Root exudate cocktails: the link between plant diversity and soil microorganisms?

Chemodiversity of dissolved organic matter and its association with the bacterial community at a zinc smelting slag site after 10 years of direct revegetation

Dissolved organic matter (DOM) plays a critical role in driving the development of biogeochemical functions in revegetated metal smelting slag sites, laying a fundamental basis for their sustainable rehabilitation. However, the DOM composition at the molecular level and its interaction with the microbial community in such sites undergoing long-term direct revegetation remain poorly understood. This study investigated the chemodiversity of DOM and its association with the bacterial community in the rhizosphere and non-rhizosphere slags of four plant species (Arundo donax, Broussonetia papyrifera, Cryptomeria fortunei, and Robinia pseudoacacia) planted at a zinc smelting slag site for 10 years. The results indicated that the relative abundance of lipids decreased from 18 % to 5 %, while the relative abundance of tannins and lignins/CRAM-like substances increased from 4 % to 10 % and from 44 % to 64 % in the revegetated slags, respectively. The chemical stability of the organic matter in the rhizosphere slag increased due to the retention of recalcitrant DOM components, such as lignins, aromatics, and tannins. As the diversity and relative abundance of the bacterial community increased, particularly within the Proteobacteria, there was better utilization of recalcitrant components (e.g., lignins/CRAM-like compounds), but this utilization was not invariable. In addition, potential preference associations between specific bacterial OTUs and DOM molecules were observed, possibly stimulated by heavy metal bioavailability. Network analysis revealed complex connectivity and strong interactions between the bacterial community and DOM molecules. These specific interactions between DOM molecules and the bacterial community enable adaptation to the harsh conditions of the slag environment. Overall, these findings provide novel insights into the transformation of DOM chemodiversity at the molecular level at a zinc smelting slag sites undergoing long-term revegetation. This knowledge could serve as a crucial foundation for developing direct revegetation strategies for the sustainable rehabilitation of metal smelting slag sites.

Changes in Soil Bacterial and Fungal Community Composition and Functional Groups During the Artificial Restoration of Degraded Grassland of "Black-Soil Mountain"

About 35% of grassland in Sanjiangyuan area of China has degenerated into black-soil mountain. Artificial grassland is considered to be an effective measure to alleviate the severely degraded grassland in the alpine region of the three rivers and has been widely used. However, the pattern, potential function, and changes of carbon and nitrogen contents of soil microorganisms in degraded grassland in Heimushan by planting artificial grassland are still unclear. In this study, mixed-sown artificial alpine grassland (AG) was the focus of our study, whereas degraded black-soil mountain grassland (BG) and natural alpine grassland (NG) served as controls. Illumina 16S and ITS gene sequence analyses were used to analyze the community structure of the soil bacteria and fungi. The functional groups of NG, AG, and BG were predicted using the FAPROTAX and FUNGuild databases. In addition, the levels of soil carbon, nitrogen, and soil enzyme activities were evaluated. The results indicated a significant increase in the aboveground biomass of BG due to the planting artificial grassland. Moreover, the contents of total carbon (TC), total nitrogen (TN), ammonium nitrogen (NH 4 + - N ), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and leucine aminopeptidase (LAP) increased in the soil. Planting artificial grasslands changed the composition of bacterial and fungal communities. Among these, the bacterial community was more sensitive to planting artificial grasslands. The relative abundance of bacterial functional groups involved in carbon and nitrogen cycling changed significantly, suggesting that bacteria may play a role in regulating nutrient cycling during artificial grassland planting. Soil TC, TN, LAP, andNH 4 + - N affected the microbial community structure related to carbon and nitrogen.NH 4 + - N and β-1,4-glucosidase were carbon and nitrogen factors, respectively, that affected functional changes in fungi. These results indicate that planting artificial grasslands can effectively enhance the productivity of degraded black-soil mountain and regulate soil microbial communities and soil physical and chemical properties.

Diversified crop rotations improve soil microbial communities and functions in a six-year field experiment

Diversified crop rotations can help mitigate the negative impacts of increased agricultural intensity on the sustainability of agroecosystems. However, the impact of crop rotation diversity on the complexity of soil microbial association networks and ecological functions is still not well understood. In this study, a 6-year field experiment was conducted to evaluate how six different crop rotations change the composition and network complexity of soil microbial communities, as well as their related ecological functions. Microbial traits were measured in six crop rotations with different crop diversity index (CDI) during 2016-2022, including winter wheat-summer maize (CDI 1, WM) as the control, sweet potato→winter wheat-summer maize (CDI 1.5, SpWM), peanut→winter wheat-summer maize (CDI 1.5, PWM), soybean→winter wheat-summer maize (CDI 1.5, SWM), spring maize→winter wheat-summer maize (CDI 1.5, SmWM), and ryegrass-sweet sorghum→winter wheat-summer maize (CDI 2, RSWM). The study findings indicated that diversified crop rotations significantly increased ASV richness of both bacterial and fungal communities after 6-year treatments, and the β-diversity profiles of bacterial and fungal communities significantly distinguished at the year of 2022 from 2016. The relative abundance of Acidobacteria and Chloroflexi was significantly enriched in SpWM rotation at 2022, while Basidiomycota significantly declined in five diversified rotations compared to WM. Diversified crop rotations at 2022 increased the complexity and density of bacterial and fungal networks than 2016. SpWM and PWM rotations had the highest functional groups involved in chemoheterotrophy and saprotroph, respectively. Structural equation modelling (SEM) also revealed that diversified crop rotations increased soil nutrients through improving the composition of bacterial communities and the augmented intricacy of the interconnections within both bacterial and fungal communities. This research underscores the importance of preserving the diversity and ecological functions of soil microorganisms in the nutrient-recycling processes for efficient agricultural practices.

