Surrounding Bulk Soil Research Articles

Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties.

Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salix purpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.

The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae).

In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound‐building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.

Forest plant cover and mineral type determine the diversity and composition of mineral-colonizing fungal communities

Soil fungi play a fundamental role in the cycling of nutrients and tree nutrition in forests. As mycorrhizal fungi are closely associated with their host trees and provide them essential base cations and phosphorus, we hypothesize that they actively mine soil minerals and transfer their nutritive content to their host. Therefore, mycorrhizal fungi are expected to be important colonizers of soil mineral surfaces relative to other fungal trophic guilds. To test this hypothesis, 50 μm nylon mesh bags were filled with three different mineral types (i.e. calcite, apatite and obsidian) and buried in the same soil colonized by three forest stands (i.e. beech, Corsican pine and coppice with standards). After an in situ incubation period of 29 months in the topsoil, mineral dissolution was detectable in the mesh bags, and the analysis of the fungal communities was therefore undertaken. Minerals presented a lower fungal biomass than the surrounding bulk soil and no difference between the three mineral types tested was observed. The high-throughput sequencing (HTS) approach showed that the fungal communities differed among the three forest stands, but in each case, mineral associated fungal taxa differed significantly from those in the bulk soil. To a lesser extent, fungal communities further varied between the three mineral types. Overall, trophic inference analyses suggested that two groups of plant-associated fungi, namely the ectomycorrhizal and endophytic fungi, were the major fungal mineral colonizers. Saprophytes also appeared significantly enriched on minerals comparatively to the surrounding bulk soil. Together, our data reveal at local scale that the mineral-associated fungal communities are first determined by the forest plant cover and then by the type of mineral.

Tillage-induced effects on organic carbon in earthworm casts through changes in their physical and structural stability parameters

Earthworm casts have been recognized as contributing to long-term carbon protection, but few studies have focused on the mechanism by which this is achieved. Most of the literature documenting earthworm casts revolves around the difference between the earthworm cast and natural soil, whereas little attention has been given to deciphering the effects of different tillage systems on earthworm casts. Further, whether or not an earthworm cast, like soil, affects its own organic carbon content through physical structure stability is still somewhat vague, and very little is known. The objective for this study was to determine the effect of tillage on organic carbon and physical structure stability parameters in earthworm casts. Undisturbed soil columns were collected from a 17-year tillage experiment including no tillage (NT), ridge tillage (RT) and mouldboard ploughing (MP) in Northeast China. Each column was seeded with ten earthworms (Eisenia foetida), incubated at 18 °C for 120 days and casts were collected and analysed. Both NT and RT led to significantly greater organic carbon (20.5% and 14.4%), total pore volume (54.6% and 75.6%), total pore area (45.4% and 60.4%), permeability (21.8% and 66.4%), fluid conductivity (26.2% and 31.1%), tensile strength (34.1% and 51.2%) and water resistance index (16.7% and 22.3%) in the casts compared to MP (P < 0.05), whereas water repellency showed a significant decrease (42.9% and 52.4%) (P < 0.05). Correlation analysis showed that total pore area, tensile strength and water repellency were the three most critical factors affecting organic carbon in earthworm casts (r = 0.943, 0.742, 0.762 and 0.715, 0.758, 0.743 for NT and RT, respectively). The results of tillage effects on organic carbon and physical structure stability parameters combined with Structural Equation Modelling analysis identified that NT and RT could increase organic carbon by increasing total pore area, tensile strength and water repellency in earthworm casts. These results demonstrate that tillage through physical structure stability (total pore area, tensile strength and water repellency) changes affect organic carbon in earthworm cast which are major new findings. This signifies similarity in the underlying processes by which tillage affects organic carbon and physical structure stability parameters in earthworm casts and the surrounding bulk soil. Moreover, the increased abundance of earthworms and greater organic carbon in earthworm casts under conservation tillage, suggest that earthworms enhance the conversion of residue into organic carbon and therefore enhance the long-term soil organic carbon sequestration.

