Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field.

Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.

Impact of two arbuscular mycorrhizal fungi on Arundo donax L. response to salt stress.

MAIN CONCLUSION: AM symbiosis did not strongly affect Arundo donax performances under salt stress, although differences in the plants inoculated with two different fungi were recorded. The mechanisms at the basis of the improved tolerance to abiotic stresses by arbuscular mycorrhizal (AM) fungi have been investigated mainly focusing on food crops. In this work, the potential impact of AM symbiosis on the performance of a bioenergy crop, Arundo donax, under saline conditions was considered. Specifically, we tried to understand whether AM symbiosis helps this fast-growing plant, often widespread in marginal soils, withstand salt. A combined approach, involving eco-physiological, morphometric and biochemical measurements, was used and the effects of two different AM fungal species (Funneliformis mosseae and Rhizophagus irregularis) were compared. Results indicate that potted A. donax plants do not suffer permanent damage induced by salt stress, but photosynthesis and growth are considerably reduced. Since A. donax is a high-yield biomass crop, reduction of biomass might be a serious agronomical problem in saline conditions. At least under the presently experienced growth conditions, and plant-AM combinations, the negative effect of salt on plant performance was not rescued by AM fungal colonization. However, some changes in plant metabolisms were observed following AM-inoculation, including a significant increase in proline accumulation and a trend toward higher isoprene emission and higher H2O2, especially in plants colonized by R. irregularis. This suggests that AM fungal symbiosis influences plant metabolism, and plant-AM fungus combination is an important factor for improving plant performance and productivity, in presence or absence of stress conditions.

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient.

Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across-habitat ß-diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil ß-diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below-ground biodiversity responses.

Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation.

Intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization, cultivation with non-host species, and pesticide use are widely reported to be detrimental for arbuscular mycorrhizal fungi (AMF), which are one of the most important plant biofertilizers. The effect of the reduction of agricultural input on AMF community dynamics following conversion from conventional non-mycorrhizal to lower input mycorrhizal crop cultivation has not yet been fully elucidated. We investigated the effect of the reduction of agricultural input, rotation, and season on AMF communities in winter wheat field soil after conversion from long-term (more than 20 years) non-mycorrhizal (sugar beet) crop cultivation. We described AMF communities from bulk soil samples by specifically targeting the 18S ribosomal gene using a combination of AMF specific primers and 454 pyrosequencing. No effect was found after 3 years' reduction of agricultural input, and only marginal effects were due to rotation with specific crops preceding winter wheat. Instead, season and year of sampling had the most appreciable influence on the AMF community. We suggest that, after conversion from long-term non-mycorrhizal to mycorrhizal crop cultivation, AMF diversity is low if compared to similar agroecosystems. Seasonal and successional dynamics play an important role as determinants of community structure.

Insights on the Impact of Arbuscular Mycorrhizal Symbiosis on Tomato Tolerance to Water Stress.

Arbuscular mycorrhizal (AM) fungi, which form symbioses with the roots of the most important crop species, are usually considered biofertilizers, whose exploitation could represent a promising avenue for the development in the future of a more sustainable next-generation agriculture. The best understood function in symbiosis is an improvement in plant mineral nutrient acquisition, as exchange for carbon compounds derived from the photosynthetic process: this can enhance host growth and tolerance to environmental stresses, such as water stress (WS). However, physiological and molecular mechanisms occurring in arbuscular mycorrhiza-colonized plants and directly involved in the mitigation of WS effects need to be further investigated. The main goal of this work is to verify the potential impact of AM symbiosis on the plant response to WS To this aim, the effect of two AM fungi (Funneliformis mosseae and Rhizophagus intraradices) on tomato (Solanum lycopersicum) under the WS condition was studied. A combined approach, involving ecophysiological, morphometric, biochemical, and molecular analyses, has been used to highlight the mechanisms involved in plant response to WS during AM symbiosis. Gene expression analyses focused on a set of target genes putatively involved in the plant response to drought, and in parallel, we considered the expression changes induced by the imposed stress on a group of fungal genes playing a key role in the water-transport process. Taken together, the results show that AM symbiosis positively affects the tolerance to WS in tomato, with a different plant response depending on the AM fungi species involved.

