Aligned grains and scattered light found in gaps of planet-forming disk.

Polarized (sub)millimetre emission from dust grains in circumstellar disks was initially thought to be because of grains aligned with the magnetic field1,2. However, higher-resolution multi-wavelength observations3-5 and improved models6-10 found that this polarization is dominated by self-scattering at shorter wavelengths (for example, 870 µm) and by grains aligned with something other than magnetic fields at longer wavelengths (for example, 3 mm). Nevertheless, the polarization signal is expected to depend on the underlying substructure11-13, and observations until now have been unable to resolve polarization in multiple rings and gaps. HL Tau, a protoplanetary disk located 147.3 ± 0.5 pc away14, is the brightest class I or class II disk at millimetre-submillimetre wavelengths. Here we show deep, high-resolution polarization observations of HL Tau at 870 µm, resolving polarization in both the rings and the gaps. We find that the gaps have polarization angles with a notable azimuthal component and a higher polarization fraction than the rings. Our models show that the disk polarization is due to both scattering and emission from the aligned effectively prolate grains. The intrinsic polarization of aligned dust grains is probably more than 10%, which is much higher than that expected in low-resolution observations (about 1%). Asymmetries and dust features that are not seen in non-polarimetric observations are seen in the polarization observations.

Four annular structures in a protostellar disk less than 500,000 years old.

Annular structures (rings and gaps) in disks around pre-main-sequence stars have been detected in abundance towards class II protostellar objects that are approximately 1,000,000 years old1. These structures are often interpreted as evidence of planet formation1-3, with planetary-mass bodies carving rings and gaps in the disk4. This implies that planet formation may already be underway in even younger disks in the class I phase, when the protostar is still embedded in a larger-scale dense envelope of gas and dust5. Only within the past decade have detailed properties of disks in the earliest star-forming phases been observed6,7. Here we report 1.3-millimetre dust emission observations with a resolution of five astronomical units that show four annular substructures in the disk of the young (less than 500,000 years old)8 protostar IRS 63. IRS 63 is a single class I source located in the nearby Ophiuchus molecular cloud at a distance of 144 parsecs9, and is one of the brightest class I protostars at millimetre wavelengths. IRS 63 also has a relatively large disk compared to other young disks (greater than 50 astronomical units)10. Multiple annular substructures observed towards disks at young ages can act as an early foothold for dust-grain growth, which is a prerequisite of planet formation. Whether or not planets already exist in the disk of IRS 63, it is clear that the planet-formation process begins in the initial protostellar phases, earlier than predicted by current planet-formation theories11.

Episodic molecular outflow in the very young protostellar cluster Serpens South.

The loss of mass from protostars, in the form of a jet or outflow, is a necessary counterpart to protostellar mass accretion. Outflow ejection events probably vary in their velocity and/or in the rate of mass loss. Such 'episodic' ejection events have been observed during the class 0 protostellar phase (the early accretion stage), and continue during the subsequent class I phase that marks the first one million years of star formation. Previously observed episodic-ejection sources were relatively isolated; however, the most common sites of star formation are clusters. Outflows link protostars with their environment and provide a viable source of the turbulence that is necessary for regulating star formation in clusters, but it is not known how an accretion-driven jet or outflow in a clustered environment manifests itself in its earliest stage. This early stage is important in establishing the initial conditions for momentum and energy transfer to the environment as the protostar and cluster evolve. Here we report that an outflow from a young, class 0 protostar, at the hub of the very active and filamentary Serpens South protostellar cluster, shows unambiguous episodic events. The (12)C(16)O (J = 2-1) emission from the protostar reveals 22 distinct features of outflow ejecta, the most recent having the highest velocity. The outflow forms bipolar lobes--one of the first detectable signs of star formation--which originate from the peak of 1-mm continuum emission. Emission from the surrounding C(18)O envelope shows kinematics consistent with rotation and an infall of material onto the protostar. The data suggest that episodic, accretion-driven outflow begins in the earliest phase of protostellar evolution, and that the outflow remains intact in a very clustered environment, probably providing efficient momentum transfer for driving turbulence.

The endosphere bacteriome of diseased and healthy tomato plants.

Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.

Spatially resolved magnetic field structure in the disk of a T Tauri star.

