Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates

The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics

Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.

Hexose/pentose ratio in rhizosphere exudates-mediated soil eutrophic/oligotrophic bacteria regulates the growth pattern of host plant in young apple-aromatic plant intercropping systems

Introduction

The positive effect of intercropping on host plant growth through plant-soil feedback has been established. However, the mechanisms through which intercropping induces interspecific competition remain unclear.

Methods

In this study, we selected young apple trees for intercropping with two companion plants: medium growth-potential Mentha haplocalyx Briq. (TM) and high growth-potential Ageratum conyzoides L. (TA) and conducted mixed intercropping treatment with both types (TMA) and a control treatment of monocropping apples (CT).

Results

Our findings revealed that TM increased the under-ground biomass of apple trees and TA and TMA decreased the above-ground biomass of apple trees, with the lowest above-ground biomass of apple trees in TA. The above- and under-ground biomass of intercrops in TA and TMA were higher than those in TM, with the highest in TA, suggesting that the interspecific competition was the most pronounced in TA. TA had a detrimental effect on the photosynthesis ability and antioxidant capacity of apple leaves, resulting in a decrease in above-ground apple biomass. Furthermore, TA led to a reduction in organic acids, alcohols, carbohydrates, and hydrocarbons in the apple rhizosphere soil (FRS) compared to those in both soil bulk (BS) and aromatic plant rhizosphere soil (ARS). Notably, TA caused an increase in pentose content and a decrease in the hexose/pentose (C6/C5) ratio in FRS, while ARS exhibited higher hexose content and a higher C6/C5 ratio. The changes in exudates induced by TA favored an increase in taxon members of Actinobacteria while reducing Proteobacteria in FRS compared to that in ARS. This led to a higher eutrophic/oligotrophic bacteria ratio relative to TM.

Discussion

This novel perspective sheds light on how interspecific competition, mediated by root exudates and microbial community feedback, influences plant growth and development.

Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars

BACKGROUND

Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome).

RESULTS

Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil.

CONCLUSIONS

Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.

Multi-factor correlation analysis of the effect of root-promoting practices on tobacco rhizosphere microecology in growth stages

Some agronomic practices not only promote the development of crop roots and increase overall plant performance but also affect colonisation by rhizosphere microorganisms. However, the composition and temporal dynamics of the tobacco rhizosphere microbiota under different root-promoting practices are poorly understood. Here, we characterised the tobacco rhizosphere microbiota at the knee-high, vigorous growing, and maturity stages under the application of potassium fulvic acid (PFA), γ-Polyglutamic acid (PGA), soymilk root irrigation (SRI), and conventional fertilization (CK) and its correlation with root characteristics and soil nutrients. The results showed that three root-promoting practices notably improved the dry and fresh root weights. Total nitrogen and phosphorus, available phosphorus and potassium, and organic matter contents in the rhizosphere markedly increased at the vigorous growing stage. The rhizosphere microbiota was changed through root-promoting practices. However, with tobacco growth, the change of rhizosphere microbiota showed a pattern of slow first and then fast and the microbiota of different treatments gradually approached. SRI reduced plant-pathogenic fungi but increased chemoheterotrophic and phototrophic bacteria, and arbuscular mycorrhizal fungi. PFA and PGA markedly increased arbuscular mycorrhizal and ectomycorrhizal fungi at the knee-high stage, which benefitted tobacco nutrient absorption. The correlation between rhizosphere microorganisms and environmental factors varied at different growth stages. Notably, the rhizosphere microbiota was more sensitive to environmental factors at the vigorous growing stage, and the interactions were more complex than in other stages. Furthermore, a variance partitioning analysis showed that the influence of root-soil interaction on the rhizosphere microbiota increased with tobacco growth. Overall, all three root-promoting practices could improve root characteristics, rhizosphere nutrient, and rhizosphere microbiota to varying degrees and increase the tobacco biomass, among which PGA had the most obvious effect and most suitable for tobacco cultivation. Our findings revealed the role of root-promoting practices in shaping the rhizosphere microbiota during plant growth and elucidated the assembly patterns and environmental drivers of crop rhizosphere microbiota driven by the application of root-promoting practices in agricultural production.

Carbon allocation in cassava is affected by water deficit and potassium application - A 13 C-CO2 pulse labelling assessment

RATIONALE

Cassava production faces challenges in a changing climate. Pulse labelling cassava with ¹³ C-CO₂ has the potential to elucidate carbon allocation mechanisms of cassava under drought stress and with potassium application. Understanding these mechanisms could guide efforts to mitigate effects of drought in cassava cropping systems.