Functional compensation dominates the assembly of plant rhizospheric bacterial community

Plant rhizosphere microbes play a key role in plant-soil feedbacks. However, the intrinsic principles governing the assembly of the rhizosphere microbial community remain unclear. To understand these principles, we studied the taxonomical and functional characteristics of the reassembled maize rhizosphere bacterial communities after transplanting between soils. The composition of the rhizosphere bacterial community was measured by high-throughput amplicon-based Illumina MiSeq sequencing of the V4 region of the 16S ribosomal RNA (rRNA) gene. The rhizosphere functional profile was assessed using 16S rRNA data in the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved State) software. We found that the reassembled rhizosphere bacterial community was recruited from both soil and endosphere communities. The assembly and functional traits of the rhizosphere bacterial community were associated with the concentrations of soil available nutrients. The most important rhizospheric functions were to improve host stress tolerance, followed by nutrient cycling functions. The rhizosphere bacterial taxa that improved host stress tolerance were in low abundance and were primarily derived from the surrounding bulk soil. Moreover, the rhizosphere nutrient cycling functions were marginalized in nutrient-excessive soils. Plants may sacrifice stress tolerance functions and enhance compensatory colonization of nutrient cycling-related endophytes in the rhizosphere in nutrient-deficient soils. Our results demonstrate that the levels of soil available nutrients mediate the assembly of rhizosphere bacterial communities to satisfy plant-required functions. This assembly principle is useful for manipulating the bacterial communities of plant roots to improve agricultural sustainability.

Microbiome Dynamics Associated With the Atacama Flowering Desert.

In a desert, plants as holobionts quickly respond to resource pulses like precipitation. However, little is known on how environment and plants modulate the rhizosphere-associated microbiome. As a model species to represent the Atacama Desert bloom, Cistanthe longiscapa (Montiaceae family) was selected to study the influence of abiotic and biotic environment on the diversity and structure of the microbiota associated to its rhizosphere. We analyzed the rhizosphere and soil microbiome along a North-South precipitation gradient and between a dry and rainy year by using Illumina high−throughput sequencing of 16S rRNA gene fragments and ITS2 regions for prokaryotes and fungi, respectively. In the rhizosphere of C. longiscapa the microbiota clearly differs in composition and structure from the surrounding bulk soil. The fungal and bacterial communities respond differently to environmental conditions. The diversity and richness of fungal OTUs were negatively correlated with aridity, as predicted. The community structure was predominantly influenced by other soil characteristics (pH, organic matter content) but not by aridity. In contrast, diversity, composition, and structure of the bacterial community were not influenced by aridity or any other evaluated soil parameter. These findings coincide with the identification of mainly site-specific microbial communities, not shared along the sites. These local communities contain a group of OTUs, which are exclusive to the rhizosphere of each site and presumably vertically inherited as seed endophytes. Their ecological functions and dispersal mechanisms remain unclear. The analysis of co-occurrence patterns highlights the strong effect of the desert habitat over the soil- and rhizosphere-microbiome. The site-independent enrichment of only a small bacterial cluster consistently associated with the rhizosphere of C. longiscapa further supports this conclusion. In a rainy year, the rhizosphere microbiota significantly differed from bulk and bare soil, whereas in a dry year, the community structure of the former rhizosphere approximates to the one found in the bulk. In the context of plant–microbe interactions in desert environments, our study contributes new insights into the importance of aridity in microbial community structure and composition, discovering the influence of other soil parameters in this complex dynamic network, which needs further to be investigated.

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient.

Serving as “natural laboratories”, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600–3,400 m a.s.l.). The research area of this study was Mount (Mt.) “Schrankogel” in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000–3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.