The Response of Rhizosphere Microbial C and N-Cycling Gene Abundance of Sand-Fixing Shrub to Stand Age Following Desert Restoration

Rhizosphere microorganisms play a pivotal role in biogeochemical cycles, particularly in relation to carbon (C) and nitrogen (N) cycles. However, the impact of stand age on the composition of rhizosphere microbial communities and the abundance involved in C and N cycling remains largely unexplored in restoration ecosystems dominated by shrubs of temperate deserts. This study focuses on revealing changes in microbial composition and functional genes in the rhizosphere soil of Caragana korshinskii after revegetation, as well as their response mechanisms to changes in environmental factors. The alpha diversity of bacteria tended to increase with stand age, whereas that of fungi decreased. The abundance of denitrification; dissimilatory nitrate reduction to ammonium, nitrification, and ammonium assimilation; and C fixation-related gene levels increased with stand age, whereas those related to the degradation of starch, pectin, hemicellulose, cellulose, and aromatics decreased. The parameters MBC, MBN, and TC were the key factors affecting the bacterial community, whereas the fungal community was regulated by TN, EC, pH, and MBC. Stand age indirectly regulated C and N cycling functions of genes through altered soil properties and microbial community structures. This study presents a novel approach to accurately evaluate the C and N cycling dynamics within ecosystems at various stages of restoration.

Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China

Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.

Diverse factors influence the amounts of carbon input to soils via rhizodeposition in plants: A review

Rhizodeposition encompasses the intricate processes through which plants generate organic compounds via photosynthesis, store these compounds within aboveground biomass and roots through top-down transport, and subsequently release this organic matter into the soil. Rhizodeposition represents one of the carbon (C) cycle in soils that can achieve long-term organic C sequestration. This function holds significant implications for mitigating the climate change that partly stems from the greenhouse effect associated with increased atmospheric carbon dioxide levels. Therefore, it is essential to further understand how the process of rhizodeposition allocates the photosynthetic C that plants create via photosynthesis. While many studies have explored the basic principles of rhizodeposition, along with the associated impact on soil C storage, there is a palpable absence of comprehensive reviews that summarize the various factors influencing this process. This paper compiles and analyzes the literature on plant rhizodeposition to describe how rhizodeposition influences soil C storage. Moreover, the review summarizes the impacts of soil physicochemical, microbial, and environmental characteristics on plant rhizodeposition and priming effects, and concludes with recommendations for future research.

Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity

Introduction

The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

Methods

Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

Results

Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

Discussion

These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.

Soil conditions are a more important determinant of microbial community composition and functional potential than neighboring plant diversity

Replanting is an important tool for ecological recovery. Management strategies, such as planting areas with monocultures or species mixtures, have implications for restoration success. We used 16S and ITS rRNA gene amplicon sequencing and shotgun metagenomics to assess how the diversity of neighboring tree species impacted soil bacterial and fungal communities, and their functional potential, within the root zone of mānuka (Leptospermum scoparium) trees. We compared data from monoculture and mixed tree species plots and confirmed that soil microbial taxonomic and functional community profiles significantly differed (p < 0.001). Compared to the diversity of neighboring tree species within the plot, soil environmental conditions and geographic distance was more important for structuring the microbial communities. The bacterial communities appeared more impacted by soil conditions, while the fungal communities displayed stronger spatial structuring, possibly due to wider bacterial dispersal. The different mechanisms structuring bacterial and fungal communities could have implications for ecological restoration outcomes.

Exploring glycine root uptake dynamics in phosphorus and iron deficient tomato plants during the initial stages of plant development

BACKGROUND

Phosphorus (P) and iron (Fe) deficiencies are relevant plants nutritional disorders, prompting responses such as increased root exudation to aid nutrient uptake, albeit at an energy cost. Reacquiring and reusing exudates could represent an efficient energy and nitrogen saving strategy. Hence, we investigated the impact of plant development, Fe and P deficiencies on this process. Tomato seedlings were grown hydroponically for 3 weeks in Control, -Fe, and -P conditions and sampled twice a week. We used Isotope Ratio Mass-Spectrometry to measure δ13C in roots and shoots after a 2-h exposure to 13C-labeled glycine (0, 50, or 500 μmol L-1). Plant physiology was assessed with an InfraRed Gas Analyzer and ionome with an Inductively Coupled Plasma Mass-Spectrometry.

RESULTS

Glycine uptake varied with concentration, suggesting an involvement of root transporters with different substrate affinities. The uptake decreased over time, with -Fe and -P showing significantly higher values as compared to the Control. This highlights its importance during germination and in nutrient-deficient plants. Translocation to shoots declined over time in -P and Control but increased in -Fe plants, suggesting a role of Gly in the Fe xylem transport.

CONCLUSIONS

Root exudates, i.e. glycine, acquisition and their subsequent shoot translocation depend on Fe and P deficiency. The present findings highlight the importance of this adaptation to nutrient deficiencies, that can potentially enhance plants fitness. A thorough comprehension of this trait holds potential significance for selecting cultivars that can better withstand abiotic stresses.

The Heterogeneous Habitat of Taiga Forests Changes the Soil Microbial Functional Diversity

The soil contains abundant and diverse microorganisms, which interrelate closely with the aboveground vegetation and impact the structure and function of the forest ecosystem. To explore the effect of vegetation diversity on soil microbial functional diversity in taiga forests, we selected significantly different important values of Larix gmelinii as experimental grouping treatments based on plant investigation from fixed plots in Da Xing'anling Mountains. Following that, we collected soil samples and applied the Biolog-ECO microplate method to investigate differences in carbon source utilization, features of functional diversity in soil microorganisms, and factors influencing them in taiga forests. The AWCD decreased as the important value of Larix gmelinii grew, and soil microorganisms preferred carboxylic acids, amino acids, and carbohydrates over polymers, phenolic acids, and amines. The Shannon and McIntosh indexes decreased significantly with the increase of the important value of Larix gmelinii (p < 0.05) and were positively correlated with soil SOC, MBC, C/N, and pH, but negatively with TN, AP, and AN. Redundancy analysis revealed significant effects on soil microbial functional diversity from soil C/N, SOC, AP, MBC, TN, pH, AN, and WC. To sum up, heterogeneous habitats of taiga forests with different important values altered soil microbial functional diversity.

Traits-based approach: leveraging genome size in plant-microbe interactions

Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.