Magnetic fields in accretion disks play a dominant part during the star formation process but have hitherto been observationally poorly constrained. Field strengths have been inferred on T Tauri stars and possibly in the innermost part of their accretion disks, but the strength and morphology of the field in the bulk of a disk have not been observed. Spatially unresolved measurements of polarized emission (arising from elongated dust grains aligned perpendicularly to the field) imply average fields aligned with the disks. Theoretically, the fields are expected to be largely toroidal, poloidal or a mixture of the two, which imply different mechanisms for transporting angular momentum in the disks of actively accreting young stars such as HL Tau (ref. 11). Here we report resolved measurements of the polarized 1.25-millimetre continuum emission from the disk of HL Tau. The magnetic field on a scale of 80 astronomical units is coincident with the major axis (about 210 astronomical units long) of the disk. From this we conclude that the magnetic field inside the disk at this scale cannot be dominated by a vertical component, though a purely toroidal field also does not fit the data well. The unexpected morphology suggests that the role of the magnetic field in the accretion of a T Tauri star is more complex than our current theoretical understanding.

The early events underlying genome evolution in a localized Sinorhizobium meliloti population.

BACKGROUND: Population genetic analyses based on genome-wide sequencing data have been carried out for Sinorhizobium medicae and S. meliloti, two closely related bacterial species forming nitrogen-fixing symbioses with plants of the genus Medicago. However, genome coverage was low or the isolates had a broad geographic distribution, making it difficult to interpret the estimated diversity and to unravel the early events underlying population genetic variations and ecological differentiation. RESULTS: Here, to gain insight into the early genome level variation and diversification within S. meliloti populations, we first used Illumina paired-end reads technology to sequence a new clone of S. meliloti strain GR4, a highly competitive strain for alfalfa nodulation. The Illumina data and the GR4 genome sequence previously obtained with 454 technology were used to generate a high-quality reference genome sequence. We then used Illumina technology to sequence the genomes of 13 S. meliloti isolates representative of the genomic variation within the GR4-type population, obtained from a single field site with a high degree of coverage. The genome sequences obtained were analyzed to determine nucleotide diversity, divergence times, polymorphism and genomic variation. Similar low levels of nucleotide diversity were observed for the chromosome, pSymB and pSymA replicons. The isolates displayed other types of variation, such as indels, recombination events, genomic island excision and the transposition of mobile elements. CONCLUSIONS: Our results suggest that the GR4-type population has experienced a process of demographic expansion and behaves as a stable genotypic cluster of genome-wide similarity, with most of the genome following a clonal pattern of evolution. Although some of genetic variation detected within the GR4-type population is probably due to genetic drift, others might be important in diversification and environmental adaptation.

Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.

Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change.

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by 'Candidatus Phytoplasma pini' as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, 'Ca. Phytoplasma pini' is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

Pitting the olive seed microbiome.

BACKGROUND: The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions. RESULTS: A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments. CONCLUSIONS: This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria.

BACKGROUND: Verticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed. RESULTS: Inoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the 'Picual' root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the 'Picual' microbial community; instead, PICF7 inoculation increased the microbiota's compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected. CONCLUSION: The absence of significant modifications on the structure and composition of the 'Picual' belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the 'Picual' microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.

Thriving beneath olive trees: The influence of organic farming on microbial communities.

Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.

Bacteriome dataset from the rhizosphere of trees in a Pinus pinaster and Pinus halepensis dominated forest subjected to drought conditions.