Edaphic factors trigger diverse AM fungal communities associated to exotic camellias in closely located Lake Maggiore (Italy) sites.

Camellia japonica L. is an acidophilic ornamental shrub of high economic value that has its center of origin in Japan and has been introduced in several European environmental niches. This exotic species forms arbuscular mycorrhizas (AM), known for their ability to positively affect plant growth. However, AM fungal communities associated to C. japonica in the field have never been characterized. For the first time, the AM fungal community naturally selected by C. japonica was screened in three sites located on the shores of Lake Maggiore (Italy), where specimens of this plant were introduced in the nineteenth century. Mycorrhizal levels were assessed, and the AM fungal communities associated to roots and soil were molecularly characterized based on the small subunit (SSU) rDNA region. The frequency of mycorrhizal roots was high in all sampled root systems (>90 %). Overall, 39 Operational Taxonomic Units (OTUs; 22 Glomerales, 9 Paraglomerales, 7 Archaeosporales, and 1 Diversisporales) were found in the root and soil samples. OTU richness did not significantly differ between the root and the soil niche (5.7 ± 0.6 and 8.0 ± 1.1 average OTUs per sample, respectively) and the three sites analyzed (7.5 ± 0.7, 5.2 ± 1.0, and 7.8 ± 1.5 average OTUs per sample in the three sites, respectively). The AM fungal community composition significantly differed between root-colonizing and soil-dwelling communities and among the three sites under study. Data show a major involvement of edaphic factors, such as available N sources, P, Mg, and K content in soil and soil compaction, in the structuring of the AM fungal communities.

Sequencing and comparison of the mitochondrial COI gene from isolates of Arbuscular Mycorrhizal Fungi belonging to Gigasporaceae and Glomeraceae families.

Arbuscular Mycorrhizal Fungi (AMF) are well known for their ecological importance and their positive influence on plants. The genetics and phylogeny of this group of fungi have long been debated. Nuclear markers are the main tools used for phylogenetic analyses, but they have sometimes proved difficult to use because of their extreme variability. Therefore, the attention of researchers has been moving towards other genomic markers, in particular those from the mitochondrial DNA. In this study, 46 sequences of different AMF isolates belonging to two main clades Gigasporaceae and Glomeraceae have been obtained from the mitochondrial gene coding for the Cytochrome c Oxidase I (COI), representing the largest dataset to date of AMF COI sequences. A very low level of divergence was recorded in the COI sequences from the Gigasporaceae, which could reflect either a slow rate of evolution or a more recent evolutionary divergence of this group. On the other hand, the COI sequence divergence between Gigasporaceae and Glomeraceae was high, with synonymous divergence reaching saturated levels. This work also showed the difficulty in developing valuable mitochondrial markers able to effectively distinguish all Glomeromycota species, especially those belonging to Gigasporaceae, yet it represents a first step towards the development of a full mtDNA-based dataset which can be used for further phylogenetic investigations of this fungal phylum.

Growth-promoting bacteria and arbuscular mycorrhizal fungus enhance maize tolerance to saline stress.

