Root biomass and exudates link plant diversity with soil bacterial and fungal biomass

A bacteria-based index of biotic integrity indicates aquatic ecosystem restoration

Intensive ecological interventions have been carried out in highly polluted shallow lakes to improve their environments and restore their ecosystems. However, certain treatments, such as dredging polluted sediment and stocking fish, can impact the aquatic communities, including benthos and fishes. These impacts can alter the composition and characteristics of aquatic communities, which makes community-based ecological assessments challenging. Here we develop a bacteria-based index of biotic integrity (IBI) that can clearly indicate the restoration of aquatic ecosystems with minimal artificial interventions. We applied this method to a restored shallow lake during 3-year intensive ecological interventions. The interventions reduced nutrients and heavy metals by 27.1% and 16.7% in the sediment, while the total organic carbon (TOC) increased by 8.0% due to the proliferation of macrophytes. Additionally, the abundance of sulfur-related metabolic pathways decreased by 10.5% as the responses to improved ecosystem. The score of bacteria-based IBI, which is calculated based on the diversity, composition, and function of benthic bacterial communities, increased from 0.62 in 2018 to 0.81 in 2021. Our study not only provides an applicable method for aquatic ecological assessment under intensive artificial interventions but also extends the application of IBI to complex application scenarios, such as ecosystems with significantly different aquatic communities and comparisons between different basins.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient

Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16-, and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities.

Association between bacterial community and cadmium distribution across Colombian cacao crops

Assessing the bacterial community composition across cacao crops is important to understand its potential role as a modulator of cadmium (Cd) translocation to plant tissues under field conditions; Cd mobility between soil and plants is a complex and multifactorial problem that cannot be captured only by experimentation. Although microbes have been shown to metabolize and drive the speciation of Cd under controlled conditions, regardless of the link between soil bacterial community (SBC) dynamics and Cd mobilization in the rhizosphere, only a few studies have addressed the relationship between soil bacterial community composition (SBCC) and Cd content in cacao seeds (Cdseed). Therefore, this study aimed to explore the association between SBCC and different factors influencing the distribution of Cd across cacao crop systems. This study comprised 225 samples collected across five farms, where we used an amplicon sequencing approach to characterize the bacterial community composition. The soil Cd concentration alone (Cdsoil) was a poor predictor of Cdseed. Still, we found that this relationship was more apparent when the variation within farms was controlled, suggesting a role of heterogeneity within farms in modulating Cd translocation and, thus, seed Cd content. Our results provide evidence of the link between soil bacterial communities and the distribution of Cd across Colombian cacao crops, and highlight the importance of incorporating fine-spatial-scale studies to advance the understanding of factors driving Cd uptake and accumulation in cacao plants.

IMPORTANCE

Cadmium (Cd) content in cacao crops is an issue that generates interest due to the commercialization of chocolate for human consumption. Several studies provided evidence about the non-biological factors involved in its translocation into the cacao plant. However, factors related to this process, including soil bacterial community composition (SBCC), still need to be addressed. It is well known that soil microbiome could impact compounds' chemical transformation, including Cd, on the field. Here, we found the first evidence of the link between soil bacterial community composition and Cd concentration in cacao soils and seeds. It highlights the importance of including the variation of bacterial communities to assess the factors driving the Cd translocation into cacao seeds. Moreover, the results highlight the relevance of the spatial heterogeneity within and across cacao farms, influencing the variability of Cd concentrations.

Rice breeding for low input agriculture

A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars

BACKGROUND

Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars.

RESULTS

This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars.

CONCLUSIONS

Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.

An investigation on the conversion of infertile soil into fertile soil using crop waste as a remedial (compost) approach and its influence on Vigna mungo biometric and biomolecule profile

The sustainable management of huge volume of agricultural waste in India can be resolved through composting and used as soil amendment. Agriculture waste compost amendments can optimistically alter the physicochemical (pH, C, N, & P) as well as biological nature (microbial activity/biomass and enzymatic activity) of infertile soil. Hence this study, the agriculture wastes such as sugarcane trash, corn stover, and pearl millet stalks were converted to composite through decomposition pit. Interestingly, test crops residues individual composites and their mixed form contained considerable quantity of vital elements like TC, TN, TP, TK, and C:N ratio and can effectively convert infertile soil to fertile soil. These test crop composites also had a significant impact on MBN (42.3 μg g-1), MBC (198.4 μg g-1), and MBP (196.4 μg g-1) in test soil, as well as dehydrogenase and alkaline phosphatase enzyme activity. However, the mixed composite effects are significantly greater than the individual test crop composite effects. Furthermore, it effectively remediates/converts infertile soil to fertile soil, and it ultimately demonstrated positive effects on Vigna mungo biometric (SH, RH, WB, and DB) and biomolecule (total chlorophyll, total carbohydrate, and total proteins) profiles, followed by individual test crop composites. According to the findings of this study, the incorporation of crop residue-based mixed composite significantly transforms infertile soil into fertile soil and promotes the growth of V. mungo.