DNA-SIP delineates unique microbial communities in the rhizosphere of the hyperaccumulator Sedum alfredii which are beneficial to Cd phytoextraction

Rhizo-microbe recruited by hyperaccumulating plants are crucial for the extraction of metals from contaminated soils. It is important, but difficult, to identify the specific rhizosphere microbes of hyperaccumulators shaped by root exudation. Continuous 13CO2 labeling, microbial DNA-based stable isotope probing (DNA-SIP), and high throughput sequencing were applied to identify those rhizosphere microorganisms using exudates from the Cd hyperaccumulator Sedum alfredii. In contrast to its non-hyperaccumulating ecotype (NAE), the hyperaccumulating ecotype (HAE) of S. alfredii strongly changed the rhizosphere environment and extracted a 5-fold higher concentration of Cd from contaminated soil. Although both HAE and NAE harbored Streptomyces, Massilia, Bacillus, and WPS-2 Uncultured Bacteria with relative abundance of more than 1% in the rhizosphere associated with plant growth and immunity, the HAE rhizosphere specifically recruited Rhodanobacter (2.66%), Nocardioides (1.16%), and Burkholderia (1.01%) through exudates to benefit the extraction of Cd from soil. Different from the bacterial network with weak cooperation in the NAE rhizosphere, a closed-loop bacterial network shaped by exudates was established in the HAE rhizosphere to synergistically resist Cd. This research reveals a specific rhizosphere bacterial community induced by exudates assisted in the extraction of Cd by S. alfredii and provides a new perspective for plant regulation of the rhizo-microbe community beneficial for optimizing phytoremediation.

Planting grass enhances relations between soil microbes and enzyme activities and restores soil functions in a degraded grassland

Introduction

Forage culture is a common way to restore degraded grasslands and soil functions, in which the reconstruction of the soil microbial community and its relationship with extracellular enzyme activity (EEAs) can characterize the recovery effects of degraded grasslands. However, the impacts of forage culture on the interaction between soil microbes and EEAs and whether the recovery effect of soil functions depends on the varying degradation statuses remain unclear.

Methods

We conducted a plantation of a dominant grass, Leymus chinensis, in the soil collected from severe, moderate, light, and non-degradation statuses in the Songnen grassland in northeastern China. We measured soil microbial diversity and soil EEAs, and predicted microbial functional groups using FUNGuild.

Results

The results showed that L. chinensis culture promoted soil bacterial alpha diversity and soil EEAs only in the moderate degradation status, indicating a dramatic dependence of the recovery effects of the grass culture on degradation status of the grassland. After planting L. chinensis for 10 weeks, a decreasing trend in the chemoheterotrophy and nitrate-reduction microbial functional groups was found. In contrast, the abundance of the nitrogen (N)-fixing microbial functional group tended to increase. The positive correlation between soil EEAs and the nitrate-reduction and N-fixing microbial functional groups was enhanced by planting L. chinensis, indicating that grass culture could promote soil N cycle functions.

Conclusion

We illuminate that grass culture may promote the restoration of soil functions, especially soil N cycling in degraded grasslands, and the recovery effect may depend on the grassland degradation status. We emphasized that selection of the plant species for restoration of grasslands needs to consider the restoration effects of microbial functional groups and soil functions.

Phylogenetic diversity drives soil multifunctionality in arid montane forest-grassland transition zone

Exploring plant diversity and ecosystem functioning in different dimensions is crucial to preserve ecological balance and advance ecosystem conservation efforts. Ecosystem transition zones serve as vital connectors linking two distinct ecosystems, yet the impact of various aspects of plant diversity (including taxonomic, functional, and phylogenetic diversity) on soil multifunctionality in these zones remains to be clarified. This study focuses on the forest-grassland transition zone in the mountains on the northern slopes of the Tianshan Mountains, and investigates vegetation and soil characteristics from forest ecosystems to grassland ecosystems to characterize plant diversity and soil functioning, as well as the driving role of plant diversity in different dimensions. In the montane forest-grassland transition zone, urease (URE) and total nitrogen (TN) play a major role in regulating plant diversity by affecting the soil nutrient cycle. Phylogenetic diversity was found to be the strongest driver of soil multifunctionality, followed by functional diversity, while taxonomic diversity was the least important driver. Diverse species were shown to play an important role in maintaining soil multifunctionality in the transition zone, especially distantly related species with high phylogeny. The study of multidimensional plant diversity and soil multifunctionality in the montane forest-grassland transition zone can help to balance the relationship between these two elements, which is crucial in areas where the ecosystem overlaps, and the application of the findings can support sustainable development in these regions.

Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.

Effects of biochar on soil microbial communities: A meta-analysis

Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.

Plant diversity and soil legacy independently affect the plant metabolome and induced responses following herbivory

Plant and soil biodiversity can have significant effects on herbivore resistance mediated by plant metabolites. Here, we disentangled the independent effects of plant diversity and soil legacy on constitutive and herbivore-induced plant metabolomes of three plant species in two complementary microcosm experiments. First, we grew plants in sterile soil with three different plant diversity levels. Second, single plant species were grown on soil with different plant diversity-induced soil legacies. We infested a subset of all plants with Spodoptera exigua larvae, a generalist leaf-chewing herbivore, and assessed foliar and root metabolomes. Neither plant diversity nor soil legacy had significant effects on overall foliar, root, or herbivore-induced metabolome composition. Herbivore-induced metabolomes, however, differed from those of control plants. We detected 139 significantly regulated metabolites by comparing plants grown in monocultures with conspecifics growing in plant or soil legacy mixtures. Moreover, plant-plant and plant-soil interactions regulated 141 metabolites in herbivore-induced plants. Taken together, plant diversity and soil legacy independently alter the concentration and induction of plant metabolites, thus affecting the plant's defensive capability. This is a first step toward disentangling plant and soil biodiversity effects on herbivore resistance, thereby improving our understanding of the mechanisms that govern ecosystem functioning.

