Root endosphere and rhizosphere soils from organic and tradicional managed olive orchards
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA925330 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23118200_1.fastq.gz | Fastqsanger.gz | |||
| SRR23118200_2.fastq.gz | Fastqsanger.gz | |||
| SRR23118201_1.fastq.gz | Fastqsanger.gz | |||
| SRR23118201_2.fastq.gz | Fastqsanger.gz | |||
| SRR23118202_1.fastq.gz | Fastqsanger.gz |
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Project description:The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. We show in this work that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a large number of as yet unclassified fungal sequences (class level) were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity here uncovered suggests that fungi with important ecological function and biotechnological potential are yet to be identified.
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Project description:Population dynamics of methanogenic genera was investigated in pilot anaerobic digesters. Cattle manure and two-phase olive mill wastes were codigested at a 3:1 ratio in two reactors operated at 37 ï¾°C and 55 ï¾°C. Other two reactors were run with either residue at 37 ï¾°C. Sludge DNA extracted from samples taken from all four reactors on days 4, 14 and 28 of digestion was used for hybridisation with the AnaeroChip, an oligonucleotide microarray targeting those groups of methanogenic archaea that are commonly found under mesophilic and thermophilic conditions (Franke-Whittle et al. 2009, in press, doi:10.1016/j.mimet.2009.09.017).
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Project description:The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants were grown in a glasshouse standardized system, and the bacterial and fungal microbiomes of 233 samples of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. The results showed highly dynamic and diverse microbial communities that changed over time, with Sphingomonas bacteria and Aspergillus, Dipodascus, and Trichoderma fungi increasing over time. Application of biocontrol Streptomyces strains promoted plant growth and maturation of wheat heads and modulated the root microbiome, decreasing Paenibacillus and increasing other bacterial and fungal OTUs. The soils with the highest levels of R. solani had increased reads of Thanatephorus (Rhizoctonia anamorph) and increased root disease levels and increased Balneimonas, Massilia, Pseudomonas, and unclassified Micrococcaceae. As we enter the era of biologically sustainable agriculture, it may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.
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Project description:This work has studied for the first time the structure and diversity of plant-parasitic nematodes (PPNs) infesting olive orchard soils in a wide-region in Spain that included 92 locations. It aims at determining which agronomical or environmental factors associated to the olive orchards are the main drivers of the PPNs community structure and diversity. Classical morphological and morphometric identification methods were used to determine the frequency and densities of PPNs. Thirteen families, 34 genera and 77 species of PPNs were identified. The highest diversity was found in Helicotylenchus genus, with six species previously reported in Spain and with H. oleae being a first report. Neodolichorhynchus microphasmis and Diptenchus sp., Diphtherophora sp., and Discotylenchus sp., usually considered fungal feeders, were also reported for the first time associated to olive rhizosphere. PPNs abundance ranged from 66 to 16,288 individuals/500-cm3 of soil with Helicotylenchus digonicus being the most prevalent species, followed by Filenchus sp., Merlinius brevidens and Xiphinema pachtaicum. Nematode abundance and diversity indexes were influenced by olive cultivar, and orchard and soil management practices; while olive variety and soil texture were the main factors driving PPN community composition. Soil physicochemical properties and climatic characteristics most strongly associated to the PPN community composition included pH, sand content and exchangeable K, and maximum and minimum average temperature of the sampled locations. Our data suggests that there is a high diversity of PPNs associated to olive in Southern Spain that can exert different damage to olive roots depending on the olive variety and their abundance. Further analysis to determine the resistance levels of most common olive varieties to the prevalent PPNs in Spain will help to choose the most appropriate ones for the establishment of new plantations. This choice will take into consideration the specific soils and environments where those olive varieties will be established.
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