Climate change intensifies soil salinization and jeopardizes the development of crops worldwide. The accumulation of salts in plant tissue activates the defense system and triggers ethylene production thus restricting cell division. We hypothesize that the inoculation of plant growth-promoting bacteria (PGPB) producing ACC (1-aminocyclopropane-1-carboxylate) deaminase favors the development of arbuscular mycorrhizal fungi (AMF), promoting the growth of maize plants under saline stress. We investigated the efficacy of individual inoculation of PGPB, which produce ACC deaminase, as well as the co-inoculation of PGPB with Rhizophagus clarus on maize plant growth subjected to saline stress. The isolates were acquired from the bulk and rhizospheric soil of Mimosa bimucronata (DC.) Kuntze in a temporary pond located in Pernambuco State, Brazil. In the first greenhouse experiment, 10 halophilic PGPB were inoculated into maize at 0, 40 and 80 mM of NaCl, and in the second experiment, the PGPB that showed the best performance were co-inoculated with R. clarus in maize under the same conditions as in the first experiment. Individual PGPB inoculation benefited the number of leaves, stem diameter, root and shoot dry mass, and the photosynthetic pigments. Inoculation with PGPB 28-10 Pseudarthrobacter enclensis, 24-1 P. enclensis and 52 P. chlorophenolicus increased the chlorophyll a content by 138%, 171%, and 324% at 0, 40 and 80 mM NaCl, respectively, comparing to the non-inoculated control. We also highlight that the inoculation of PGPB 28-10, 28-7 Arthrobacter sp. and 52 increased the content of chlorophyll b by 72%, 98%, and 280% and carotenoids by 82%, 98%, and 290% at 0, 40 and 80 mM of NaCl, respectively. Co-inoculation with PGPB 28-7, 46-1 Leclercia tamurae, 70 Artrobacter sp., and 79-1 Micrococcus endophyticus significantly increased the rate of mycorrhizal colonization by roughly 50%. Furthermore, co-inoculation promoted a decrease in the accumulation of Na and K extracted from plant tissue, with an increase in salt concentration, from 40 mM to 80 mM, also favoring the establishment and development of R. clarus. In addition, co-inoculation of these PGPB with R. clarus promoted maize growth and increased plant biomass through osmoregulation and protection of the photosynthetic apparatus. The tripartite symbiosis (plant-fungus-bacterium) is likely to reprogram metabolic pathways that improve maize growth and crop yield, suggesting that the AMF-PGPB consortium can minimize damages caused by saline stress.

Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia.

Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.

Modeling geographic distribution of arbuscular mycorrhizal fungi from molecular evidence in soils of Argentinean Puna using a maximum entropy approach.

The biogeographic region of Argentinean Puna mainly extends at elevations higher than 3,000 m within the Andean Plateau and hosts diverse ecological communities highly adapted to extreme aridity and low temperatures. Soils of Puna are typically poorly evolved and geomorphology is shaped by drainage networks, resulting in highly vegetated endorheic basins and hypersaline basins known as salar or salt flats. Local communities rely on soil fertility for agricultural practices and on pastures for livestock rearing. From this perspective, investigating the scarcely explored microbiological diversity of these soils as indicators of ecosystems functioning might help to predict the fragility of these harsh environments. In this study we collected soil samples from 28 points, following a nested design within three different macro-habitats, i.e., Puna grassland, hypersaline salar and family-run crop fields. Total fungi and arbuscular mycorrhizal fungi (AMF) occurrence were analyzed using eDNA sequencing. In addition, the significance of soil salinity and organic matter content as significant predictors of AMF occurrence, was assessed through Generalized Linear Mixed Modeling. We also investigated whether intensive grazing by cattle and lama in Puna grasslands may reduce the presence of AMF in these highly disturbed soils, driving or not major ecological changes, but no consistent results were found, suggesting that more specific experiments and further investigations may address the question more specifically. Finally, to predict the suitability for AMF in the different macro-habitats, Species Distribution Modeling (SDM) was performed within an environmental coherent area comprising both the phytogeographic regions of Puna and Altoandino. We modeled AMF distribution with a maximum entropy approach, including bioclimatic and edaphic predictors and obtaining maps of environmental suitability for AMF within the predicted areas. To assess the impact of farming on AMF occurrence, we set a new series of models excluding the cultivated Chaupi Rodeo samples. Overall, SDM predicted a lower suitability for AMF in hypersaline salar areas, while grassland habitats and a wider temperature seasonality range appear to be factors significantly related to AMF enrichment, suggesting a main role of seasonal dynamics in shaping AMF communities. The highest abundance of AMF was observed in Vicia faba crop fields, while potato fields yielded a very low AMF occurrence. The models excluding the cultivated Chaupi Rodeo samples highlighted that if these cultivated areas had theoretically remained unmanaged habitats of Puna and Altoandino, then large-scale soil features and local bioclimatic constraints would likely support a lower suitability for AMF. Using SDM we evidenced the influence of bioclimatic, edaphic and anthropic predictors in shaping AMF occurrence and highlighted the relevance of considering human activities to accurately predict AMF distribution.