Impact of PGPR inoculation on root morphological traits and root exudation in rapeseed and camelina: interactions with heat stress

Root exudation is involved in the recruitment of beneficial microorganisms by trophic relationships and/or signalling pathways. Among beneficial microorganisms, Plant Growth-Promoting Rhizobacteria (PGPR) are known to improve plant growth and stress resistance. These interactions are of particular importance for species that do not interact with mycorrhizal fungi, such as rapeseed (Brassica napus L.) and camelina (Camelina sativa (L.) Crantz). However, heat stress is known to have a quantitative and qualitative impact on root exudation and could affect the interactions between plants and PGPR. We aimed to analyse the effects of PGPR inoculation on root morphology and exudation in rapeseed and camelina at the reproductive stage. The modulation of the effects of these interactions under heat stress was also investigated. The plants were inoculated twice at the reproductive stage with two different Pseudomonas species and were exposed to heat stress after the second inoculation. In non-stressing conditions, after bacterial inoculation, rapeseed and camelina exhibited two contrasting behaviours in C root allocation. While rapeseed plants seemed to suffer from the interactions with the bacteria, camelina plants appeared to control the relationship with the PGPR by modifying the composition of their root exudates. Under heat stress, the plant-PGPR interaction was unbalanced for rapeseed, for which the C allocation strategy is mainly driven by the C cost from the bacteria. Alternatively, camelina plants prioritized C allocation for their own above-ground development. This work opens up new perspectives for understanding plant-PGPR interactions, especially in an abiotic stress context.

Urban land uses shape soil microbial abundance and diversity

Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.

Species phylogeny, ecology, and root traits as predictors of root exudate composition

Root traits including root exudates are key factors affecting plant interactions with soil and thus play an important role in determining ecosystem processes. The drivers of their variation, however, remain poorly understood. We determined the relative importance of phylogeny and species ecology in determining root traits and analyzed the extent to which root exudate composition can be predicted by other root traits. We measured different root morphological and biochemical traits (including exudate profiles) of 65 plant species grown in a controlled system. We tested phylogenetic conservatism in traits and disentangled the individual and overlapping effects of phylogeny and species ecology on traits. We also predicted root exudate composition using other root traits. Phylogenetic signal differed greatly among root traits, with the strongest signal in phenol content in plant tissues. Interspecific variation in root traits was partly explained by species ecology, but phylogeny was more important in most cases. Species exudate composition could be partly predicted by specific root length, root dry matter content, root biomass, and root diameter, but a large part of variation remained unexplained. In conclusion, root exudation cannot be easily predicted based on other root traits and more comparative data on root exudation are needed to understand their diversity.

Root exudates and rhizosphere microbiomes jointly determine temporal shifts in plant-soil feedbacks

Plants influence numerous soil biotic factors that can alter the performance of later growing plants-defined as plant-soil feedback (PSF). Here, we investigate whether PSF effects are linked with the temporal changes in root exudate diversity and the rhizosphere microbiome of two common grassland species (Holcus lanatus and Jacobaea vulgaris). Both plant species were grown separately establishing conspecific and heterospecific soils. In the feedback phase, we determined plant biomass, measured root exudate composition, and characterised rhizosphere microbial communities weekly (eight time points). Over time, we found a strong negative conspecific PSF on J. vulgaris in its early growth phase which changed into a neutral PSF, whereas H. lanatus exhibited a more persistent negative PSF. Root exudate diversity increased considerably over time for both plant species. Rhizosphere microbial communities were distinct in conspecific and heterospecific soils and showed strong temporal patterns. Bacterial communities converged over time. Using path models, PSF effects could be linked to the temporal dynamics of root exudate diversity, whereby shifts in rhizosphere microbial diversity contributed to temporal variation in PSF to a lesser extent. Our results highlight the importance of root exudates and rhizosphere microbial communities in driving temporal changes in the strength of PSF effects.

Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.)

BACKGROUND

Crop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations.

RESULTS

After 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO₃, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years.

CONCLUSIONS

Long-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.

Root exudates increased arsenic mobility and altered microbial community in paddy soils

Root exudates are crucial for plants returning organic matter to soils, which is assumed to be a major source of carbon for the soil microbial community. This study investigated the influence of root exudates on the fate of arsenic (As) with a lab simulation experiment. Our findings suggested that root exudates had a dose effect on the soil physicochemical properties, As speciation transformation and the microbial community structure at different concentrations. The addition of root exudates increased the soil pH while decreased the soil redox potential (Eh). These changes in the soil pH and Eh increased As and ferrous (Fe(II)) concentrations in soil porewater. Results showed that 40 mg/L exudates addition significantly increased arsenite (As(III)) and arsenate (As(V)) by 541 and 10 times respectively within 30 days in soil porewater. The relative abundance of Fe(III)-reducing bacteria Geobacter and Anaeromyxobacter increased with the addition of root exudates, which enhanced microbial Fe reduction. Together these results suggest that investigating how root exudates affect the mobility and transformation of As in paddy soils is helpful to systematically understand the biogeochemical cycle of As in soil-rice system, which is of great significance for reducing the health risk of soil As contamination.

New insights into the occurrence of continuous cropping obstacles in pea (Pisum sativum L.) from soil bacterial communities, root metabolism and gene transcription

BACKGROUND

Continuous cropping is a significant obstacle to sustainable development in the pea (Pisum sativum L.) industry, but the underlying mechanisms of this remain unclear. In this study, we used 16 S rDNA sequencing, transcriptomics, and metabolomics to analyze the response mechanism of roots and soil bacteria to continuous cropping and the relationship between soil bacteria and root phenotypes of different pea genotypes (Ding wan 10 and Yun wan 8).

RESULTS

Continuous cropping inhibited pea growth, with a greater effect on Ding wan 10 than Yun wan 8. Metabolomics showed that the number of differentially accumulated metabolites (DAMs) in pea roots increased with the number of continuous cropping, and more metabolic pathways were involved. Transcriptomics revealed that the number of differentially expressed genes (DEGs) increased with the number of continuous cropping. Continuous cropping altered the expression of genes involved in plant-pathogen interaction, MAPK signal transduction, and lignin synthesis pathways in pea roots, with more DEGs in Ding wan 10 than in Yun wan 8. The up-regulated expression of genes in the ethylene signal transduction pathway was evident in Ding wan 10. Soil bacterial diversity did not change, but the relative abundance of bacteria significantly responded to continuous cropping. Integrative analysis showed that the bacteria with significant relative abundance in the soil were strongly associated with the antioxidant synthesis and linoleic acid metabolism pathway of pea roots under continuous cropping once. Under continuous cropping twice, the bacteria with significant relative abundance changes were strongly associated with cysteine and methionine metabolism, fatty acid metabolism, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, linoleic acid, and amino sugar and nucleotide sugar metabolism.

