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Fmicb-11-01622.Pdf (484.1Kb) fmicb-11-01622 July 28, 2020 Time: 15:57 # 1 ORIGINAL RESEARCH published: 28 July 2020 doi: 10.3389/fmicb.2020.01622 Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica Fatma Karray1*†, Mahmoud Gargouri2*†, Asma Chebaane2, Najla Mhiri1, Ahmed Mliki2 and Sami Sayadi3*† Edited by: 1 Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia, 2 Laboratory of Plant Molecular Nikolay Vassilev, Physiology, Centre of Biotechnology of Borj Cedria, Hammam-Lif, Tunisia, 3 Center for Sustainable Development, College University of Granada, Spain of Arts and Sciences, Qatar University, Doha, Qatar Reviewed by: Laila Pamela Partida-Martinez, Instituto Politécnico Nacional de Recent microbiome research has shown that soil fertility, plant-associated microbiome, México (CINVESTAV), Mexico and crop production can be affected by abiotic environmental parameters. The effect Ignacio D. Rodriguez-Llorente, Universidad de Sevilla, Spain of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) *Correspondence: prokaryotic structure and diversity associated with cacti remain poorly investigated and Fatma Karray understood. In the current study, next-generation sequencing approaches were used to [email protected] characterize the diversity and composition of bacteria and archaea associated with the Mahmoud Gargouri [email protected] rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic Sami Sayadi zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that [email protected] bacterial and archaeal cactus microbiomes changed in inside and outside roots and †ORCID: Fatma Karray along the aridity gradient. Plant compartment and aridity gradient were the influencing orcid.org/0000-0002-7390-2270 factors on the differentiation of microbial communities in rhizosphere and endosphere Mahmoud Gargouri samples. The co-occurrence correlations between increased and decreased OTUs orcid.org/0000-0002-7476-9854 Sami Sayadi in rhizosphere and endosphere samples and soil parameters were determined orcid.org/0000-0002-2115-2981 according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were Specialty section: This article was submitted to considered as specific biomarkers taxa, which could play a crucial role on the aridity Plant Microbe Interactions, stress. Overall, our findings highlighted the prominence of the climatic aridity gradient a section of the journal Frontiers in Microbiology on the equilibrium and diversity of microbial community composition in the rhizosphere Received: 11 March 2020 and endosphere of cactus. Accepted: 22 June 2020 Keywords: Opuntia ficus-indica, bacterial and archaeal microbiome, aridity gradient, rhizosphere soil, Published: 28 July 2020 endosphere root, co-occurrence network Citation: Karray F, Gargouri M, Chebaane A, Mhiri N, Mliki A and INTRODUCTION Sayadi S (2020) Climatic Aridity Gradient Modulates the Diversity Semi-arid and arid zones occupy nearly 40% of the world’s terrestrial surface and are the most of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia vulnerable to climate changes (Schlaepfer et al., 2017; Canter, 2018). These zones are characterized ficus-indica. by high temperatures and low precipitations, and they are probably the most threatened by Front. Microbiol. 11:1622. desertification. Abiotic stress, including high and low temperature, water deficit (drought) and doi: 10.3389/fmicb.2020.01622 flooding, salinity, UV radiation, light, and poor nutrient soils, have a significant impact on soil Frontiers in Microbiology | www.frontiersin.org 1 July 2020 | Volume 11 | Article 1622 fmicb-11-01622 July 28, 2020 Time: 15:57 # 2 Karray et al. Aridity Modulates Cactus Bacterial Microbiome fertility and subsequently on agricultural production in semi-arid Bezerra et al., 2017). Cactus endophytic plant growth-promoting and arid regions (Shahid and Al-Shankiti, 2013; Cuevas et al., bacteria (PGPR) are known to facilitate plant growth by 2019; Hussain et al., 2019). promoting production of phytohormones (auxins, gibberelins, Cacti (Cactaceae) represent one of the most xerophyte plants cytokinins, and ethylene), diazotrophic fixation of nitrogen, and that have their origin in arid and semi-arid ecosystems of central solubilization of phosphate. Moreover, they enhance the plant’s Mexico and the American continent (Hernandez-Hernandez tolerance to various stresses, such as high salinity, drought, et al., 2014). Cactaceae are an extremely diverse family of metal toxicity, pesticide load, and activity against a broad plants among which the genus Opuntia is the most numerous spectrum of phytopathogens (Puente et al., 2009a; Lopez et al., (Hernandez-Hernandez