Alpine constructed wetlands: A metagenomic analysis reveals microbial complementary structure.

Constructed wetlands (CWs) are used to water treatment worldwide, however their application at high-altitude is poorly studied. In order to survive mountain winters, CWs rely on native flora and associated microbial communities. However, the choice of plant-microbes pairs more suitable for water treatment is challenging in alpine environments. Using a metagenomic approach, we investigated the composition of prokaryotes and fungal communities, through extensive sampling inside a constructed wetland in the SW-Alps. Best performing plant species were searched among those hosting the most diverse and resilient microbial communities and to this goal, we analysed them in the natural environment also. Our results showed that microbial communities were less diverse in the CW than at natural conditions, and they differed from plant to plant, revealing a clear variation in taxonomic composition between forbs and gramineous plants. Carex rostrata, Deschampsia caespitosa and Rumex alpinus hosted bacteria very active in N-cycles. Moreover, fungal and prokaryotic communities associated to R. alpinus (Polygonaceae) turned to be the richest and stable among the studied species. In our opinion, this species should be prioritized in CWs at high elevations, also in consideration of its low maintenance requirements.

Different farming and water regimes in Italian rice fields affect arbuscular mycorrhizal fungal soil communities.

Arbuscular mycorrhizal fungi (AMF) comprise one of the main components of soil microbiota in most agroecosystems. These obligate mutualistic symbionts colonize the roots of most plants, including crop plants. Many papers have indicated that different crop management practices could affect AMF communities and their root colonization. However, there is little knowledge available on the influence of conventional and low-input agriculture on root colonization and AMF molecular diversity in rice fields. Two different agroecosystems (continuous conventional high-input rice monocropping and organic farming with a five-year crop rotation) and two different water management regimes have been considered in this study. Both morphological and molecular analyses were performed. The soil mycorrhizal potential, estimated using clover trap cultures, was high and similar in the two agroecosystems. The diversity of the AMF community in the soil, calculated by means of PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) and 18S rDNA sequencing on clover trap cultures roots, was higher for the organic cultivation. The rice roots cultivated in the conventional agrosystem or under permanent flooding showed no AMF colonization, while the rice plants grown under the organic agriculture system showed typical mycorrhization patterns. Considered together, our data suggest that a high-input cropping system and conventional flooding depress AMF colonization in rice roots and that organic managements could help maintain a higher diversity of AMF communities in soil.

Unique arbuscular mycorrhizal fungal communities uncovered in date palm plantations and surrounding desert habitats of Southern Arabia.

The main objective of this study was to shed light on the previously unknown arbuscular mycorrhizal fungal (AMF) communities in Southern Arabia. We explored AMF communities in two date palm (Phoenix dactylifera) plantations and the natural vegetation of their surrounding arid habitats. The plantations were managed traditionally in an oasis and according to conventional guidelines at an experimental station. Based on spore morphotyping, the AMF communities under the date palms appeared to be quite diverse at both plantations and more similar to each other than to the communities under the ruderal plant, Polygala erioptera, growing at the experimental station on the dry strip between the palm trees, and to the communities uncovered under the native vegetation (Zygophyllum hamiense, Salvadora persica, Prosopis cineraria, inter-plant area) of adjacent undisturbed arid habitat. AMF spore abundance and species richness were higher under date palms than under the ruderal and native plants. Sampling in a remote sand dune area under Heliotropium kotschyi yielded only two AMF morphospecies and only after trap culturing. Overall, 25 AMF morphospecies were detected encompassing all study habitats. Eighteen belonged to the genus Glomus including four undescribed species. Glomus sinuosum, a species typically found in undisturbed habitats, was the most frequently occurring morphospecies under the date palms. Using molecular tools, it was also found as a phylogenetic taxon associated with date palm roots. These roots were associated with nine phylogenetic taxa, among them eight from Glomus group A, but the majority could not be assigned to known morphospecies or to environmental sequences in public databases. Some phylogenetic taxa seemed to be site specific. Despite the use of group-specific primers and efficient trapping systems with a bait plant consortium, surprisingly, two of the globally most frequently found species, Glomus intraradices and Glomus mosseae, were not detected neither as phylogenetic taxa in the date palm roots nor as spores under the date palms, the intermediate ruderal plant, or the surrounding natural vegetation. The results highlight the uniqueness of AMF communities inhabiting these diverse habitats exposed to the harsh climatic conditions of Southern Arabia.

