Root exudates regulate soil fungal community composition and diversity

Are drivers of root-associated fungal community structure context specific?

The composition and structure of plant-root-associated fungal communities are determined by local abiotic and biotic conditions. However, the relative influence and identity of relationships to abiotic and biotic factors may differ across environmental and ecological contexts, and fungal functional groups. Thus, understanding which aspects of root-associated fungal community ecology generalise across contexts is the first step towards a more predictive framework. We investigated how the relative importance of biotic and abiotic factors scale across environmental and ecological contexts using high-throughput sequencing (ca. 55 M Illumina metabarcoding sequences) of >260 plant-root-associated fungal communities from six UK salt marshes across two geographic regions (South-East and North-West England) in winter and summer. Levels of root-associated fungal diversity were comparable with forests and temperate grasslands, quadrupling previous estimates of salt-marsh fungal diversity. Whilst abiotic variables were generally most important, a range of site- and spatial scale-specific abiotic and biotic drivers of diversity and community composition were observed. Consequently, predictive models of diversity trained on one site, extrapolated poorly to others. Fungal taxa from the same functional groups responded similarly to the specific drivers of diversity and composition. Thus site, spatial scale and functional group are key factors that, if accounted for, may lead to a more predictive understanding of fungal community ecology.

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.

Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill

The plant microbiome, composed of diverse interacting microorganisms, is thought to undergird host integrity and well-being. Though it is well understood that environmental perturbations like oil pollution can alter the diversity and composition of microbiomes, remarkably little is known about how disturbance alters plant-fungal associations. Using Next-Generation sequencing of the 18S rDNA internal transcribed spacer (ITS1) region, we examined outcomes of enduring oil exposure on aboveground leaf and belowground endophytic root and rhizosphere fungal communities of Spartina alterniflora, a highly valued ecosystem engineer in southeastern Louisiana marshes affected by the 2010 Deepwater Horizon accident. We found that aboveground foliar fungal communities exhibited site-dependent compositional turnover with consequent loss in diversity according to oiling history. Rhizosphere soil communities also exhibited shifts in community composition associated with oiling history, whereas root endophytic communities did not. Oiling did not increase or decrease similarities among aboveground and belowground communities within an individual host, indicating that host plant characteristics exert stronger control than external factors on fungal community composition. These results show that fungal community responses to oiling vary within tissues of the same host plant, and that differences in the local environment, or alternatively, site-specific differences in residual oil constrain the magnitude of exposure responses. Our study offers novel perspectives on how environmental contaminants and perturbations can influence plant microbiomes, highlighting the importance of assessing long-term ecological outcomes of oil pollution to better understand how shifts in microbial communities influence plant performance and ecosystem function. Our findings are relevant to coastal management programs tasked with responding to oil spills and increasing pressures arising from intensifying development and climate change. Understanding how modification of plant-microbiome associations influences plant performance, particularly of ecosystem engineers like S. alterniflora, can help guide efforts to protect and restore at-risk coastal ecosystems.

An in Vivo Imaging Assay Detects Spatial Variability in Glucose Release from Plant Roots

Plants secrete a plethora of metabolites into the rhizosphere that allow them to obtain nutrients necessary for growth and modify microbial communities around the roots. Plants release considerable amounts of photosynthetically fixed carbon into the rhizosphere; hence, it is important to understand how carbon moves from the roots into the rhizosphere. Approaches used previously to address this question involved radioactive tracers, fluorescent probes, and biosensors to study sugar movement in the roots and into the rhizosphere. Although quite effective for studying sugar movement, it has been challenging to obtain data on spatial and temporal variability in sugar exudation using these techniques. In this study, we developed a gel-based enzyme-coupled colorimetric and fluorometric assay to image glucose (Glc) in vivo and used this assay to show that there is spatial variability in Glc release from plant roots. We found that the primary roots of maize (Zea mays) released more Glc from the base of the root than from the root tip and that the Glc release rate is reduced in response to water stress. These findings were confirmed independently by quantifying Glc release in well-watered and water-stressed maize primary roots using high-performance anion-exchange chromatography. Additionally, we demonstrated differential patterns of Glc exudation in different monocot and eudicot plant species. These findings and their implications on root-rhizosphere interactions are discussed.