et al., 2014). Several morphological and 2011; Kavamura et al., 2013). Two rhizobacteria related to the physiological adaptations have been developed by the genus genus Bacillus were isolated from Brazilian cacti exhibiting Opuntia in arid environments where water is the main factor plant growth-promotion abilities under drought conditions limiting the development of most plant species. Prominent (Kavamura et al., 2013). among these adaptations is the Crassulacean acid metabolism In North Africa, particularly in Tunisia, wild and cultivated (CAM), a water-efficient type of photosynthesis, which allows populations of Opuntia ficus-indica (Cactaceae) exist from north plants to fix carbon dioxide through the night and prevent water to south in all bioclimatic zones, from the humid to the semi- loss during the day (Nobel, 2010). Besides, their morphologies are arid zones (Nefzaoui and Salem, 2001). It is mainly cultivated characterized by succulent bodies, thick epidermis of cladodes for fruit production and forage, particularly in upper-arid covered with spines, and shallow and extensive root systems regions (Nefzaoui et al., 2010). The investigation on microbial that enable cacti to exploit scarce rainfall and high temperatures. communities and the mechanisms by which particular bacteria These physiological and biochemical strategies developed by cacti associated with cactus plants induce abiotic stress tolerance have permitted them to resist and spread under conditions of in plants is still poorly understood. The main focus of the high temperatures and scarce and erratic rainfall (Nefzaoui et al., present research was to characterize the prokaryotic (bacteria 2010, 2014). They play a significant role in the protection of and archaea) community’s diversity and composition in Opuntia local fauna in arid ecosystems. Moreover, plantations of cactus ficus-indica using DGGE and high-throughput sequencing for fruit and forage production have been developed in all (Illumina MiSeq) approaches. The impact of the aridity gradient continents (Nefzaoui et al., 2010). The increasing interest in and soil physical and chemical properties on the diversity and cactus cultivation, particularly Opuntia ficus-indica, is due to its the composition of the prokaryotic communities associated with implication in the future achievement of sustainable agriculture spineless cacti were evaluated. in arid and semi-arid zones. It is widely documented that a significant diversity of microbes associated with plants form a biological unit named “holobiont” (Bordenstein and Theis, 2015; MATERIALS AND METHODS Vandenkoornhuyse et al., 2015). These microorganisms can affect host fitness, development, adaptation, survival, and distribution Sampling of plants. Several previous studies, based on culture-dependent Prickly pear trees (Opuntia ficusindica f. inermis) growing in and culture-independent approaches, reported that bacteria and wild areas protected by the forest administration in Tunisia fungi live in different plant compartments, and some of them were selected for this study: rhizosphere soil (5 mm of soil are involved in promoting plant growth and/or tolerance to adhering to the root surface) and root endosphere (the interior abiotic stress in arid ecosystems. Numerous factors influencing of the root). The studied locations were chosen to represent the plant microbiome, such as the host genotype, the physical an increased aridity gradient characterized by a decreased total and chemical properties of soil, the seasonal variations, the annual precipitation and mean temperature ranging from 1200 agricultural practices, the plant compartment, the biogeography to 100 mm (Verner et al., 2018) and from 18 to 20.2◦C of the plant species, and the plant development, have been studied (meteorological stations in Tunisia), respectively, and covering using high-throughput sequencing technologies (Coleman-Derr four bioclimatic zones (humid, semi-arid, upper-arid, lower- et al., 2016; Fonseca-García et al., 2016; Eida et al., 2018; Lee arid) (Table 1). The latitude and longitude for each site were et al., 2019; Zheng and Gong, 2019). However, despite many noted using a GPS device during the field work (Table 1). Roots studies carried out using culture and uncultured-based methods collected from cactus plants aged between 3 and 4 years were to characterize cactus-associated microbiome in arid zones, the considered as young wild plantations. The height of cactus plants effect of aridity on microbiome assembly has not been fully is about 3–3.5 m. After digging until the first primary root explored. Several studies have cataloged
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