METHODS

Forty-eight cassava plants received a nutrient solution high or low in potassium. Water deficit was imposed on half of the plants at bulk root initiation stage, after which they were labelled for 8 h with ¹³ C-CO₂ in a 15 m³ growth chamber. Plants were harvested 8 h, 9 days and 24 days after labelling, and separated into leaves, stems and roots. δ¹³ C values of the different parts were measured using an isotope ratio mass spectrometer, from which ¹³ C excess was calculated.

RESULTS

Water deficit decreased transpiration (P < 0.001) and increased carbon respiration (P < 0.05). Potassium application increased assimilate distribution to the roots (P < 0.05) at 9 days after labelling, more strongly for plants under water deficit. The opposite was found at 24 days (P < 0.05) with the legacy of water deficit additionally increasing assimilate distribution to roots (P < 0.05). Youngest, fully expanded leaves contained up to 47% of initial ¹³ C excess at 24 days after labelling.

CONCLUSIONS

Pulse labelling proved to be successful in shedding light on carbon allocation in relation to water and potassium availability. This technique, once adapted to field conditions, could further be used to improve fertilizer recommendations or change agronomic practices to cope with plant stress.

Revealing the relative importance among plant species, slope positions, and soil types on rhizosphere microbial communities in northern tropical karst and non-karst seasonal rainforests of China

Rhizosphere microbes have an extremely close relationship with plants and the study on the relationship between rhizosphere microorganisms and their influencing factors is conducive to the protection of vegetation and the maintenance of biodiversity. Here we investigated how plant species, slope positions and soil types affect the rhizosphere microbial community. Slope positions and soil types were collected from northern tropical karst and non-karst seasonal rainforests. The results indicated that soil types played a predominant role in the development of rhizosphere microbial communities (28.3% of separate contribution rate), more than plant species identity (10.9% of separate contribution rate) and slope position (3.5% of separate contribution rate). Notably, environmental factors closely related to soil properties were the major influence factors that controlling the rhizosphere bacterial community structure in the northern tropical seasonal rainforest, especially pH. Additionally, plant species also influenced the rhizosphere bacterial community. In low nitrogen content soil environments, rhizosphere biomarkers of dominant plant species were often nitrogen-fixing strains. It suggested that plants might have a selective adaptation mechanism to rhizosphere microorganisms to obtain the advantages of nutrient supply. Overall, soil types exerted the biggest influence on rhizosphere microbial community structure, followed by plant species and finally slope positions.

Plant Interaction Patterns Shape the Soil Microbial Community and Nutrient Cycling in Different Intercropping Scenarios of Aromatic Plant Species

Intercropping systems improve the soil nutrient cycle through microbial community activity and then land productivity. However, their interactions mechanism underlying that the mixed aromatic plant species intercropping regulate the soil microbiome and nutrient cycling on the perennial woody orchard is still uncovered. We designed treatments with 0, 1, and 3 aromatic plant species intercropped in two scenarios of clean tillage (T model, T1, T2, and T4) and natural grass (G model, G1, G2, and G4) in apple orchards, and investigated intercrops effects at the branch growing stage (BGS) and fruit development stage (FDS), respectively. Compared with T model, G model in FDS increased alpha diversity of bacterial community and Shannon index fungal community, the relative abundance of dominant taxa, such as Acidobacteria and Actinobacteria, and also the numbers of up and down-regulated OTUs, the most of indices of co-occurrence network in both bacterial and fungal community, and then improved invertase activity and available nitrogen content. Relative to G1, G2 and G4 reduced diversity bacterial community in FDS, the relative abundance of dominant taxa, the most of indices of co-occurrence network, and then improved soil invertase activity and total phosphorus content in soil. Moreover, Shannon index of fungal community, the altered number of OTUs and the most indices of co-occurrence network were higher in G4 than those in G2 in FDS. These changes above in FDS were more markedly than those in BGS, suggesting that chemical diversity of litter from mixed species of aromatic plants in natural grass scenario led to diversity, complexity, and stability of soil microbial community and then nutrient cycling. It provided a novel highlight and method to modulate biocenosis and then improve the soil nutrient cycling.

Influence of different phytoremediation on soil microbial diversity and community composition in saline-alkaline land

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land.HIGHLIGHTSThe effects of different phytoremediation on microbial diversity and community structure were different.Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil.All plants increased the activity of nitrite reductase and decreased the activity of urease.