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.

Use of sugarcane-soybean intercropping in acid soil impacts the structure of the soil fungal community

Although sugarcane-soybean intercropping has been widely used to control disease and improve productivity in the field, the response of soil fungal communities to intercropping has not been fully understood. In this study, the rhizosphere fungal communities of sugarcane and soybean under monoculture and intercropping systems were investigated using Illumina MiSeq sequencing of ITS gene. Intercropping decreased the alpha-diversity and changed fungal community composition compared to monocultures. Taxonomic analyses showed that the dominant phyla were Ascomycota, Zygomycota and Basidiomycota. The abundance of Ascomycota decreased in intercropping sugarcane-grown soil compared to monoculture, while it increased in soybean-grown soil in the intercropping system. In addition, intercropping increased the abundance of important fungal genera, such as Trichoderma, Hypocreales and Fusarium but decreased the relative abundance of Gibberella and Chaetomium. The results of canonical correspondence analysis and automatic linear modelling indicated that fungal community compositions were closely associated with soil parameters such as total nitrogen (TN), soil organic matter (SOC), pH and NO3-, which suggests that the impacts of intercropping on the soil fungal community are linked to the alteration of soil chemical properties.

Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.

Less abundant bacterial groups are more affected than the most abundant groups in composted tannery sludge-treated soil

The application of composted tannery sludge (CTS) has promoted shifts in soil chemical properties and, therefore, can affect the soil bacterial community. This study assessed the effect of the CTS on the soil bacterial community over time. The CTS was applied at five rates (0, 2.5, 5, 10 and 20 t/ha), and the bacterial community was evaluated for 180 days. The principal curve response (PRC) analysis showed that the most abundant phyla were not influenced by the CTS rates over time, while the analysis of the bacterial community showed that some of the less abundant phyla were influenced by the CTS rates. Similarly, the PRC analysis for the bacterial classes showed the significant effect of the CTS rates. The redundancy analyses for the bacterial phyla and classes showed the relationship between the significant chemical properties and the bacterial community of the soil after the CTS amendment over time. Therefore, there was a shift in the bacterial community over time with the application of the composted tannery sludge. Our study has shown that the less abundant bacterial groups were more influenced by the CTS than the most abundant bacterial groups and that these bacterial groups were driven by soil chemical properties, primarily chromium (Cr) and the soil pH.

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau

Thinning can effectively improve forest production and maintain ecological stability. However, the changes in soil microbial community compositions after thinning are still not well understood. In this study, we investigated the changes in the soil microbial community of mature Chinese pine (Pinus tabuliformis) plantations in the Loess Plateau after 11years of four different thinning intensity treatments. Furthermore, the responses of the soil microbial community to changes in understory plants and soil properties were analyzed. The ratios of wood removal investigated were 0 (CK), 15% (LIT), 30% (MIT) and 45% (HIT). Compared with the CK, thinning significantly increased the Shannon index, species richness, coverage and biomass of the understory plants, and these values were highest for the HIT. The soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO₃^--N) and available phosphorus (AP) concentrations increased with increasing thinning intensity. Thinning intensity did not significantly affect soil microbial community diversity indices. With respect to the dominant bacterial groups, the relative abundance of Proteobacteria was much higher in the HIT, while that of Acidobacteria was much higher in the LIT and CK. For the dominant fungal groups, the relative abundance of Basidiomycota was lowest in the HIT, while that of Ascomycota was highest in the same treatment. Redundancy analysis (RDA) showed that SOC, TN, and AP significantly correlated with soil bacterial communities and that SOC, TN, TP, AP and NO₃^--N significantly correlated with soil fungal communities. The understory vegetation influenced soil fungal communities rather than soil bacterial communities. These findings suggest that the aboveground vegetation diversity and soil nutrients were improved with the increased thinning intensity after 11years. The copiotrophic groups (e.g. Proteobacteria) and oligotrophic groups (e.g. Acidobacteria) differed significantly among the four thinning treatments, indicating a dependence of the soil microbial community composition on soil nutrients.

Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems

Intercropping plays a vital role in greenhouse production, and affects soil physicochemical properties and soil microbial communities structure, but influences of intercropping on the relationship of microorganisms are reported in continuous cropping soil rarely. Here, we investigated the effects of seven intercropping systems [alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber] on soil bacterial and fungal communities compared to the cucumber continuous cropping system in the greenhouse. The results showed that intercropping increased microbial OTU richness and fungal communities diversity, soil bacterial communities diversity was abundant in the trifolium-cucumber and mustard-cucumber systems. Nevertheless, there was no significant differences of microbial communities structure between intercropping and monoculture systems. Redundancy analysis indicated that soil microbial communities composition was indirectly influenced by soil properties. In addition, network analysis demonstrated that simple inter-relationships of fungal taxa were observed in the intercropping soil, and trifolium, wheat, and mustard intercropping systems had a complex connection between bacterial taxa. Taken together, trifolium and mustard as the intercrops significantly increased cucumber continuous cropping soil bacterial and fungal communities diversity. Moreover, intercropping strongly changed the relationships of microbial taxa, though did not shape notably soil microbial communities structure.

The Effects of Arbuscular Mycorrhizal Fungal Colonisation on Nutrient Status, Growth, Productivity, and Canker Resistance of Apple (Malus pumila)

We assess whether arbuscular mycorrhizal fungi (AMF) improve growth, nutritional status, phenology, flower and fruit production, and disease resistance in woody perennial crops using apple (Malus pumila) as a study system. In a fully factorial experiment, young trees were grown for 3 years with or without AMF (Funneliformis mosseae and Rhizophagus irregularis), and with industrial standard fertiliser applications or restricted fertiliser (10% of standard). We use two commercial scions (Dabinett and Michelin) and rootstocks (MM111 and MM106). Industrial standard fertiliser applications reduced AMF colonisation and root biomass, potentially increasing drought sensitivity. Mycorrhizal status was influenced by above ground genotypes (scion type) but not rootstocks, indicating strong interactions between above and below ground plant tissue. The AMF inoculation significantly increased resistance to Neonectria ditissima, a globally economically significant fungal pathogen of apple orchards, but did not consistently alter leaf nutrients, growth, phenology or fruit and flower production. This study significantly advances understanding of AMF benefits to woody perennial crops, especially increased disease resistance which we show is not due to improved tree nutrition or drought alleviation. Breeding programmes and standard management practises can limit the potential for these benefits.

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH₄-N, NO₃-N, NO₂-N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere.

Diversity of cultivable fungal endophytes in Paullinia cupana (Mart.) Ducke and bioactivity of their secondary metabolites

Paullinia cupana is associated with a diverse community of pathogenic and endophytic microorganisms. We isolated and identified endophytic fungal communities from the roots and seeds of P. cupana genotypes susceptible and tolerant to anthracnose that grow in two sites of the Brazilian Amazonia forest. We assessed the antibacterial, antitumor and genotoxic activity in vitro of compounds isolated from the strains Trichoderma asperellum (1BDA) and Diaporthe phaseolorum (8S). In concert, we identified eight fungal species not previously reported as endophytes; some fungal species capable of inhibiting pathogen growth; and the production of antibiotics and compounds with bacteriostatic activity against Pseudomonas aeruginosa in both susceptible and multiresistant host strains. The plant genotype, geographic location and specially the organ influenced the composition of P. cupana endophytic fungal community. Together, our findings identify important functional roles of endophytic species found within the microbiome of P. cupana. This hypothesis requires experimental validation to propose management of this microbiome with the objective of promoting plant growth and protection.