Metagenomic survey of the bacterial communities in the rhizosphere of three Andean tuber crops

Microbes colonizing the rhizosphere are important drivers of plant health, supplying nutrients and antagonizing pathogens, among other beneficial activities. Tubers are important staple crops in the Andean highlands, produced by thousands of small-farmers and consumed by millions. Here we report the composition of the bacterial communities colonizing the rhizospheres of three Andean tuber crops (ATCs), namely oca (Oxalis tuberosa), ullucu (Ullucus tuberosus) and mashua (Tropaeolum tuberosum). We used high throughput sequence analysis of 16S rRNA genes to describe the bacterial diversity of rhizospheric soils associated to thee crops. Between 4862 and 5080 OTUs were exclusively detected in each one of the ATCs’ rhizospheres; the majority of the 100 most abundant OTUs belonged to the Bacteroidetes and Proteobacteria phyla. Beta diversity indices revealed a low similarity between the three communities, suggesting differences in their specific composition. Only 566 bacterial OTUs were shared by all three tuber’s rhizospheres and absent from the surrounding bulk soil. Apart from studies in potato, this is the first report concerning the diversity and abundance of bacterial taxa associated with the rhizosphere of other important and traditional ATCs.

Combination of Magnetic Resonance Imaging and Neutron Computed Tomography for Three‐Dimensional Rhizosphere Imaging

Core Ideas 3D MRI relaxation time maps reflect water mobility in root, rhizosphere, and soil. 3D NCT water content maps of the same plant complement relaxation time maps. The relaxation time T1 decreases from soil to root, whereas water content increases. Parameters together indicate modification of rhizosphere pore space by gel phase. The zone of reduced T1 corresponds to the zone remaining dry after rewetting. In situ investigations of the rhizosphere require high‐resolution imaging techniques, which allow a look into the optically opaque soil compartment. We present the novel combination of magnetic resonance imaging (MRI) and neutron computed tomography (NCT) to achieve synergistic information such as water mobility in terms of three‐dimensional (3D) relaxation time maps and total water content maps. Besides a stationary MRI scanner for relaxation time mapping, we used a transportable MRI system on site in the NCT facility to capture rhizosphere properties before desiccation and after subsequent rewetting. First, we addressed two questions using water‐filled test capillaries between 0.1 and 5 mm: which root diameters can still be detected by both methods, and to what extent are defined interfaces blurred by these imaging techniques? Going to real root system architecture, we demonstrated the sensitivity of the transportable MRI device by co‐registration with NCT and additional validation using X‐ray computed tomography. Under saturated conditions, we observed for the rhizosphere in situ a zone with shorter T1 relaxation time across a distance of about 1 mm that was not caused by reduced water content, as proven by successive NCT measurements. We conclude that the effective pore size in the pore network had changed, induced by a gel phase. After rewetting, NCT images showed a dry zone persisting while the MRI intensity inside the root increased considerably, indicating water uptake from the surrounding bulk soil through the still hydrophobic rhizosphere. Overall, combining NCT and MRI allows a more detailed analysis of the rhizosphere's functioning.

Preferential flow pathways in paddy rice soils as hot spots for nutrient cycling

Crop rotations with maize and flooded rice lead to temporally aerobic soil conditions. This promotes the development of desiccation cracks in the soil, which can act as preferential flow pathways for water and solutes. We hypothesized that these cracks are enriched with organic carbon (C), plant nutrients and microbial residues (amino sugars) and that they can thus also serve as hot spots of fertilizer and C cycling. To test this hypothesis, we applied 13C-labelled rice straw and 15N-labelled urea to rice fields of the International Rice Research Institute (Los Baños, Philippines). We then traced the fate of the 13C-labelled rice straw and the 15N-labelled urea in crack and bulk soil and in microbial residues in two approaches, i) in the short term, i.e., 24 h after application of straw and fertilizer jointly with a dye tracer (Brilliant Blue) prior to maize seeding in the paddy - maize cropping system, as well as ii) in the long-term, i.e., during one year and for three different crop rotations (continuous paddy rice, paddy rice – maize, and paddy rice – maize with straw mulching and cover cropping). The short-term analyses of the dye tracer depth profiles showed that flow path areas decreased with increasing depth. A typical impermeable plough pan was not identified. Instead, we observed rapid infiltration of irrigation water down to 60 cm soil depth. The dyed flow paths were enriched in organic C (+12%) and plant nutrients (N: +21%, Ca2+: +59%, K+: +39%, Mg2+: +39%) relative to the bulk soil. The labelled straw and fertilizer quickly reached 60 cm depth with the dye tracer. We could not identify elevated microbial biomass along the flow paths, however, we did find larger microbial activities along the cracks in the long-term experiment than in the surrounding bulk soil. The increased activity fostered microbial uptake of fertilizer 15N along the cracks, which was detected mainly for fungal residues and only in the trials receiving straw (crack soil: 0.6 ± 0.1 mg glucosamine-15N kg soil−1, bulk soil: 0.2 ± 0.1 mg glucosamine-15N kg soil−1). We conclude that analysis of homogenized bulk soil samples can underestimate C and nutrient availability, as well as their microbial processing in paddy rice soils, when crack systems are not considered.

