, donde los microorganismos contribuyen a los ciclos bioquímicos, la mineralización-estabilización de materia orgánica, la estructura del suelo y al crecimiento y desarrollo de las plantas. Esta tesis propone un estudio de los microorganismos del suelo mediante técnicas genómicas y metabolómicas, que nos aportaran gran cantidad de información en el impacto de su complejo ecosistema, como es el suelo. La aplicación de técnicas bioinformáticas nos permitirá obtener resultados para entender su ecosistema en profundidad, también la relación entre las propiedades abióticas y el tipo de cultivo, con el objetivo de alcanzar una producción más productiva, económica y ecológica. [ENG] The increasing implementation of intensive agriculture has resulted in soil degradation, which has provoked the diversity reduction and growing economic risks for farmers. As a consequence, we need a more sustainable system that would allow us to keep our current lifestyle without damaging the environment. Crop diversification is an alternative. It is base in growing two or more crops in proximity or using crop rotation technique. It is main benefits are greater diversity and soil stability, greater environmental sustainability and economic benefit. Soil is formed by abiotic and biotic natural elements (which are) closely related, where microorganisms contribute to biochemical cycles, mineralization-stabilization of organic matter, soil structure and growth and development of plants. This thesis proposes a study of soil microorganisms through genomic and metabolomic techniques, which will provide us with a great amount of information on their impact on a complex ecosystem as it is the soil. The application of bioinformatics tools to generate and analyse such huge data will allows us to get outcomes to understand their ecosystem in depth, as well as their relationship with both the abiotic properties and the type of crop, as a way to achieve a more profitable, economic and ecological production.Agradecer al proyecto Diverfarming del programa H2020 perteneciente a la unión europea (Grant Agreement (728003)) la financiación necesaria para poder realizar esta tesis. También quiero agradecerle al grupo de investigación E079-06 “Estadística: Modelos, Métodos y Aplicaciones” de la Universidad de Murcia el asesoramiento estadístico de todo el proyecto

Effects of solarisation combined with compost on soil pathogens and the microbial community in a spinach cropping system

This study compares the effects of solarization combined with compost (72% vineyard prunings and 28% leek residues) (CAS) versus solarization (NAS) in soils used for intensive spinach cultivation in the Mediterranean area. The objective was to study the beneficial effects of the compost on the soil microbial community, soil fertility and soil functionality related to C and N cycling during solarization, during the spinach crop growth period and after harvesting. CAS did increase soil fertility and microbial activity, in addition, CAS increased the microbial alpha diversity in the soil to a greater extent than NAS, and the Principal Coordinate Analysis (PCoA) of the beta diversity in the soil revealed changes in the bacterial and fungal community at the different sampling times, except after the plastic was lifted. During solarization and after harvesting, different beneficial bacteria and fungi related to C and N cycling were more abundant in CAS than in NAS, in the same way as the genera involved in plant defense and plant growth (Pseudomonas, Sphingomonas, Bacillus, Thermomyces, Streptomyces, NMD1 or Nitrospira). CAS also had a notable effect on the abundance of predictive genes involved in the C and N cycles. The functional genes showed their lowest activity level a week after covering the soil with plastic, but they increased after lifting the plastic and after harvesting. Compared to NAS, CAS also showed higher N2-fixation and greater conversion of N2O to N2. Moreover, the abundance of several predictive genes involved in hemicellulose, lignin and cellulose degradation suggested that CAS produced an increase in nutritional availability. From this study, it can be concluded that the combination of solarization and compost increased soil fertility, microbial activity, microbial diversity and functionality. Compost could provide added value by stimulating the microbiological community in the soil until harvest.This work was supported by the Spanish Ministry of Economy and Competitiveness and with European Regional Development Funds (ERDF, “Una manera de hacer Europa”) in the framework of the project “Compoleaf” (Compost as biofertilizer, resistance inductor against plant pathogens and healthy property promoter under a crop intensive sustainable production). Project (AGL2017–84085-C3–1-R, C3–2-R and C3–3-R) and grant (PRE2018–085802). Thanks to Ansley Evans for having made the corrections of this work in English