Phenolic root exudate and tissue compounds vary widely among temperate forest tree species and have contrasting effects on soil microbial respiration

Root-soil interactions fundamentally affect the terrestrial carbon (C) cycle and thereby ecosystem feedbacks to climate change. This study addressed the question of whether the secondary metabolism of different temperate forest tree species can affect soil microbial respiration. We hypothesized that phenolics can both increase and decrease respiration depending on their function as food source, mobilizer of other soil resources, signaling compound, or toxin. We analyzed the phenolic compounds from root exudates and root tissue extracts of six tree species grown in a glasshouse using high-performance liquid chromatography. We then tested the effect of individual phenolic compounds, representing the major identified phenylpropanoid compound classes, on microbial respiration through a 5-d soil incubation. Phenolic root profiles were highly species-specific. Of the eight classes identified, flavonoids were the most abundant, with flavanols being the predominating sub-class. Phenolic effects on microbial respiration ranged from a 26% decrease to a 46% increase, with reduced respiration occurring in the presence of compounds possessing a catechol ring. Tree species variation in root phenolic composition influences the magnitude and direction of root effects on microbial respiration. Our data support the hypothesis that functional group rather than biosynthetic class determines the root phenolic effect on soil C cycling.

Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.

Effect of Solid Biological Waste Compost on the Metabolite Profile of Brassica rapa ssp. chinensis

Large quantities of biological waste are generated at various steps within the food production chain and a great utilization potential for this solid biological waste exists apart from the current main usage for the feedstuff sector. It remains unclear how the usage of biological waste as compost modulates plant metabolites. We investigated the effect of biological waste of the processing of coffee, aronia, and hop added to soil on the plant metabolite profile by means of liquid chromatography in pak choi sprouts. Here we demonstrate that the solid biological waste composts induced specific changes in the metabolite profiles and the changes are depending on the type of the organic residues and its concentration in soil. The targeted analysis of selected plant metabolites, associated with health beneficial properties of the Brassicaceae family, revealed increased concentrations of carotenoids (up to 3.2-fold) and decreased amounts of glucosinolates (up to 4.7-fold) as well as phenolic compounds (up to 1.5-fold).

Mycobiome of Cysts of the Soybean Cyst Nematode Under Long Term Crop Rotation

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe (Phylum Nematoda), is a major pathogen of soybean. It causes substantial yield losses worldwide and is difficult to control because the cyst protects the eggs which can remain viable for nearly a decade. Crop rotation with non-host crops and use of biocontrol organisms such as fungi and bacteria offer promising approaches, but remain hampered by lack of knowledge of the biology of nematode parasitic organisms. We used a high-throughput metabarcoding approach to characterize fungal communities associated with the SCN cyst, a microenvironment in soil that may harbor both nematode parasites and plant pathogens. SCN cysts were collected from a long-term crop rotation experiment in Southeastern Minnesota at three time points over two growing seasons to characterize diversity of fungi inhabiting cysts and to examine how crop rotation and seasonal variation affects fungal communities. A majority of fungi in cysts belonged to Ascomycota and Basidiomycota, but the presence of several early diverging fungal subphyla thought to be primarily plant and litter associated, including Mortierellomycotina and Glomeromycotina (e.g., arbuscular mycorrhizal fungi), suggests a possible role as nematode egg parasites. Species richness varied by both crop rotation and season and was higher in early years of crop rotation and in fall at the end of the growing season. Crop rotation and season also impacted fungal community composition and identified several classes of fungi, including Eurotiomycetes, Sordariomycetes, and Orbiliomycetes (e.g., nematode trapping fungi), with higher relative abundance in early soybean rotations. The relative abundance of several genera was correlated with increasing years of soybean. Fungal communities also varied by season and were most divergent at midseason. The percentage of OTUs assigned to Mortierellomycotina_cls_Incertae_sedis and Sordariomycetes increased at midseason, while Orbiliomycetes decreased at midseason, and Glomeromycetes increased in fall. Ecological guilds of fungi containing an animal-pathogen lifestyle, as well as potential egg-parasitic taxa previously isolated from parasitized SCN eggs, increased at midseason. The animal pathogen guilds included known (e.g., Pochonia chlamydosporia) and new candidate biocontrol organisms. This research advances knowledge of the ecology of nematophagous fungi in agroecosystems and their use as biocontrol agents of the SCN.