CONCLUSION

Ding wan 10 was more sensitive to continuous cropping than Yun wan 8. Continuous cropping times and pea genotypes determined the differences in root metabolic pathways. There were common metabolic pathways in the two pea genotypes in response to continuous cropping, and the DEGs and DAMs in these metabolic pathways were strongly associated with the bacteria with significant changes in relative abundance in the soil. This study provides new insights into obstacles to continuous cropping in peas.

Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)

Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilis Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.

Contrasting distribution of enzyme activities in the rhizosphere of European beech and Norway spruce

Recent policies and silvicultural management call for forest regeneration that involve the selection of tree species able to cope with low soil nutrient availability in forest ecosystems. Understanding the impact of different tree species on the rhizosphere processes (e.g., enzyme activities) involved in nutrient mobilisation is critical in selecting suitable species to adapt forests to environmental change. Here, we visualised and investigated the rhizosphere distribution of enzyme activities (cellobiohydrolase, leucine-aminopeptidase, and acid phosphomonoesterase) using zymography. We related the distribution of enzyme activities to the seedling root morphological traits of European beech (Fagus sylvatica) and Norway spruce (Picea abies), the two most cultivated temperate tree species that employ contrasting strategies in soil nutrient acquisition. We found that spruce showed a higher morphological heterogeneity along the roots than beech, resulting in a more robust relationship between rhizoplane-associated enzyme activities and the longitudinal distance from the root apex. The rhizoplane enzyme activities decreased in spruce and increased in beech with the distance from the root apex over a power-law equation. Spruce revealed broader rhizosphere extents of all three enzymes, but only acid phosphomonoesterase activity was higher compared with beech. This latter result was determined by a larger root system found in beech compared with spruce that enhanced cellobiohydrolase and leucine-aminopeptidase activities. The root hair zone and hair lengths were significant variables determining the distribution of enzyme activities in the rhizosphere. Our findings indicate that spruce has a more substantial influence on rhizosphere enzyme production and diffusion than beech, enabling spruce to better mobilise nutrients from organic sources in heterogeneous forest soils.

Effects of seasonal grazing on plant and soil microbial diversity of typical temperate grassland

Biodiversity is the decisive factor of grassland ecological function and process. As the most important human use of grassland, grazing inevitably affects the grassland biodiversity. However, comprehensive studies of seasonal grazing on plant and soil bacterial, archaeal and fungal diversity of typical temperate grassland are still lacking. We examined the impact of seasonal grazing, including no-grazing (NG), continuous grazing (CG), grazing in May and July (G57), grazing in June and August (G68), and grazing in July and September (G79) on grassland plant and soil microbial diversity based on a long-term field grazing experiment. The results showed that the aboveground plant biomass (AGB) of the seasonal grazing plots was significantly higher than that of the CG plots. Compared with NG, CG increased significantly the Margalef richness index of plant community, while did not significantly change the Shannon, Simpson and Pielou evenness of plant community. Grazing changed the composition and biomass of dominant vegetation. Long-term grazing decreased the proportion of Leymus chinensis (Trin.) Tzvel. and increased the proportion of Cleistogenes squarrosa (Trin.) Keng. There was no significant change in the Shannoneven, Shannon and Coverage indices of soil bacteria, archaea and fungi between NG and the grazing plots. But the Chao index of soil fungi in G57, G68 and G79 and archaea in G57, G79 was significantly higher than that in CG. The results of correlation analysis showed that the plant diversity in the CG plots was significantly negatively correlated with the soil bacterial diversity. The plant richness in the G57 and G68 plots was significantly positively correlated with the soil archaea richness. Our study showed that seasonal grazing was a sustainable grazing management strategy for maintaining typical grassland plant and soil microbial diversity in northern of China.

Artificial root exudates restore microbial functioning in a metal contaminated, barren, inactive soil

Restoring enzyme function in barren, brownfield soils using green strategies can improve microbial functioning and enable phytoremediation. It is known that adding simple, readily metabolized substrates secreted by growing plant roots (root exudates) or a laboratory prepared solution of root exudates (artificial root exudates) can stimulate soil microbial function. It is not known whether and how well this strategy works in a contaminated, low functioning soil from an industrial barren site because contaminants in the barren soil might inhibit microbial survival and functioning, or the microbial community might not be adapted to functionally benefit from root exudates. The objective of this study was to determine whether artificial root exudates stimulate microbial function in a barren soil. We collected soils from a barren brownfield (25R) site and an adjacent vegetated brownfield site (25F), with low and high enzyme activities, respectively. We subjected both soils to three treatments: switchgrass (native to the site), artificial root exudates, and a combination of switchgrass and artificial root exudates. We measured enzymatic activity, plant growth, soil moisture, organic matter content, and easily extractable glomalin content over 205 days. By day 157, artificial root exudates increased the phosphatase activity by 9-fold in previously vegetated brownfield soil and by 351-fold in barren brownfield soil. When exudates were added to the barren soil, the plant shoot mass was higher (52.2 ± 2.5 mg) than when they were not (35.4 ± 3.6 mg). In both soils, adding artificial root exudates significantly increased the percent moisture, organic matter, and glomalin content. Treating contaminated, barren soil with artificial root exudates resulted in increased soil microbial function and improved soil properties that might promote a hospitable habitat to support vegetation in such extreme environments. Summary: We added artificial root exudates to stimulate enzymatic function in two contaminated soils. Plant shoot mass, soil percent moisture, glomalin content, and organic matter content significantly increased due to the addition of artificial root exudates to the study soils. Microbially-mediated phosphatase activity was established in a barren, previously inactive, polluted soil.

Differential Response of Soil Microbial Community Structure in Coal Mining Areas during Different Ecological Restoration Processes

Micro-organisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the more sensitive and indicative microbial structures or the responses of microbial diversity to environmental change. In this study, based on high-throughput sequencing and molecular ecological network analyses, the structural characteristics of bacterial communities were investigated in response to four different ecological restoration modes in a coal mining subsidence area located in northwest China. The results showed that among soil nutrients, nitrate-nitrogen and fast-acting potassium were the most strongly associated with microbial community structure under different ecological restoration types. Proteobacteria, Actinobacteria, and Acidobacteria were identified as important phyla regarding network connectivity and structural composition. The central natural recovery zone was found to have the smallest network size and low complexity, but high modularity and good microbial community stability. Contrastingly, a highly complex molecular ecological network of soils in the photovoltaic economic zone existed beneath the photovoltaic modules, although no key species, strong bacterial competition, poor resistance to disturbance, and a significant increase in the relative abundance of Gemmatimonadetes were found. Furthermore, the reclamation zone had the highest soil nutrient content, the most complex network structure, and the most key and indicator species; however, the ecological network was less stable and readily disturbed.