Metabarcoding of Soil Fungal Communities Associated with Alpine Field-Grown Saffron (Crocus sativus L.) Inoculated with AM Fungi.

Soil fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. Arbuscular mycorrhizal fungi (AMF) establish mutualistic symbiotic associations with plant roots and act as biofertilizers by enhancing plant nutrients and water uptake. Information about the AMF association with Crocus sativus L. (saffron) and their impact on crop performances and spice quality has been increasing in recent years. Instead, there is still little data on the biodiversity of soil microbial communities associated with this crop in the Alpine environments. The aims of this study were to investigate the fungal communities of two Alpine experimental sites cultivated with saffron, and to rank the relative impact of two AMF inocula, applied to soil as single species (R = Rhizophagus intraradices, C. Walker & A. Schüßler) or a mixture of two species (M = R. intraradices and Funneliformis mosseae, C. Walker & A. Schüßler), on the resident fungal communities which might be influenced in their diversity and composition. We used Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region to characterize the fungal communities associated to Crocus sativus cultivation in two fields, located in the municipalities of Saint Christophe (SC) and Morgex (MG), (Aosta Valley, Italy), treated or not with AMF inocula and sampled for two consecutive years (Y1; Y2). Data analyses consistently indicated that Basidiomycota were particularly abundant in both sites and sampling years (Y1 and Y2). Significant differences in the distribution of fungal taxa assemblages at phylum and class levels between the two sites were also found. The main compositional differences consisted in significant abundance changes of OTUs belonging to Dothideomycetes and Leotiomycetes (Ascomycota), Agaricomycetes and Tremellomycetes (Basidiomycota), Mortierellomycetes and Mucoromycetes. Further differences concerned OTUs, of other classes, significantly represented only in the first or second year of sampling. Concerning Glomeromycota, the most represented genus was Claroideoglomus always detected in both sites and years. Other AMF genera such as Funneliformis, Septoglomus and Microdominikia, were retrieved only in MG site. Results highlighted that neither sites nor inoculation significantly impacted Alpine saffron-field fungal communities; instead, the year of sampling had the most appreciable influence on the resident communities.

Arbuscular Mycorrhizal Fungi from Argentinean Highland Puna Soils Unveiled by Propagule Multiplication.

Low arbuscular-mycorrhizal (AM) sporulation in arid field soils limits our knowledge of indigenous species when diversity studies are based only on spore morphology. Our aim was to use different approaches (i.e., spore morphological approach and PCR-SSCP (single-strand-conformation-polymorphism) analysis after trap plant multiplication strategies to improve the knowledge of the current richness of glomalean AM fungi (Glomerales; Glomeromycota) from the Argentine Puna. Indigenous propagules from two pristine sites at 3870 and 3370 m of elevation were multiplied using different host plants; propagation periods (2-6 months), and subculture cycles (1; 2; or 3) from 5 to 13 months. The propagule multiplication experiment allowed the detection of different glomoid taxa of Funneliformis spp. and Rhizoglomus spp., which were considered cryptic species since they had never been found in Puna soils before. On the other hand; almost all the generalist species previously described were recovered from cultures; except for Glomus ambisporum. Both plant host selection and culture times are critical for Glomerales multiplication. The SSCP analysis complemented the morphological approach and showed a high variability of Glomus at each site; revealing the presence of Funneliformis mosseae. This study demonstrates that AMF trap culture (TC) is a useful strategy for improving the analysis of AM fungal diversity/richness in the Argentinean highlands.

Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach.