Response of microbial community to soil disinfection with compost

[SPA] Evaluamos una enmienda de compost incorporada a un proceso de solarización en comparación con la solarización de suelos agrícolas para determinar si produce algún efecto beneficioso sobre la comunidad microbiana, la fertilidad y la funcionalidad del suelo relacionado con el ciclo del N y C. Se tomaron muestras al inicio (T1), una semana después de añadir los tratamientos (T2) y justo al terminar los tratamientos (T3). La solarización del suelo con enmienda de compost (SEC) enriqueció el suelo con diferentes bacterias y hongos, que se caracterizaron por estar involucradas en diferentes funciones relacionadas con el ciclo del N y C; promotores del crecimiento de las plantas o defensa contra patógenos en comparación con el suelo no modificado (SNM). El compost dio un valor agregado al suelo al aumentar la actividad microbiana, la diversidad microbiana y la composición de la comunidad, aumentando la fertilidad funcional del suelo manteniendo el ciclo del C y N del suelo. [ENG] We evaluated a compost amendment incorporated into a solarization process compared to solarization of agricultural soils to determine if it produced any enhanced effects on the microbial community, fertility, and soil functionality related to N and C cycling. at the beginning (T1), one week after adding the treatments (T2) and just after finishing the treatments (T3). Soil solarization with compost amendment (CAS) enriched the soil with different bacteria and fungi, which were characterized by being involved in different functions related to the N and C cycle; plant growth promoters or defense against pathogens compared to unmodified soil (NAS). CAS brought added value to the soil by increasing microbial activity, microbial diversity, and community composition, increasing functional soil fertility maintaining the soil C and N cycle.Al Ministerio de Economía, Industria y Competitividad por la financiación recibida para llevar a cabo el proyecto AGL 2017-84085-C3-1-R

Changes in bacterial and fungal soil communities in long-term organic cropping systems

Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.Raúl Zornoza acknowledges the financial support received from the Spanish Ministry of Science, Innovation and Universities through the “Ramón y Cajal” Program (RYC-2015-18758). We would like to thank Ansley Evans for providing English corrections

A depth study of changed bacterial structure from soil under different cropping systems by co-occurrence network approach

[SPA] Debido al desgaste de los suelos por el uso indiscriminado de pesticidas y herbicidas, la búsqueda de alternativas a la agricultura convencional ha ido ganando interés alrededor del mundo. En este sentido, los microorganismos son importantes, ya que están incluidos en muchas funciones indispensables en los suelos, como la fijación de nitrógeno. En este trabajo se estudiaron 3 tipos de agricultura diferentes i) convencional, ii) ecológica con estiércol y iii) ecológica con compost, con el objetivo de estudiar los cambios ocurridos en las comunidades bacterianas, así como su funcionalidad, las parcelas estaban ubicadas en Cartagena (España). Para estudiar estas funciones, se utilizó el gen 16S obtenido a través de la secuenciación masiva y seguidamente se realizaron aproximaciones matemáticas a través de PICRUSt para predecir la función de esos microorganismos en el suelo. Por otro lado, se realizó un análisis de redes ecológicas moleculares (MENA) para estudiar las interacciones entre esas bacterias. Los resultados de esta investigación mostraron como el compost puede incrementar algunas rutas metabólicas y puede influir en la organización bacteriana, favoreciendo la modulación y las conexiones entre los nodos. [ENG] Due to soil degradation caused by indiscriminate use of pesticides and herbicides, search for sustainable alternatives to conventional agriculture has taken interest around the world. In this sense, microorganisms are important since they are involved in many indispensable functions on soils such a nitrogen fixation. In this work, three different cropping systems were studied i) conventional ii) organic with manure and iii) organic with compost, with the aim to study changes occurred on bacterial communities as well as their functionality. Experimental plots were located in Cartagena (Spain). To study these functions, 16S gen obtain through high-throughput then a mathematical approximations using PICRUST algorithm were used to predict functionality on soils. On the other hand, a molecular ecological network analysis (MENA) was made to study the interactions among these bacteria. Results of this research showed how compost can enhance some metabolic pathways and can influence the bacterial organization favoring modulation and connections among nodes.Este proyecto está financiado por la Unión Europea a través del proyecto del Programa Horizonte 2020 Diverfarming (GA 728003)

Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness

Composting is an advantageous and efficient process for recycling organic waste and producing organic fertilizers, and many kinds of microorganisms are involved in obtaining quality compost with suppressive activity against soil-borne pathogens. The aim of this work was to evaluate the main differences in the effects of three composting piles on the whole bacterial and fungal communities of baby-leaf lettuce crops and to determine the specific communities by high-throughput sequencing related to suppressiveness against the soil-borne plant pathogen Pythium irregulare- (P. irregulare). Compost pile A was composed of 47% vineyard pruning waste, 34% tomato waste and 19% leek waste; pile B was composed of 54% vineyard pruning waste and 46% tomato waste; and pile C was composed of 42% vineyard pruning waste, 25% tomato waste and 33% olive mill cake. The temperature and the chemical properties of the piles were monitored throughout the composting process. In addition, the potential suppressive capacity of the three composts (C_A, C_B and C_C) against P. irregulare in baby-leaf lettuce was assessed. We found that the bacterial community changed according to the composting phases and composting pile and was sensitive to chemical changes throughout the composting process. The fungal community, on the other hand, did not change between the composting piles and proved to be less influenced by chemical properties, but it did change, principally, according to the composting phases. All composts obtained were considered stable and mature, while compost C_C showed higher maturity than composts C_A and C_B. During composting, the three piles contained a greater relative abundance of Bacterioidetes, Proteobacterias and Actinobacterias related to the suppression of soil-borne pathogens such as Pythium irregulare. Composts C_A and C_B, however, showed higher suppressiveness against P. irregulare than compost C_C. Deeper study showed that this observed suppressiveness was favored by a higher abundance of genera that have been described as potential suppressive against P. irregulare, such as Aspergillus, Penicillium, Truepera and Luteimonas.This study was supported by the Spanish Ministry of Economy and Competitiveness and by European Regional Development Funds (ERDF, “Una manera de hacer Europa”) in the framework of the project “Compoleaf” (Compost as biofertilizer, resistance inductor against plant pathogens and healthy property promoter under a crop intensive sustainable production) (Project AGL2017-84085-C3-1-R, C3-2-R and C3- 3-R). Alicia Hernández-Lara acknowledges the financial support she has received from the Spanish Ministry of Science, Innovation and Universities through the "FPI" Program [PRE2018-085802] for the training of research personne

Long-term adoption of reduced tillage and green manure improves soil physicochemical properties and increases the abundance of beneficial bacteria in a Mediterranean rainfed almond orchard

Soil health and function is one of the most important components for sustainable management of woody orchards. Intensive use of machinery and tillage creates heavy pressure on agroecosystems by altering the soil physicochemical and biological characteristics. In this study we aimed to assess the changes in soil physicochemical properties and the soil bacterial community structure, as well as the main drivers involved in shifts in the microbial community following 10 years implementing reduced tillage and reduced tillage plus green manure in a rainfed Mediterranean almond orchard. The treatments were: i) conventional tillage (CT); ii) reduced tillage (RT); and iii) reduced tillage and diversification with Avena sativa and Vicia sativa (RTD). After ten years, the results showed that the different managements had no significant effect on almond yields. RTD significantly increased total organic carbon (TOC), with an average content of 19.5 g kg−1 compared to 17.1 g kg−1 in CT. RTD also contributed to an increase in the fraction of soil macro-aggregates. Both RT and RTD significantly increased soil total nitrogen (NT) and particulate organic carbon (POC). However, other physical and chemical variables such as exchangeable Ca, Mg and K, bioavailable Fe, Cu, Zn and Mn, cation exchange capacity, bulk density, wilting point and field capacity were not significantly affected by the management. The bacterial community significantly changed with management: RTD showed a higher relative abundance of the family Solirubrobacteraceae and the genera Streptomyces and Solirubrobacter. The bacterial community structure was explained by changes in TOC, POC, pH, and NT values. Thus, a combination of reduced tillage and green manure could represent an appropriate sustainable management for rainfed almond orchards in very fragile environmental conditions, due to an increase in soil organic matter, total nitrogen, and the higher presence of beneficial bacteria related to soil productivity.This work was supported by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003]. We acknowledge the owners of the farm “Los Alhagüeces”, Antonio and Pepe Escámez, for generously letting us work in their farm for the last 12 years

How binomial (traditional rainfed olive grove-Crocus sativus) crops impact the soil bacterial community and enhance microbial capacities

Intercropping can favour the yield of the main crop. However, because of the potential competition among woody crops, this system is rarely used by farmers. To increase knowledge about the intercropping system, we have explored three different combinations of alley cropping in rainfed olive groves compared to conventional management (CP): (i) Crocus sativus (D-S); (ii) Vicia sativa/Avena sativa in annual rotation (D-O); and (iii) Lavandula x intermedia (D-L). Different soil chemical properties were analyzed to evaluate the effects of alley cropping, while 16S rRNA amplification and enzymatic activities were determined to study the changes that occurred in soil microbial communities and activity. In addition, the influence of intercropping on the potential functionality of the soil microbial community was measuredThis research was funded by the European Commission Horizon 2020 project Diverfarming (Crop diversification and low-input farming across Europe: From practitioners' engagement and ecosystems services to increased revenues and value chain organisation), grant agreement 728003Peer reviewe