Eco-Stoichiometric Characteristics of Rhizosphere and Bulk Soils of Smilax china L. along Vertical Zone Spectrum of Fanjing Mountain

To explore the correlations between nutrients and stoichiometric characteristics in the rhizosphere and bulk soils of understory Smilax china L. in forest ecosystems at different altitudes and to clarify the rhizosphere effect of understory vegetation in forest ecosystems and its response strategy to altitude, providing a theoretical basis for better forest ecological environment protection and high-quality development in Fanjing Mountain. Understory Smilax china L. at four different altitudes were selected, with the differences and influencing factors of carbon (C), nitrogen (N), phosphorus (P) and potassium (K) mass fractions and stoichiometric ratios in their rhizosphere and bulk soils analyzed. The average mass fractions of total C, total N and alkali-hydrolyzed N in the rhizosphere and bulk soils of Smilax china L. at different altitudes were 224.43 and 181.55 g·kg⁻¹; 9.56 and 6.81 g·kg⁻¹; and 648.19 and 600.70 g·kg⁻¹, respectively. The rhizosphere effect of Smilax china L. was significant at altitudes of 500 m and 1000 m but became not so prominent with the rise of altitude. The C:N ratio in the rhizosphere and bulk soils ranged from 19.51 to 39.75 and the C:P ratio ranged from 225.29 to 543.05. C accumulation is greater than N accumulation in the rhizosphere and bulk soils of Smilax china L., and both present P limitation. Based on the comprehensive analysis of the mass fractions and eco-stoichiometric ratios of soil nutrients, the P limitation in Fanjing Mountain forest ecosystem is commonly seen and should be addressed.

Plant diversity enhances soil fungal network stability indirectly through the increase of soil carbon and fungal keystone taxa richness

Plant diversity is critical to the stability of ecosystems. However, our knowledge about the plant diversity effect on the stability of belowground communities is limited. Here, we characterized soil fungal diversity and co-occurrence network across a plant diversity gradient in a diversity manipulation experiment. We found that higher plant diversity resulted in higher fungal diversity, network complexity and stability. The positive plant diversity effect on fungal network stability was indirect via the increase of soil carbon and fungal keystone taxa richness based on structural equation modeling analysis. The model explained 44% variations of network stability when combining soil carbon and fungal keystone taxa richness, but explained approximate 30% variations of network stability when considering either one of the two factors, indicating that environmental filtering and biotic interaction processes play comparable roles in mediating the plant diversity effect on soil fungal network stability. The plant diversity-induced fungal network stability was significantly correlated with community-level functions including community resistance and enzyme activities. This study, from the view of networks, provides new insights into the plant diversity effect on the stability of soil microbial communities, which have implications for biodiversity conservation and policy development.

Exploring an enhanced rhizospheric phenomenon for pluricontaminated soil remediation: Insights from tripartite metatranscriptome analyses

Phytoremediation involving the use of microorganisms with tolerant plant species represents a new frontier for on-site remediation of pluricontaminated soils. In this study, the effectiveness of a biotechnological strategy, involving the use of Festuca arundinacea and a pool of microorganisms, was assessed by a mesocosm experiment and an in-depth rhizospheric metatranscriptomic analysis. The chemical profile of mesocosm soil at the end of the experiment (240 days) showed that the decrease of trace elements such as Cd, Hg, Pb, Sn, Tl, V and Zn in the soil was enhanced by our biological combination. Additionally, also the organic pollutants (PAHs and PCBs) were strongly reduced up to 40.5%. About two million transcripts were identified and used for taxonomic and functional profiling. Transcripts read counts, tripartite among plant, bacteria and fungi were identified and quantified to provide an overview of the complex soil community composition. We observed that Actinobacteria and fungi abundance might be involved in remediation success. Functional analyses showed that Trehalose Biosynthesis and the antioxidant activity might have played a key-role in metaorganism effective interactions. The biotechnological approach remodeled the transcriptional profile toward organic pollutant degradation and heavy metal stress response.

Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau

There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.

Abundance, Diversity, and Function of Soil Microorganisms in Temperate Alley-Cropping Agroforestry Systems: A Review

Modern temperate alley-cropping systems combine rows of trees with rows of crops (agroforestry), which allows for diverse interspecific interactions such as the complementary and competitive use of resources. The complementary use of resources between trees and crops is considered the main advantage of these multifunctional land use systems over cropland monocultures. Moreover, several studies demonstrated that agroforestry systems are environmentally more sustainable than cropland monocultures. Over two decades of research on soil microorganisms in temperate alley-cropping systems are characterized by a variety of different methodological approaches and study designs to investigate the impact of agroforestry on the soil microbiome. Here, we review the available literature on the abundance, diversity, and functionality of soil microorganisms in temperate alley-cropping systems. Further, we identify current knowledge gaps as well as important experimental factors to consider in future studies. Overall, we found that temperate alley-cropping systems increase soil microbial abundance, diversity, and functions as compared to cropland monocultures, which is expected to contribute to enhanced biological soil fertility in these systems.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Applying cover crop residues as diverse mixtures increases initial microbial assimilation of crop residue-derived carbon

Increasing the diversity of crops grown in arable soils delivers multiple ecological functions. Whether mixtures of residues from different crops grown in polyculture contribute to microbial assimilation of carbon (C) to a greater extent than would be expected from applying individual residues is currently unknown. In this study, we used 13C isotope labelled cover crop residues (buckwheat, clover, radish, and sunflower) to track microbial assimilation of plant residue-derived C using phospholipid fatty acid (PLFA) analysis. We also quantified microbial assimilation of C derived from the soil organic matter (SOM) because fresh residue inputs also prime the decomposition of SOM. To consider the initial stages of residue decomposition, and preclude microbial turnover, we compared a quaternary mixture of residues with the average effect of their four components 1 day after incorporation. Our results show that the microbial biomass carbon (MBC) in the treatment receiving the mixed residue was significantly greater, by 132% (3.61 μg C g-1), than the mean plant residue-derived MBC in treatments receiving the four individual components of the mixture. However, there was no evidence that the mixture resulted in any additional assimilation of C derived from native SOM than the average observed in individual residue treatments. We surmise that, during the initial stages of crop residue decomposition, a greater biodiversity of residues increases microbial assimilation to a greater extent than would be expected from applying individual residues either due to faster decomposition or greater carbon use efficiency (CUE). This might be facilitated by functional complementarity in the soil microbiota, permitted by a greater diversity of substrates, reducing competition for any single substrate. Therefore, growing and incorporating crop polycultures (e.g., cover crop mixtures) could be an effective method to increase microbial C assimilation in the early stages of cover crop decomposition.