Denitrifying pathways dominate nitrous oxide emissions from managed grassland during drought and rewetting

Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade.

The abundance of nirS-type denitrifiers and anammox bacteria in rhizospheres was affected by the organic acids secreted from roots of submerged macrophytes

Excessive nitrogen has been a global concern to cause lake eutrophication. The denitrification and anammox processes are considered to be effective biological pathways for nitrogen removal. Submerged macrophytes also play a key role in the nitrogen cycle of lakes. However, the mechanism of submerged macrophytes on regulating biological nitrogen removal pathways has not been well quantified. Therefore, this study investigated the impacts of submerged macrophytes on the community structures and abundance of the nirS-type denitrifiers and anammox bacteria in the rhizospheres. The qPCR results indicated that the abundance of two bacteria in the near-rhizospheres of submerged macrophytes was significantly lower than the root compartments and non-rhizospheres, while the concentrations of organic acids in the near-rhizospheres were higher than those of the root compartments and non-rhizospheres. Redundancy analysis results illustrated that concentrations of NO₃^--N, NO₂^--N, citric acid and oxalic acid were the key environmental indicators which had the significant impact on the microbial community. The concentrations of citric acid and oxalic acid were negatively correlated with the nirS-type denitrifiers abundance, and the oxalic acid concentrations were negatively correlated with the anammox bacteria abundance. These results indicated that submerged macrophytes could reduce the abundance of nirS-type denitrifiers and anammox bacteria by releasing organic acids. In addition, the highest diversity of denitrifier community were found in the rhizosphere of the Hydrilla verticillata, while the highest diversity of anammox community were found in the Potamogeton maackianus rhizosphere. These results indicate that the impacts of submerged macrophytes on the biological nitrogen removal pathways were species-dependent.

Structure and variation of root-associated microbiomes of potato grown in alfisol

Root-associated fungi and bacteria play a pivotal role in the plant-soil ecosystem by influencing both plant growth and immunity. The aim of this study was to unravel the biodiversity of the bacterial and fungal rhizosphere (RS) and rhizoplane (RP) microbiota of Zhukovskij rannij potato (Solanum tuberosum L.) cultivar growing in the Alfisol of Tatarstan, Russia. To assess the structure and diversity of microbial communities, we employed the 16S rRNA and internal transcribed spacer gene library technique. Overall, sequence analysis showed the presence of 3982 bacterial and 188 fungal operational taxonomic units (OTUs) in the RP, and 6018 bacterial and 320 fungal OTUs for in the RS. Comparison between microbial community structures in the RS and RP showed significant differences between these compartments. Biodiversity was higher in the RS than in the RP. Although members of Proteobacteria (RS-59.1 ± 4.9%; RP-54.5 ± 9.2%), Bacteroidetes (RS-23.19 ± 10.2%; RP-34.52 ± 10.4%) and Actinobacteria (RS-11.55 ± 4.9%; RP-7.7 ± 5.1%) were the three most dominant phyla, accounting for 94-98% of all bacterial taxa in both compartments, notable variations were observed in the primary dominance of classes and genera in RS and RP samples. In addition, our results demonstrated that the potato rhizoplane was significantly enriched with the genera Flavobacterium, Pseudomonas, Acinetobacter and other potentially beneficial bacteria. The fungal community was predominantly inhabited by members of the Ascomycota phylum (RS-81.4 ± 8.1%; RP-81.7 ± 5.7%), among which the genera Fusarium (RS-10.34 ± 3.41%; RP-9.96 ± 4.79%), Monographella (RS-7.66 ± 4.43%; RP-9.91 ± 5.87%), Verticillium (RS-4.6 ± 1.43%; RP-8.27 ± 3.63%) and Chaetomium (RS-4.95 ± 2.07%; RP-8.33 ± 4.93%) were particularly abundant. Interestingly, potato rhizoplane was significantly enriched with potentially useful fungal genera, such as Mortierella and Metacordiceps. A comparative analysis revealed that the abundance of Fusarium (a cosmopolitan plant pathogen) varied significantly depending on rotation variants, indicating a possible control of phytopathogenic fungi via management-induced shifts through crop rotational methods. Analysis of the core microbiome of bacterial and fungal community structure showed that the formation of bacterial microbiota in the rhizosphere and rhizoplane is dependent on the host plant.

Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection

Root knot nematodes (RKN, Meloidogyne spp.) are serious pathogens of numerous crops worldwide. Understanding the roles plant rhizosphere soil microbiome play during RKN infection is very important. The current study aims at investigating the impacts of soil microbiome on the activity of RKN. In this study, the 16S rRNA genes of the bacterial communities from nematode-infested and non-infested rhizosphere soils from four different plants were sequenced on the Illumina Hi-Seq platform. The soil microbiome effects on RKN infection were tested in a greenhouse assay. The non-infested soils had more microbial diversity than the infested soils from all plant rhizospheres, and both soil types had exclusive microbial communities. The inoculation of the microbiomes from eggplant and cucumber non-infested soils to tomato plants significantly alleviated the RKN infection, while the microbiome from infested soil showed increased the RKN infection. Furthermore, bacteria Pseudomonas sp. and Bacillus sp. were screened out from non-infested eggplant soil and exhibited biocontrol activity to RKN on tomato. Our findings suggest that microbes may regulate RKN infection in plants and are involved in biocontrol of RKN.

Pathogenic Streptomyces spp. Abundance Affected by Potato Cultivars

Potato cultivars vary in their tolerance to common scab; however, how they affect common scab-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a common scab-infested field: (i) soil close to the plant (SCP); (ii) rhizosphere soil (RS); and (iii) geocaulosphere soil (GS). Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon, and nitrogen concentrations) explained 68 and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced common scab pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with five to six times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems

Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS), semi-separation intercropping (SS) using a nylon net, and complete separation intercropping (CS) using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs) showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS) showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS) improved levels of soil-available nutrients (nitrogen (N) and phosphorus (P)) and enzymes (urease and acid phosphomonoesterase) as compared to intercropping without belowground interactions (CS). Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillusbrevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P) supply capacity and soil microecosystem stability.

Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napusIMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development

The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The 'stable' component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the 'dynamic' component comprised OTUs that were enriched at specific vegetation stages.

Long-term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide-derived carbon in soil

Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source.

Soil fungal resources in annual cropping systems and their potential for management

Soil fungi are a critical component of agroecosystems and provide ecological services that impact the production of food and bioproducts. Effective management of fungal resources is essential to optimize the productivity and sustainability of agricultural ecosystems. In this review, we (i) highlight the functional groups of fungi that play key roles in agricultural ecosystems, (ii) examine the influence of agronomic practices on these fungi, and (iii) propose ways to improve the management and contribution of soil fungi to annual cropping systems. Many of these key soil fungal organisms (i.e., arbuscular mycorrhizal fungi and fungal root endophytes) interact directly with plants and are determinants of the efficiency of agroecosystems. In turn, plants largely control rhizosphere fungi through the production of carbon and energy rich compounds and of bioactive phytochemicals, making them a powerful tool for the management of soil fungal diversity in agriculture. The use of crop rotations and selection of optimal plant genotypes can be used to improve soil biodiversity and promote beneficial soil fungi. In addition, other agronomic practices (e.g., no-till, microbial inoculants, and biochemical amendments) can be used to enhance the effect of beneficial fungi and increase the health and productivity of cultivated soils.

¹³C pulse-chase labeling comparative assessment of the active methanogenic archaeal community composition in the transgenic and nontransgenic parental rice rhizospheres

More and more investigations indicate that genetic modification has no significant or persistent effects on microbial community composition in the rice rhizosphere. Very few studies, however, have focused on its impact on functional microorganisms. This study completed a ¹³C-CO₂ pulse-chase labeling experiment comparing the potential effects of cry1Ab gene transformation on ¹³C tissue distribution and rhizosphere methanogenic archaeal community composition with its parental rice variety (Ck) and a distant parental rice variety (Dp). Results showed that ¹³C partitioning in aboveground biomass (mainly in stems) and roots of Dp was significantly lower than that of Ck. However, there were no significant differences in ¹³C partitioning between the Bt transgenic rice line (Bt) and Ck. RNA-stable isotope probing combined with clone library analyses inferred that the group Methanosaetaceae was the predominant methanogenic Archaea in all three rice rhizospheres. The active methanogenic archaeal community in the Bt rhizosphere was dominated by Methanosarcinaceae, Methanosaetaceae, and Methanomicrobiaceae, while there were only two main methanogenic clusters (Methanosaetaceae and Methanomicrobiaceae) in the Ck and Dp rhizospheres. These results indicate that the insertion of cry1Ab gene into the rice genome has the potential to result in the modification of methanogenic community composition in its rhizosphere.

Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines

BACKGROUND

In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds.

METHODOLOGY/PRINCIPAL FINDINGS

The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.

CONCLUSIONS/SIGNIFICANCE

Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.

13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline

• The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving (13)C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.