Soil zymography as a powerful tool for exploring hotspots and substrate limitation in undisturbed subsoil

It is widely accepted that soil microorganisms are not evenly distributed but are often concentrated in spatially segregated hotspots that are characterized by higher substrate availability compared to the surrounding bulk soil. However, microorganisms outside of hotspots may be in a dormant or inactive state, since they have depleted all available substrates within their vicinity. So far, the knowledge about the spatial distribution and dynamics of microbial activity in subsoil is very scarce, since most available data has been acquired from either homogenized soil samples or as bulk signals from undisturbed soil cores. In this study, we introduced a new incubation approach combining soil zymography and substrate addition on undisturbed soil core surfaces. We mapped three extracellular enzymes (β-glucosidase, chitinase and acid phosphatase) on a subsoil sample from 60 cm depth and analyzed their activity-patterns using different geostatistical and spatial analyses. After initial enzyme mapping, the soil was homogenously sprayed with 14C glucose as model substrate and incubated for 14 days. Soil zymography was suitable for detecting hotspots in undisturbed soil, making up a proportion of 2.4% on average of the total area. Consequently, microbial-driven biogeochemical processes can be expected to be limited to small areas in this subsoil, while the major part of the soil volume is not contributing. Glucose additions considerably increased enzyme activities up to 900% in initial non-hotspots, while the effect was far lower in initial hotspots. These results show that microorganisms in the subsoil outside of hotspots can be activated and release enzymes when substrate is supplied. Thus, dormant or inactive microorganisms outside of hotspots are able to contribute to SOC mineralization when substrate limitation is overcome, thus most likely inducing positive priming effects. Our results clearly demonstrate the benefits of combining enzyme mapping with substrate additions on undisturbed soil to gain new insights about microbial hotspots and C-cycling in subsoils using spatial analyses. In contrast to traditional incubation experiments, this method gives high spatial information about microbial activity, allowing a more differentiated interpretation of incubation results.

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem

The effect of thermoclimatic changes on microbial communities in the rhizosphere of a wild thyme species, Thymus zygis L., and its surrounding bulk soil was studied along elevational gradients in the Sierra Nevada National Park (Spain). Multiplex amplicon sequencing of bacterial and fungal taxonomic markers revealed that the richness, diversity and structure of bacterial and fungal communities were affected by thermoclimatic changes, with environmental parameters (mean annual atmospheric temperature and precipitation) and edaphic properties (mainly pH and nutrients) as the major drivers. Although both bulk soil and rhizosphere communities were structured according to the thermoclimatic zones, the response of microorganisms to thermoclimatic changes was different depending on the rhizosphere effect. On the contrary, the microbial functional gene diversity was not affected by thermoclimatic changes suggesting functional redundancy in the microbial communities along the altitudinal gradients. However, the functional gene diversity was clearly different between bulk soil and the rhizosphere, with the latter harbouring a larger number of gene copies and more different functional genes than bulk soils. Finally, a set of microbial bioindicators are defined for the thermoclimatic zones as a starting point to develop improved biological tools and models to monitor and predict the effects of climate changes. To the best of our knowledge, this is the first study where the response of bulk soil and rhizosphere microbial communities to thermoclimatic changes has been studied in parallel.