Highlights

The effect of mixing crop residues on assimilation of C by soil microbial biomass was investigated.The study is important due to recent interest in diverse cover crop mixtures for arable systems.Mixing crop residues enhanced the assimilation of plant residue-derived C into microbial biomass.Growing and incorporating cover crop polycultures may enhance C storage in arable soils.

Herbaceous plant species support soil microbial performance in deciduous temperate forests

Although herbaceous plant layer may contribute significantly to plant diversity and nutrient turnover, its effects on the soil environment in forest ecosystems remain largely unexplored. In this study, we compared the effects of mono-dominant and multi-species assemblages of herb plants on soil physicochemical and microbial properties in two temperate deciduous (beech and riparian) forests. We hypothesized that the presence of herbaceous plants would increase microbial activity and biomass, and nutrient availability in soil when compared to bare soil. This increase would be the highest in multi-species assemblages as high plant diversity supports microbial performance and soil processes, and the expected patterns would be essentially similar in both forests. Allium ursinum L. and Dentaria enneaphyllos L. represented herb species forming mono-dominant patches in beech forest, while Aegopodium podagraria L. and Ficaria verna Huds. represented herb species forming mono-dominant patches in riparian forest. Our hypotheses were only partly supported by the data. We found that herb plant species affected soil microbial communities and processes, particularly in the riparian forest, but they generally did not influence soil physicochemical properties. In the beech forest, herbaceous plants increased saprotrophic fungi biomass, fungi/bacteria ratio, and arylsulfatase activity, with the highest values under D. enneaphyllos. In the riparian forest, a number of microbial parameters, namely bacteria, G+ bacteria, and saprotrophic fungi biomass, fungi/bacteria ratio, and soil respiration exhibited the lowest values in bare soil and the highest values in soil under A. podagraria. Contrary to expectations, soils under multi-species assemblages were characterized by intermediate values of microbial parameters. Concluding, herbaceous plant species largely supported soil microbial communities in deciduous temperate forests but did not affect soil chemical properties. The potential reasons for the positive influence of herb plants on soil microbes (litterfall, rhizodeposition) require further investigation.

Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices

Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor's microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus, Populus with Pinus, and Pinus with Pinus. Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus-associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

Functional diversity and identity of plant genotypes regulate rhizodeposition and soil microbial activity

Our understanding of the linkages between plant diversity and soil carbon and nutrient cycling is primarily derived from studies at the species level, while the importance and mechanisms of diversity effects at the genotype level are poorly understood. Here we examine how genotypic diversity and identity, and associated variation in functional traits, within a common grass species, Anthoxanthum odoratum, modified rhizodeposition, soil microbial activity and litter decomposition. Root litter quality was not significantly affected by plant genotypic diversity, but decomposition was enhanced in soils with the legacy of higher genotypic diversity. Plant genotypic diversity and identity modified rhizodeposition and associated microbial activity via two independent pathways. Plant genotypic diversity enhanced soil functioning via positive effects on variation in specific leaf area and total rhizodeposition. Genotype identity affected both rhizodeposit quantity and quality, and these effects were mediated by differences in mean specific leaf area, shoot mass and plant height. Rhizodeposition was more strongly predicted by aboveground than belowground traits, suggesting strong linkages between photosynthesis and root exudation. Our study demonstrates that functional diversity and identity of plant genotypes modulates belowground carbon supply and quality, representing an important but overlooked pathway by which biodiversity affects ecosystem functioning.

Effects of a compound microbial agent and plants on soil properties, enzyme activities, and bacterial composition of Pisha sandstone

The objective of this study was to investigate the effects of the microbial agent on the improvement of Pisha sandstone soil and find out an effective measure for the control of soil erosion in the Pisha sandstone area. Pisha sandstone containing the microbial agent composed of Bacillus halotolerans P75, Sinorhizobium meliloti D10, Bacillus megaterium H3, Bacillus subtilis HB01, and organic substrate was utilized to be the soil matrix for pot experiment, and then alfalfa, ryegrass, and caragana were planted, respectively. Effects of the microbial agent plus plants on the soil properties of Pisha sandstone were evaluated, and the results showed that the microbial agent plus plants significantly increased the organic matter content, alkali hydrolyzed nitrogen content, available phosphorus content, available potassium content, invertase activity, and urease activity. Meanwhile, inoculation with the microbial agent significantly promoted the growth of alfalfa, ryegrass, and caragana and also influenced the number of soil bacteria and the relative abundance of Proteobacteria, Bacteroidetes, Actinobacteria, and others. However, the effects of the microbial agent plus different plants on the soil properties and bacterial composition of Pisha sandstone were different, while the growth of different plants showed differences, suggesting that there was a different interaction between microbes and different plants in Pisha sandstone soil. In conclusion, the microbial agent plus plants could improve Pisha sandstone soil which could provide some theoretical and experimental references for soil erosion control in the Pisha sandstone area.