Investigations of microbial degradation of polycyclic aromatic hydrocarbons based on 13C-labeled phenanthrene in a soil co-contaminated with trace elements using a plant assisted approach

Co-contaminations of soils with organic and inorganic pollutants are a frequent environmental problem. Due to their toxicity and recalcitrance, the heterogeneous pollutants may persist in soil. The hypothesis of this study was that degradation of polycyclic aromatic hydrocarbons (PAHs) is enhanced if heavy metals in soil are immobilized and their bioavailability reduced. For metal immobilization and enhanced biodegradation, distinct mineral and organic soil amendments (iron oxides, gravel sludge, biochar) were deployed in an incubation batch experiment. The second part of the experiment consisted of a greenhouse pot experiment applying fast-growing and pollution-tolerant woody plants (willow and black locust). Soil amendments initially immobilized NH₄NO₃-extractable zinc, cadmium, and lead; after 100 days of incubation, soil amendments showed reductions only for cadmium and a tendency to enhance arsenic mobility. In order to monitor the remediation success, a ¹³C-phenanthrene (PHE) label was applied. ¹³C-phospholipid fatty acid analysis (¹³C-PLFA) further enabled the identification of PHE-degrading soil microorganisms. Both experiments exhibited a similar PLFA profile. Gram-negative bacteria (esp. cy17:0, 16:1ω7 + 6, 18:1ω7c) were the most significant microbial group taking up ¹³C-PHE. Plants effectively increased the label uptake by gram-positive bacteria and increased the biomass of the fungal biomarker, although their contribution to the degradation process was minor. Plants tended to prolong PAH dissipation in soil; at the end of the experiment, however, all treatments showed equally low total PAH concentrations in soil. While black locust plants tended not to take up potentially toxic trace elements, willows accumulated them in their leaves. The results of this study show that the chosen treatments did not enhance the remediation of the experimental soil.

Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor

Our results show that Sorghum bicolor is able to recognize bacteria through its volatile compounds and differentially respond to beneficial or pathogens via eliciting nutritional or defense adaptive traits. Plants establish beneficial, harmful, or neutral relationships with bacteria. Plant growth promoting rhizobacteria (PGPR) emit volatile compounds (VCs), which may act as molecular cues influencing plant development, nutrition, and/or defense. In this study, we compared the effects of VCs produced by bacteria with different lifestyles, including Arthrobacter agilis UMCV2, Bacillus methylotrophicus M4-96, Sinorhizobium meliloti 1021, the plant pathogen Pseudomonas aeruginosa PAO1, and the commensal rhizobacterium Bacillus sp. L2-64, on S. bicolor. We show that VCs from all tested bacteria, except Bacillus sp. L2-64, increased biomass and chlorophyll content, and improved root architecture, but notheworthy A. agilis induced the release of attractant molecules, whereas P. aeruginosa activated the exudation of growth inhibitory compounds by roots. An analysis of the expression of iron-transporters SbIRT1, SbIRT2, SbYS1, and SbYS2 and genes related to plant defense pathways COI1 and PR-1 indicated that beneficial, pathogenic, and commensal bacteria could up-regulate iron transporters, whereas only beneficial and pathogenic species could induce a defense response. These results show how S. bicolor could recognize bacteria through their volatiles profiles and highlight that PGPR or pathogens can elicit nutritional or defensive traits in plants.

The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions

The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.

Fagopyrum esculentum Alters Its Root Exudation after Amaranthus retroflexus Recognition and Suppresses Weed Growth