The biodiversity of arbuscular mycorrhizal fungi (AMF) communities present in five Sardinian soils (Italy) subjected to different land-use (tilled vineyard, covered vineyard, pasture, managed meadow and cork-oak formation) was analysed using a pyrosequencing-based approach for the first time. Two regions of the 18S ribosomal RNA gene were considered as molecular target. The pyrosequencing produced a total of 10924 sequences: 6799 from the first and 4125 from the second target region. Among these sequences, 3189 and 1003 were selected to generate operational taxonomic units (OTUs) and to evaluate the AMF community richness and similarity: 117 (37 of which were singletons) and 28 (nine of which were singletons) unique AMF OTUs were detected respectively. Within the Glomeromycota OTUs, those belonging to the Glomerales order were dominant in all the soils. Diversisporales OTUs were always detected, even though less frequently, while Archaeosporales and Paraglomerales OTUs were exclusive of the pasture soil. Eleven OTUs were shared by all the soils, but each of the five AMF communities showed particular features, suggesting a meaningful dissimilarity among the Glomeromycota populations. The environments with low inputs (pasture and covered vineyard) showed a higher AMF biodiversity than those subjected to human input (managed meadow and tilled vineyard). A reduction in AMF was found in the cork-oak formation because other mycorrhizal fungal species, more likely associated to trees and shrubs, were detected. These findings reinforce the view that AMF biodiversity is influenced by both human input and ecological traits, illustrating a gradient of AMF communities which mirror the land-use gradient. The high number of sequences obtained by the pyrosequencing strategy has provided detailed information on the soil AMF assemblages, thus offering a source of light to shine on this crucial soil microbial group.

Water management and phenology influence the root-associated rice field microbiota.

Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

High-Throughput DNA Sequence-Based Analysis of AMF Communities.

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic impacts as they support plant nutrition and water supply, soil structure, and plant resistance to pathogens. Investigating AMF presence and distribution at small and large scales is critical. Therefore, research requires standard protocols to be easily implemented. In this chapter, we describe a workflow for AMF identification by high-throughput sequencing through Illumina MiSeq platform of two DNA target regions: small subunit (SSU) and internal transcribed spacer (ITS). The protocol can apply to both soil and root AMF communities.

Impact of land use history on the arbuscular mycorrhizal fungal diversity in arid soils of Argentinean farming fields.

Arbuscular mycorrhizal fungi (AMF) are a key soil functional group, with an important potential to increase crop productivity and sustainable agriculture including food security. However, there is clear evidence that land uses, crop rotations and soil features affect the AMF diversity and their community functioning in many agroecosystems. So far, the information related to AMF biodiversity in ecosystems like the Argentinean Puna, an arid high plateau where plants experience high abiotic stresses, is still scarce. In this work, we investigated morphological and molecular AMF diversity in soils of native corn, bean and native potato Andean crops, under a familiar land use, in Chaupi Rodeo (Jujuy, Argentina), without agrochemical supplements but with different histories of crop rotation. Our results showed that AMF morphological diversity was not only high and variable among the three different crop soils but also complemented by Illumina MiSeq data. The multivariate analyses highlighted that total fungal diversity is significantly affected by the preceding crop plants and the rotation histories, more than from the present crop species, while AMF communities are significantly affected by preceding crop only in combination with the effect of nitrogen and calcium soil concentration. This knowledge will give useful information on appropriate familiar farming.

Native Arbuscular Mycorrhizal Fungi Characterization from Saline Lands in Arid Oases, Northwest China.

Arbuscular mycorrhizal fungi (AMF) colonize land plants in almost every ecosystem, even in extreme conditions, such as saline soils. In the present work, we report the mycorrhizal capacity of rhizosphere soils collected in the dry desert region of the Minqin Oasis, located in the northwest of China (Gansu province), which is characterized by several halophytes. Lycium spp. and Peganum nigellastrum were used as trap plants in a greenhouse experiment to identify autochthonous AMF associated with the halophytes' rhizospheres. Morphological observations showed the typical AMF structures inside roots. Twenty-six molecularly distinct AMF taxa were recovered from soil and root DNA. The taxonomical diversity mirrors the several AMF adapted to extreme environmental conditions, such as the saline soil of central China. Knowledge of the AMF associated with halophytes may contribute to select specific fungal isolates to set up agriculture strategies for protecting non-halophyte crop plants in saline soils.