Bulk soil bacterial community mediated by plant community in Mediterranean ecosystem, Israel

The Israeli Mediterranean ecosystem has a distinctive flora with high levels of plant diversity. Previous studies of soil microbial ecology from the region have paid little attention to the possibility of distinctive soil bacterial communities associated with particular habitats. This study looked at bacterial communities present in the bulk soil from the closed canopy of four indigenous plants – Quercus ithaburensis, Calicotome villosa, Sarcopoterium spinosum, and Rhamnus puncata. Soil DNA was amplified for the 16S rRNA gene and sequenced using MiSeq Illumina platform. Results indicated that the bacterial communities differed between open and closed canopy with no significant difference in community structure within closed canopy, with soil moisture and organic matter content significantly influenced the community. Only the relative abundance of Gemmatimonadetes varied significantly with the open canopy having the highest abundance, and the relative abundance of Spartobacteria and Saprospirae was unusually high compared to other Mediterranean soils. There was no difference in OTU richness between plant species. Additionally, this study revealed that open canopy community between plants was nested within closed canopy bacterial community implying that open canopy community potentially serves as a source for the closed canopy. It is then possible that the rhizospheric influence extends beyond the root-soil interface and to the surrounding bulk soil. Overall, this study indicates that in Israeli Mediterranean ecosystems native plants extend a selection beyond the rhizosphere, and like other studies from Mediterranean ecosystems pH does not seem to play an integral role in structuring bacterial communities.

Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata

Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil. Two bacterial (Alphaproteobacteria and Gammaproteobacteria) and two fungal (Pezizomycetes and Agaricomycetes) classes were enriched in the rhizosphere compared with bulk soils. Changes in nutritional status, possibly induced by A. dealbata, primarily shaped rhizosphere soil communities. Despite a high degree of geographic variability in the diversity and composition of microbial communities, invasive A. dealbata populations shared a core of bacterial and fungal taxa, some of which are known to be involved in N and P cycling, while others are regarded as plant pathogens. Shotgun metagenomic analysis also showed that several functional genes related to plant growth promotion were overrepresented in the rhizospheres of A. dealbata. Overall, results suggest that rhizosphere microbes may contribute to the widespread success of this invader in novel environments.

Exploring the pathways of earthworm-induced phosphorus availability

As many soils are unable to supply sufficient amounts of phosphorus (P) to plants, P availability is often a growth-limiting factor. Literature shows that levels of readily available P can be considerably higher in earthworm casts than in the surrounding bulk soil, possibly resulting in increased plant P uptake. However, the underlying mechanisms through which this increase of readily available P occurs are unclear. In a greenhouse pot experiment with annual ryegrass (Lolium multiflorum) on a soil with low P availability, we tested whether the presence of the anecic earthworm Lumbricus terrestris resulted in increased grass growth and P uptake and explored the possible mechanisms behind such an effect. During the pot experiment, earthworm casts were collected and analysed for water-extractable P as well as for most other relevant ions. The earthworm's presence significantly increased grass yield from 9.80 to 10.80g dry matter per pot (p=0.044) and P uptake from 6.32 to 8.04mg per pot (p=0.002). Due to increased microbial activity, the solution chemistry in the water extracts of the casts was dramatically changed compared to the bulk soil samples. The concentrations of dissolved inorganic P in cast were enhanced by a factor ~30–1000 compared to the levels found in bulk soil. The pH in earthworm casts increased from 5.9 to values between 7.4 and 9.0 and the Ca concentrations decreased by about a factor ~2-3 compared to bulk soil samples. In addition, there was an increase in dissolved organic carbon (35mgL−1 in casts versus 3mgL−1 in soil). Surface complexation modelling, using the Charge Distribution model, suggests that, besides an increase in pH, particularly an enhanced interaction of dissolved organic matter with reactive surface of metal (hydr)oxides is likely to be a major driving force for the augmented release of orthophosphate (PO4) via competitive adsorption and desorption. This competition for adsorption sites is an alternative pathway, next to mineralisation of organic matter, through which earthworms can increase soil fertility.

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities.

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

Comparison of the phytoremediation potentials of Medicago falcata L. And Medicago sativa L. in aged oil-sludge-contaminated soil.