Weed control by crops through growth suppressive root exudates is a promising alternative to herbicides. Buckwheat (Fagopyrum esculentum) is known for its weed suppression and redroot pigweed (Amaranthus retroflexus) control is probably partly due to allelopathic root exudates. This work studies whether other weeds are also suppressed by buckwheat and if the presence of weeds is necessary to induce growth repression. Buckwheat and different weeds were co-cultivated in soil, separating roots by a mesh allowing to study effects due to diffusion. Buckwheat suppressed growth of pigweed, goosefoot and barnyard grass by 53, 42, and 77% respectively without physical root interactions, probably through allelopathic compounds. Root exudates were obtained from sand cultures of buckwheat (BK), pigweed (P), and a buckwheat/pigweed mixed culture (BK-P). BK-P root exudates inhibited pigweed root growth by 49%. Characterization of root exudates by UHPLC-HRMS and principal component analysis revealed that BK and BK-P had a different metabolic profile suggesting that buckwheat changes its root exudation in the presence of pigweed indicating heterospecific recognition. Among the 15 different markers, which were more abundant in BK-P, tryptophan was identified and four others were tentatively identified. Our findings might contribute to the selection of crops with weed suppressive effects.

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.

Post photosynthetic carbon partitioning to sugar alcohols and consequences for plant growth

The occurrence of sugar alcohols is ubiquitous among plants. Physiochemical properties of sugar alcohols suggest numerous primary and secondary functions in plant tissues and are often well documented. In addition to functions arising from physiochemical properties, the synthesis of sugar alcohols may have significant influence over photosynthetic, respiratory, and developmental processes owing to their function as a large sink for photosynthates. Sink strength is demonstrated by the high concentrations of sugar alcohols found in plant tissues and their ability to be readily transported. The plant scale distribution and physiochemical function of these compounds renders them strong candidates for functioning as stress metabolites. Despite this, several aspects of sugar alcohol biosynthesis and function are poorly characterised namely: 1) the quantitative characterisation of carbon flux into the sugar alcohol pool; 2) the molecular control governing sugar alcohol biosynthesis on a quantitative basis; 3) the role of sugar alcohols in plant growth and ecology; and 4) consequences of sugar alcohol synthesis for yield production and yield quality. We highlight the need to adopt new approaches to investigating sugar alcohol biosynthesis using modern technologies in gene expression, metabolic flux analysis and agronomy. Combined, these approaches will elucidate the impact of sugar alcohol biosynthesis on growth, stress tolerance, yield and yield quality.

Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity

Future increases in temperature and cloud cover will alter plant growth and decomposition of the large carbon pools stored in Arctic soils. A better understanding of interactions between above- and belowground processes and communities of plants and microorganisms is essential for predicting Arctic ecosystem responses to climate change. We measured ecosystem CO2 fluxes during the growing season for seven years in a dwarf-shrub tundra in West Greenland manipulated with warming and shading and experiencing a natural larvae outbreak. Vegetation composition, soil fungal community composition, microbial activity, and nutrient availability were analyzed after six years of treatment. Warming and shading altered the plant community, reduced plant CO2 uptake, and changed fungal community composition. Ecosystem carbon accumulation decreased during the growing season by 61% in shaded plots and 51% in warmed plots. Also, plant recovery was reduced in both manipulations following the larvae outbreak during the fifth treatment year. The reduced plant recovery in manipulated plots following the larvae outbreak suggests that climate change may increase tundra ecosystem sensitivity to disturbances. Also, plant community changes mediated via reduced light and reduced water availability due to increased temperature can strongly lower the carbon sink strength of tundra ecosystems.

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.

Temperature drives the assembly of endophytic communities' seasonal succession

Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. The variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field were studied. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures. The findings revealed the succession of endophytic communities over the year. Endophytic communities of roots and stems differ in terms of composition and dynamic response to temperature. Noticeably, compositional differences during the seasons affected bacterial taxa more in stems than in roots, suggesting that roots offer a more stable and less easily perturbed environment. Correlation abundance networks showed that the presence of several taxa (including Bradyrhizobium, Burkholderia, Dyella, Mesorhizobium, Propionibacterium and Ralstonia) is linked in both the field and the greenhouse.

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the long-term use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly Massilia and Herbaspirillum) was enriched in the RP-amended soil. Klebsiella was the second most abundant taxon in the RP-treated soil. Burkholderia sp. and Bacillus sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were Scutellospora and Racocetra. These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.