Influence of soil quality factors on capsaicin biosynthesis, pungency, yield, and produce quality of chili: An insight on Csy1, Pun1, and Pun12 signaling responses

Hotness or pungency is the major trait of genetically diverse and economically valuable chili (Capsicum sp.) cultivars. However, little is known about the influence of soil characteristics on genetic regulation of pungency vis-à-vis capsaicin formation in endemic chilies. Hence, the present work was conducted by growing two endemic chili cultivars in two types (alluvial and lateritic) of soil. Capsaicin content, pungency, and capsaicin synthase activity were significantly greater in chilies grown in alluvial soil than in lateritic soil. Correspondingly, Csy1, the gene that encodes capsaicin synthase, was significantly upregulated in alluvial soil grown plants. Interestingly, upregulation of Pun1, the gene responsible for capsaicin accumulation in fruits, was more in lateritic soil than in alluvial soil; but pungency was inhibited in lateritic soil by the overexpression of Pun1², a recessive allele of Pun1 locus. Statistical analyses revealed that high organic C, microbial activity, and NPK status in alluvial soil were responsible for high pungency, capsaicin synthase activity, capsaicin accumulation, and suppression of Pun1². Fruit yield, dry matter, crude protein, titratable acidity, and soluble solids were also significantly high in chilies grown in alluvial soil. Therefore, we postulate that soil quality attributes play vital roles in genetic regulation of pungency, capsaicin biosynthesis, fruit yield, and produce quality of endemic chili cultivars.

Effects of root exudates on rhizosphere bacteria and nutrient removal in pond-ditch circulation systems (PDCSs) for rural wastewater treatment

Pond-ditch circulation system (PDCS) is a promising remediation strategy for rural wastewater treatment. Aquatic plants play nonnegligible roles in the nutrient removal of the PDCS. However, mechanisms of root exudates regulating nutrient removal in PDCSs remained unclear. In our study, the PDCS achieved higher total nitrogen (TN) and phosphorus (TP) removal rates (72.7-97.4%) compared to the static system. Protein contents in root exudates of the PDCS ranged from 0.041 to 1.332 mg L^-1, showing negative associations with Simpson index. Lactic acid and tartaric acid in the PDCS varied from 0.045 to 0.380 mg L^-1 and 0.024 to 5.446 mg L^-1, which were tightly linked with TN, TP, and TP removal rates and most sediment properties, especially sediment total nitrogen (STN) and total organic carbon (TOC), and sediment inorganic phosphorus (SIP). Moreover, the top 3 relative dominant genus were Bacillus (0.11%-17.90%), Geobacter (0.35%-12.04%), and Clostridium sensu stricto 1 (0.14%-12.05%), which might be the predominant groups in nutrient removal of PDCSs. RDA results indicated that lactic acid, protein, and amino acids were positively correlated with Geobacter; while Bacillus was significantly affected by water content. Path analysis further demonstrated that the indirect effect of secretion from plant roots on nutrient removal rates was mainly through modulating bacteria diversity and relative abundance. Taken together, root exudates, especially protein, amino acids, and lactic acid, altered rhizosphere microbial relative abundance and diversity, where the impacts were bacterial species-dependent.

Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System

Soil fungi are strongly affected by plant species or genotypes since plants modify their surrounding environment, but the effects of plant genotype diversity on fungal diversity and function have not been extensively studied. The interactive responses of fungal community composition to plant genotypic diversity and environmental drivers were investigated in Salix biomass systems, posing questions about: (1) How fungal diversity varies as a function of plant genotype diversity; (2) If plant genotype identity is a strong driver of fungal community composition also in plant mixtures; (3) How the fungal communities change through time (seasonally and interannually)?; and (4) Will the proportion of ECM fungi increase over the rotation? Soil samples were collected over 4 years, starting preplanting from two Salix field trials, including four genotypes with contrasting phenology and functional traits, and genotypes were grown in all possible combinations (four genotypes in Uppsala, Sweden, two in Rostock, Germany). Fungal communities were identified, using Pacific Biosciences sequencing of fungal ITS2 amplicons. We found some site-dependent relationships between fungal community composition and genotype or diversity level, and site accounted for the largest part of the variation in fungal community composition. Rostock had a more homogenous community structure, with significant effects of genotype, diversity level, and the presence of one genotype ("Loden") on fungal community composition. Soil properties and plant and litter traits contributed to explaining the variation in fungal species composition. The within-season variation in composition was of a similar magnitude to the year-to-year variation. The proportion of ECM fungi increased over time irrespective of plant genotype diversity, and, in Uppsala, the 4-mixture showed a weaker response than other combinations. Species richness was generally higher in Uppsala compared with that in Rostock and increased over time, but did not increase with plant genotype diversity. This significant site-specificity underlines the need for consideration of diverse sites to draw general conclusions of temporal variations and functioning of fungal communities. A significant increase in ECM colonization of soil under the pioneer tree Salix on agricultural soils was evident and points to changed litter decomposition and soil carbon dynamics during Salix growth.

Changes in Soil Microbial Communities across an Urbanization Gradient: A Local-Scale Temporal Study in the Arid Southwestern USA

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.

Rhizosphere Microbial Communities and Heavy Metals

The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants’ functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.

Mycorrhizal-Assisted Phytoremediation and Intercropping Strategies Improved the Health of Contaminated Soil in a Peri-Urban Area

Soils of abandoned and vacant lands in the periphery of cities are frequently subjected to illegal dumping and can undergo degradation processes such as depletion of organic matter and nutrients, reduced biodiversity, and the presence of contaminants, which may exert an intense abiotic stress on biological communities. Mycorrhizal-assisted phytoremediation and intercropping strategies are highly suitable options for remediation of these sites. A two-year field experiment was conducted at a peri-urban site contaminated with petroleum hydrocarbons and polychlorinated biphenyls, to assess the effects of plant growth (spontaneous plant species, Medicago sativa, and Populus × canadensis, alone vs. intercropped) and inoculation of a commercial arbuscular mycorrhizal and ectomycorrhizal inoculum. Contaminant degradation, plant performance, and biodiversity, as well as a variety of microbial indicators of soil health (microbial biomass, activity, and diversity parameters) were determined. The rhizosphere bacterial and fungal microbiomes were assessed by measuring the structural diversity and composition via amplicon sequencing. Establishment of spontaneous vegetation led to greater plant and soil microbial diversity. Intercropping enhanced the activity of soil enzymes involved in nutrient cycling. The mycorrhizal treatment was a key contributor to the establishment of intercropping with poplar and alfalfa. Inoculated and poplar-alfalfa intercropped soils had a higher microbial abundance than soils colonized by spontaneous vegetation. Our study provided evidence of the potential of mycorrhizal-assisted phytoremediation and intercropping strategies to improve soil health in degraded peri-urban areas.