Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3.
ABSTRACT: Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere ?-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3.
Project description:The species-specific responses of plant growth to elevated atmospheric CO<sub>2</sub> concentration (eCO<sub>2</sub>) could lead to N limitation and potentially influence the sustainability of ecosystem. Questions remain unanswered with regards to the response of soil N<sub>2</sub>-fixing community to eCO<sub>2</sub> when developing high-yielding agroecosystem to dampen the future rate of increase in CO<sub>2</sub> levels and associated climate warming. This study demonstrates the divergent eCO<sub>2</sub> influences on the paddy diazotrophic community between weak- and strong-responsive rice cultivars. In response to eCO<sub>2</sub>, the diazotrophic abundance increased more for the strong-responsive cultivar treatments than for the weak-responsive ones. Only the strong-responsive cultivars decreased the alpha diversity and separated the composition of diazotrophic communities in response to eCO<sub>2</sub>. The topological indices of the ecological networks further highlighted the different co-occurrence patterns of the diazotrophic microbiome in rice cultivars under eCO<sub>2</sub>. Strong-responsive cultivars destabilized the diazotrophic community by complicating and centralizing the co-occurrence network as well as by shifting the hub species from <i>Bradyrhizobium</i> to <i>Dechloromonas</i> in response to eCO<sub>2</sub>. On the contrary, the network pattern of the weak-responsive cultivars was simplified and decentralized in response to eCO<sub>2</sub>, with the hub species shifting from <i>Halorhodospira</i> under aCO<sub>2</sub> to <i>Sideroxydans</i> under eCO<sub>2</sub>. Collectively, the above information indicates that the strong-responsive cultivars could potentially undermine the belowground ecosystem from the diazotrophs perspective in response to eCO<sub>2</sub>. This information highlights that more attention should be paid to the stability of the belowground ecosystem when developing agricultural strategies to adapt prospective climatic scenarios by growing high-yielding crop cultivars under eCO<sub>2</sub>.
Project description:Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
Project description:Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.
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.
Project description:BACKGROUND:Verticillium wilt of olive (VWO) is caused by the soilborne fungal pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant/resistant olive cultivars. Knowledge on the olive-associated microbiome and its potential relationship with tolerance to biotic constraints is almost null. The aims of this work are (1) to describe the structure, functionality, and co-occurrence interactions of the belowground (root endosphere and rhizosphere) microbial communities of two olive cultivars qualified as tolerant (Frantoio) and susceptible (Picual) to VWO, and (2) to assess whether these communities contribute to their differential disease susceptibility level. RESULTS:Minor differences in alpha and beta diversities of root-associated microbiota were detected between olive cultivars regardless of whether they were inoculated or not with the defoliating pathotype of V. dahliae. Nevertheless, significant differences were found in taxonomic composition of non-inoculated plants' communities, "Frantoio" showing a higher abundance of beneficial genera in contrast to "Picual" that exhibited major abundance of potential deleterious genera. Upon inoculation with V. dahliae, significant changes at taxonomic level were found mostly in Picual plants. Relevant topological alterations were observed in microbial communities' co-occurrence interactions after inoculation, both at structural and functional level, and in the positive/negative edges ratio. In the root endosphere, Frantoio communities switched to highly connected and low modularized networks, while Picual communities showed a sharply different behavior. In the rhizosphere, V. dahliae only irrupted in the microbial networks of Picual plants. CONCLUSIONS:The belowground microbial communities of the two olive cultivars are very similar and pathogen introduction did not provoke significant alterations in their structure and functionality. However, notable differences were found in their networks in response to the inoculation. This phenomenon was more evident in the root endosphere communities. Thus, a correlation between modifications in the microbial networks of this microhabitat and susceptibility/tolerance to a soilborne pathogen was found. Moreover, V. dahliae irruption in the Picual microbial networks suggests a stronger impact on the belowground microbial communities of this cultivar upon inoculation. Our results suggest that changes in the co-occurrence interactions may explain, at least partially, the differential VWO susceptibility of the tested olive cultivars. Video abstract.
Project description:Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines' rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.
Project description:Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.
Project description:Elevated atmospheric CO<sub>2</sub> (eCO<sub>2</sub>) enhances the yield of vegetables and could also affect their nutritional quality. We conducted a meta-analysis using 57 articles consisting of 1,015 observations and found that eCO<sub>2</sub> increased the concentrations of fructose, glucose, total soluble sugar, total antioxidant capacity, total phenols, total flavonoids, ascorbic acid, and calcium in the edible part of vegetables by 14.2%, 13.2%, 17.5%, 59.0%, 8.9%, 45.5%, 9.5%, and 8.2%, respectively, but decreased the concentrations of protein, nitrate, magnesium, iron, and zinc by 9.5%, 18.0%, 9.2%, 16.0%, and 9.4%. The concentrations of titratable acidity, total chlorophyll, carotenoids, lycopene, anthocyanins, phosphorus, potassium, sulfur, copper, and manganese were not affected by eCO<sub>2</sub>. Furthermore, we propose several approaches to improving vegetable quality based on the interaction of eCO<sub>2</sub> with various factors, including species, cultivars, CO<sub>2</sub> levels, growth stages, light, O<sub>3</sub> stress, nutrient, and salinity. Finally, we present a summary of the eCO<sub>2</sub> impact on the quality of three widely cultivated crops, namely, lettuce, tomato, and potato.
Project description:As atmospheric [CO<sub>2</sub>] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO<sub>2</sub> (eCO<sub>2</sub>) were studied in genotypes from the two major traded coffee species: the allopolyploid <i>Coffea arabica</i> (Icatu) and its diploid parent, <i>C. canephora</i> (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO<sub>2</sub>. Although many genes were found to be commonly expressed by the two genotypes under eCO<sub>2</sub>, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO<sub>2</sub>. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO<sub>2</sub> with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO<sub>2</sub> in these coffee genotypes.
Project description:The data presented in this article are related to the research article entitled "Phase stability and transport characteristics of (ZrO<sub>2</sub>)<sub>1-x</sub>(Sc<sub>2</sub>O<sub>3</sub>)<sub>x</sub>(?eO<sub>2</sub>)<sub>y</sub> and (ZrO<sub>2</sub>)<sub>1-x-y-z</sub>(Sc<sub>2</sub>O<sub>3</sub>)<sub>x</sub>(?eO<sub>2</sub>)<sub>y</sub>(Y<sub>2</sub>O<sub>3</sub>)<sub>z</sub> solid solution crystals" https://www.sciencedirect.com/science/article/pii/S2352340917302329 . It contains data on densities and microhardness of the as-grown crystals. The data on the specific conductivity of the as-grown and annealing at 1000 °? for 400 h ScCeSZ and ScCeYSZ crystals in the temperature range 623-1173 K is also included in this article. The article describes also the growth of the (ZrO<sub>2</sub>)<sub>1-x</sub>(Sc<sub>2</sub>O<sub>3</sub>)<sub>x</sub>(?eO<sub>2</sub>)<sub>y</sub> and (ZrO<sub>2</sub>)<sub>1-x-y-z</sub>(Sc<sub>2</sub>O<sub>3</sub>)<sub>x</sub>(?eO<sub>2</sub>)<sub>y</sub>(Y<sub>2</sub>O<sub>3</sub>)<sub>z</sub> solid solution crystals using directional melt crystallization in a cold crucible.