Effect of microbial activity on penetrometer resistance and elastic modulus of soil at different temperatures

We explore the effect of microbial activity stimulated by root exudates on the penetrometer resistance of soil and its elastic modulus. This is important because it is a measure of the mechanical strength of soil and it correlates closely with the rate of elongation of roots. A sandy soil was incubated with a synthetic root exudate at different temperatures, for different lengths of time and with selective suppression of either fungi or bacteria. The shape of the temperature response of penetrometer resistance in soil incubated with synthetic exudate was typical of a poikilothermic temperature response. Both penetrometer resistance and small strain shear modulus had maximum values between 25 and 30°C. At temperatures of 20°C and less, there was little effect of incubation with synthetic root exudate on the small strain shear modulus, although penetrometer resistance did increase with temperature over this range (4-20°C). This suggests that in this temperature range the increase in penetrometer resistance was related to a greater resistance to plastic deformation. At higher temperatures (> 25°C) penetrometer resistance decreased. Analysis of the DNA sequence data showed that at 25°C the number of Streptomyces (Gram-positive bacteria) increased, but selective suppression of either fungi or bacteria suggested that fungi have the greater role with respect to penetrometer resistance.

HIGHLIGHTS

Effect of microbial activity stimulated by synthetic root exudates on the mechanical properties.We compared penetrometer measurements and estimates of elastic modulus with microbial community.Penetrometer resistance of soil showed a poikilothermic temperature response.Penetrometer resistance might be affected more by fungi than bacteria.

Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities

Peatlands play an important role in global climate change through sequestration of atmospheric CO₂. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO₂ concentrations). Peat litterbags were placed in mesocosms, and fungal communities in litterbags were monitored over 12 months to assess the impacts of climate change variables on peat-inhabiting fungi. Changes in fungal richness, diversity, and community composition were assessed using Illumina MiSeq sequencing of ribosomal DNA (rDNA). While general fungal richness reduced under warming conditions, Ascomycota exhibited higher diversity under increased temperature treatments over the course of the experiment. Both increased temperature and lowered water table position drove shifts in fungal community composition with a strong positive effect on endophytic and mycorrhizal fungi (including one operational taxonomic unit (OTU) tentatively identified as Barrenia panicia) and different groups of saprotrophs identified as Mortierella, Galerina, and Mycena. These shifts were observed during a predicted degradative succession in the decomposer community as different carbon substrates became available. Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change.

Emergence of plant and rhizospheric microbiota as stable interactomes

The growing human population and depletion of resources have necessitated development of sustainable agriculture. Beneficial plant-microbe associations have been known for quite some time now. To maintain sustainability, one could show better reliance upon beneficial attributes of the rhizosphere microbiome. To harness the best agronomic traits, understanding the entire process of recruitment, establishment, and maintenance of microbiota as stable interactome within the rhizosphere is important. In this article, we highlight the process of recruitment and establishment of microbiota within rhizosphere. Further, we have discussed the interlinkages and the ability of multiple (microbial and plant) partners to interact with one another forming a stable plant holobiont system. Lastly, we address the possibility of exploring the knowledge gained from the holobiont system to tailor the rhizosphere microbiome for better productivity and maintenance of agroecosystems. The article provide new insights into the broad principles of stable plant-microbe interactions which could be useful for sustaining agriculture and food security.

Suppression of Fusarium wilt of cucumber by ammonia gas fumigation via reduction of Fusarium population in the field

Cucumber plants subjected to consecutive monoculture for 9 years were found to suffer from severe Fusarium wilt disease, caused by the soil-borne fungus Fusarium oxysporum f. sp. Cucumerinum J. H. Owen. In the present study, greenhouse experiments were performed to evaluate the influence of ammonia gas fumigation on Fusarium wilt suppression, fungal abundance and fungal community composition. Results showed that ammonia gas fumigation remarkably reduced disease incidence from 80% to 27%, resulting in a four-fold increase in yield, compared to the control. Total fungal abundance declined dramatically after fumigation and reached the lowest level at day 32, at 243 times lower than the control. Moreover, fumigation significantly increased soil fungal diversity, though it also decreased considerably coinciding with cucumber growth. Fumigation also significantly altered soil fungal community composition, relative to the control. Fusarium was strongly inhibited by fumigation in both relative abundance (3.8 times lower) and targeted quantification (a decrease of 167 fold). Collectively, the application of ammonia gas fumigation to control Fusarium wilt of cucumber resulted in a re-assembly of the fungal community to resemble that of a non-disease conducive consortium. Additional strategies, such as bioorganic fertilizer application, may still be required to develop sustainable disease suppression following fumigation.