Thirteen-year monitoring of the vegetation growing in the industrial and adjacent areas of an oil refinery showed the prevalence of yellow medick (Medicago falcata L.) over other plant species, including alfalfa (Medicago sativa L.). A comparative field study of the two Medicago species established that yellow medick and alfalfa exhibited similar resistance to soil petroleum hydrocarbons and that the pollutant concentration in their rhizosphere was 30% lower than that in the surrounding bulk soil. In laboratory pot experiments, yellow medick reduced the contaminant content by 18% owing to the degradation of the major heavy oil fractions, such as paraffins, naphthenes, and alcohol and benzene tars; and it was more successful than alfalfa. Both species were equally effective in stimulating the total number of soil microorganisms, but the number of hydrocarbon-oxidizing microorganisms, including polycyclic aromatic hydrocarbon degraders, was larger in the root zone of alfalfa. In turn, yellow medick provided a favorable balance of available nitrogen. Both Medicago species equally stimulated the dehydrogenase and peroxidase activities of the soil, and yellow medick increased the activity of soil polyphenol oxidase but reduced the activity of catalase. The root tissue activity of catalase, ascorbate oxidase, and tyrosinase was grater in alfalfa than in yellow medick. The peroxidase activity of plant roots was similar in both species, but nondenaturing polyacrylamide gel electrophoresis showed some differences in the peroxidase profiles of the root extracts of alfalfa and yellow medick. Overall, this study suggests that the phytoremediation potentials of yellow medick and alfalfa are similar, with some differences.

Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees

Rhizosphere represents a nutrient-rich environment and a hotspot of bacterial activities compared to the surrounding bulk soil. However, few studies have investigated how this rhizosphere effect depends on the soil conditions, and never for trees. Contrary to annual plants, trees need decades to grow and strongly depend on the access and recycling of soil nutrients and water. In this context, we aimed at understanding if contrasted soil types impact the taxonomy and functions of bacterial communities inhabiting beech rhizosphere. To test this hypothesis, we considered the natural toposequence of Montiers, which is characterized by a same land cover dominated by beech (Fagus sylvatica) trees of the same age, growing under the same climatic conditions and under the same forestry practices. We used a combination of in vitro bioassays and 16S rRNA gene sequences analyses on a collection of 370 bacterial strains generated from beech rhizosphere and surrounding bulk soil samples collected in the organo-mineral horizon along the toposequence. Our study highlighted an increasing beech rhizosphere effect from the nutrient-rich to nutrient-poor soils, with specific bacterial functions related to inorganic nutrient mobilization largely and exclusively enriched in the rhizosphere of the nutrient-poor soils. This functional selection in the rhizosphere came with an enrichment of bacterial strains assigned to the Burkholderia and Collimonas genus, which appeared to be the dominant and most effective mineral-weathering bacteria. Our data corroborate the hypothesis of a variable selection of specific rhizosphere bacterial communities by beech trees according to the soil conditions and the tree nutritional requirements.

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil.

Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.

Illumina high-throughput sequencing and comparative analysis of bacterial communities in cherry orchard soil

ABSTRACTMicrobial diversity in the rhizosphere is affected by soil physical and chemical properties, which may be determined by plant species and growth stage. Exploring the bacterial communities in cherry rhizospheres may help in monitoring and conservation of soil quality. The aim of this study was to characterize the bacterial community structure between bulk soil and rhizosphere, using Illumina pyrosequencing of bacterial 16S rRNA genes, to determine the effect of soil types and seasons on bacterial diversity in cherry orchard. Sequences of 199,615 (30,162–35,399/sample) genes were obtained. Rhizosphere communities shared features with the surrounding bulk soil, such as predominance of Proteobacteria, Acidobacteria, and Actinobacteria. The relative abundance of certain bacterial lineages differed: Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were more abundant in the rhizosphere than in bulk soil. At the genus level, Burkholderia, Rhodococcus, Streptomyces, and Varivorax were more abundant in the rhizosphere, compared with the bulk. Specifically, Burkholderia and Rhodanobacter were abundant in the rhizosphere and bulk soil, respectively, and changed greatly with different growth stages. These results indicated that season variations and soil types affected the bacterial community composition in cherry orchard soil, which may have implications for understanding the status of cherry orchard nutrients in North China.