The Mediterranean basin is drastically affected by intense and frequent droughts, which jeopardize the diversity and survival of its forest, for example, Pinus pinaster forests. The dynamics of the bacterial communities inhabiting the rhizosphere of Pinus pinaster and other plants from a pine dominated forest under contrasting hydric conditions was monitored. The forest was located in Sierra de Oria (southeast Spain), and it was mainly composed by P. pinaster, P. halepensis, woody shrub species and herbaceous plants. 18 trees visually belonging to P. pinaster located along the perimeter and across the forest were selected for the analysis. All the trees were separated at least 50 m each other. Although all of them belonged to P. pinaster morphologically according to visual identification, the genotyping of the roots confirmed that they corresponded to P. pinaster, P. halepensis, and other plant species different from genus Pinus, although in the last case it was not possible to identify the plant species. At a distance less than 50 cm from the trunk, the litter and topsoil were removed, and the soil closely attached to non-suberified roots (rhizosphere soil) was collected (depth of 5-25 cm). Sampling was carried out in two seasons with contrasting temperature and rainfall patterns: on July 18, 2017 (summer) and April 24, 2018 (spring). After rhizosphere soil DNA and RNA extraction (and cDNA synthesis), a metabarcoding approach was followed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene and its derived transcripts by Illumina MiSeq platform. Sequencing reads were bioinformatically processed; specifically, they were filtered, trimmed, clustered into ASV (Amplicon Sequence Variants), and taxonomically identified. As a result, a total of 1,123,209 and 1,089,359 quality sequences were obtained from DNA and RNA-derived libraries, which resulted in 5,241 and 5,231 ASVs, respectively. Total communities (DNA) were mainly dominated by phyla Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Bacteroidetes in summer and spring, while potentially active populations (RNA libraries) were rich in Proteobacteria, Acidobacteria, Candidate division WPS-1, Actinobacteria and Verrucomicrobia both in summer and spring. On the other hand, DNA libraries were mainly dominated by genera Sphingomonas and acidobacterial groups Gp4 and Gp6, while potentially active bacteria (RNA) were rich in acidobacterial Gp3, Gp4, Gp6 and Phenylobacterium, although their relative abundance depended on the considered season. This dataset can provide valuable information about bacterial candidates which could be used as bioindicators of drought conditions. In addition to shifts in the bacterial relative abundance due to seasonal changes, the ratio RNA-based cDNA:DNA could be calculated as proxy of the potential activity of bacterial taxa. Moreover, these data could aid in developing bioformulations based on microorganisms which could be resistant to desiccation and involved in the drought resistance mechanisms of the host plant.

How harmful are exotic plantations for soils and its microbiome? A case study in an arid island.

The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses.

The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.

Corrigendum to "Coupling the endophytic microbiome with the host transcriptome in olive roots" [Comput. Struct. Biotechnol. J. 19 (2021) 4777-4789].

[This corrects the article DOI: 10.1016/j.csbj.2021.08.035.].

Correlating the above- and belowground genotype of Pinus pinaster trees and rhizosphere bacterial communities under drought conditions.

Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed.

Use of RmInt1, a group IIB intron lacking the intron-encoded protein endonuclease domain, in gene targeting.

The group IIA intron Ll.LtrB from Lactococcus lactis and the group IIB intron EcI5 from Escherichia coli have intron-encoded proteins (IEP) with a DNA-binding domain (D) and an endonuclease domain (En). Both have been successfully retargeted to invade target DNAs other than their wild-type target sites. RmInt1, a subclass IIB3/D intron with an IEP lacking D and En domains, is highly active in retrohoming in its host, Sinorhizobium meliloti. We found that RmInt1 was also mobile in E. coli and that retrohoming in this heterologous host depended on temperature, being more efficient at 28°C than at 37°C. Furthermore, we programmed RmInt1 to recognize target sites other than its wild-type site. These retargeted introns efficiently and specifically retrohome into a recipient plasmid target site or a target site present as a single copy in the chromosome, generating a mutation in the targeted gene. Our results extend the range of group II introns available for gene targeting.

The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense.

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

Coupling the endophytic microbiome with the host transcriptome in olive roots.

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.

Involvement of the metabolically active bacteria in the organic matter degradation during olive mill waste composting.

RNA-based high-throughput sequencing is a valuable tool in the discernment of the implication of metabolically active bacteria during composting. In this study, "alperujo" composting was used as microbial model for the elucidation of structure-function relationships with physicochemical transformation of the organic matter. DNA and RNA, subsequently retrotranscribed into cDNA, were isolated at the mesophilic, thermophilic and maturation phases. 16S rRNA gene was amplified by quantitative PCR (qPCR) and Illumina MiSeq platform to assess bacterial abundance and diversity, respectively. The results showed that the abundance of active bacteria assessed by qPCR was maximum at thermophilic phase, which confirm it as the most active stage of the process. Concerning diversity, Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the main phyla presented in composts. Concomitantly, three different behaviours were observed for bacterial dynamics: some genera decreased during the whole process meanwhile others proliferated only at thermophilic or maturation phase. Statistical correlation between physicochemical transformations of the organic matter and bacterial diversity revealed bacterial specialisation. This result indicated that specific groups of bacteria were only involved in the organic matter degradation during bio-oxidative phase or humification at maturation. Metabolic functions predictions confirmed that active bacteria were mainly involved in carbon (C) and nitrogen (N) cycles transformations, and pathogen reduction.