Plant diversity and plant identity influence Fusarium communities in soil

Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.

Impact of fertilization by natural manure on the microbial quality of soil: Molecular approach

The quality of soil is strongly bound by several interactions between chemical and biological components, including microbial composition, which are a key importance for soil performance. Cultural activities have a huge induction on soil health, through both modification of physicochemical proprieties and changing on soil microbial communities. This usually affects the safety of soil, and then the crop production and water.

In the present work, the information on bacterial community composition was determined from a set of 6 soils collected from 2 farms in agricultural land of Marrakech (Morocco), one of which used poultry manure (PM) and the other cow manure (CM) as fertilizers. To profile this structure of the bacterial community Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA fragments has been used.

These amendments resulted in the appearance of several novel bands and different relative intensities of bands between the control station and other sites studied. The stations most affected are those receiving a supply of manure rather high, which results in an organic and bacterial load in the soil. The results showed a bacterial diversity very important indicating a fecal contamination like Bacteroides, Pseudomonas, Staphylococcus,… etc. Bacteria pertain to the phylum Firmicutes and Bacteroidetes were noted to be the dominant ribotype in amended soil.

Moreover, this work demonstrates also the existence of pathogens strains in soil amended by poultry manure (PM) belonging to the Clostridiales order and Pseudomonadales. The pathogenic bacteria detected posing a hazard of human contagion when they are used for soil practice.

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach

Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach

Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Microbial community structure and functions of rhizosphere soil of rice were investigated after applying low and high doses of nitrogenous fertilizer and Phomopsis liquidambari. Average well color development, substrate richness, catabolic diversity and soil enzymes activities varied after applying N-fertilizer and P. liquidambari and were greater in P. liquidambari treated soil than only N-fertilization. Multivariate analysis distinctly separated the catabolic and enzymes activity profile which statistically proved alteration of microbial functional diversity. Nitrogen fertilizer altered microbial community structure revealed by the increased content of total PLFAs, specific subgroup marker PLFAs except fungal PLFAs and by the decreased ratio of G(+)/G(-), sat/monunsat, iso/anteiso, F/B except trans/cis while P. liquidambari inoculation enhanced N-fertilization effect except increased fungal PLFA and decreased trans/cis. PCA using identified marker PLFAs revealed definite discrimination among the treatments which further statistically confirmed structural changed of microbial community. Nitrogenase activity representative of N-fixing community decreased in N-fertilizer treatment while P. liquidambari inoculation increased. In short, application of P. liquidambari with low doses of N-fertilizer improved rice growth and reduced N-fertilizer requirement by increasing enzymes activities involved in C, N and P cycling, structural and functional diversity of microbes, nitrogenase activity involved in N2 fixation and accumulation of total-N.

Divergent habitat filtering of root and soil fungal communities in temperate beech forests

Distance decay, the general reduction in similarity of community composition with increasing geographical distance, is known as predictor of spatial variation and distribution patterns of organisms. However, changes in fungal communities along environmental gradients are little known. Here we show that distance decays of soil-inhabiting and root-associated fungal assemblages differ, and identify explanatory environmental variables. High-throughput sequencing analysis of fungal communities of beech-dominated forests at three study sites across Germany shows that root-associated fungi are recruited from the soil fungal community. However, distance decay is substantially weaker in the root-associated than in the soil community. Variance partitioning of factors contributing to the observed distance decay patterns support the hypothesis that host trees stabilize the composition of root-associated fungi communities, relative to soil communities. Thus, they not only have selective impacts on associated communities, but also buffer effects of changes in microclimatic and environmental variables that directly influence fungal community composition.