How Rhizosphere Microbial Assemblage Is Influenced by Dragon Fruits with White and Red Flesh

The synthesis of betalain using microorganisms is an innovative developmental technology, and the excavation of microorganisms closely related to betalain can provide certain theoretical and technical support to this technology. In this study, the characteristics of soil microbial community structures and their functions in the rhizospheres of white-fleshed dragon fruit (Hylocereus undatus) and red-fleshed dragon fruit (Hylocereus polyrhizus) were analyzed. The results show that the soil bacterial and fungal compositions in the rhizospheres were shaped differently between H. undatus and H. polyrhizus. Bacterial genera such as Kribbella and TM7a were the unique dominant soil bacterial genera in the rhizospheres of H. undatus, whereas Bradyrhizobium was the unique dominant soil bacterial genus in the rhizospheres of H. polyrhizus. Additionally, Myrothecium was the unique dominant soil fungal genus in the rhizospheres of H. polyrhizus, whereas Apiotrichum and Arachniotus were the unique dominant soil fungal genera in the rhizospheres of H. undatus. Moreover, TM7a, Novibacillus, Cupriavidus, Mesorhizobium, Trechispora, Madurella, Cercophora, and Polyschema were significantly enriched in the rhizospheres of H. undatus, whereas Penicillium, Blastobotrys, Phialemonium, Marasmius, and Pseudogymnoascus were significantly enriched in the rhizospheres of H. polyrhizus. Furthermore, the relative abundances of Ascomycota and Penicillium were significantly higher in the rhizospheres of H. polyrhizus than in those of H. undatus.

Mycorrhizal type and tree diversity affect foliar elemental pools and stoichiometry

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of this potential role of mycorrhizae is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and soil microbial biomass elemental dynamics showed weak responses to tree species richness and none to mycorrhizal type. However, foliar elemental concentrations, stoichiometry, and pools were significantly affected by both treatments. Tree species richness increased foliar C and P pools but not N pools. Additive partitioning analyses showed that net biodiversity effects of foliar C, N, P pools in EM tree communities were driven by selection effects, but in mixtures of both mycorrhizal types by complementarity effects. Furthermore, increased tree species richness reduced soil nitrate availability, over 2 yr. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies and highlight the importance of using mixtures composed of tree species with different types of mycorrhizae to achieve more multifunctional afforestation.

Influence of tree mycorrhizal type, tree species identity, and diversity on forest root-associated mycobiomes

Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree-tree interactions and their root-associated fungal communities remains poorly understood. Our study addresses this gap by investigating root-associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two-species, and multi-species mixtures, utilizing Illumina sequencing of the ITS2 region. The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root-associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree-related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi-species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi-species mixtures. This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation.

Nitrogen deposition suppresses soil respiration by reducing global belowground activity

Soil respiration (Rs) indicates below-ground biological activities. Previous studies have suggested that higher nitrogen (N) deposition due to human activities exerts an increasingly negative effect on Rs. However, the mechanisms underlying this negative effect remain highly uncertain on a global scale. Using a global dataset of 262 N addition experiments, here we show the overall N addition effects on Rs changed from positive to negative with increasing N addition rate and duration. By constructing a structural equation model (SEM) that explained 41 % variation in the responses of Rs to N addition, we revealed that Rs under increasing N addition was simultaneously associated with decreases in soil pH, root biomass and microbial biomass, with the strongest influence by root biomass. Decreasing soil pH had cascading effects on root and microbial biomass, while N-addition-induced root biomass reduction further manifested a decrease in microbial biomass. Across global variations in the environment, lower background soil pH amplified the negative impacts of N addition on root and microbial biomass, which consequently exhilarated the negative impact of high N on Rs. Our results highlight that predicting the response of belowground biological activities to global changes is complex with the essence of integrative understanding for the multivariate pathways through soil physical properties, plants and microorganisms.

Lithology and niche habitat have significant effect on arbuscular mycorrhizal fungal abundance and their interspecific interactions

The chemical properties of bedrock play a crucial role in shaping the communities of soil and root-associated arbuscular mycorrhizal fungi (AMF). We investigate AMF community composition and diversity in bulk soil, rhizosphere soil, and roots in karst and non-karst forests. Chemical properties of bedrock of the calcium oxide (CaO) and ratio of calcium oxide and magnesium oxide (Ca/Mg), soil pH, and exchangeable Ca2+ were higher in karst carbonate rocks compared to non-karst clastic rocks. Conversely, bedrock phosphorus content (P-rock), silicon dioxide (SiO2) content, and tree diversity exhibited an opposing trend. AMF abundance was higher in non-karst clastic rocks than in karst carbonate rocks. Stronger interspecific interactions among AMF taxa occurred in the bulk soil and rhizosphere soil of non-karst clastic rocks compared to karst carbonate rocks. AMF abundance and diversity were higher in rhizosphere soil and roots, attributed to increasing nutrient availability when compared to the bulk soil. A more complex network within AMF taxa was observed in rhizosphere soil and roots compared to bulk soil due to an increase in AMF abundance and diversity in rhizosphere soil and roots. Comparing non-karst clastic rocks, karst carbonate rocks increased soil nitrogen (N) and P levels, which can be attributed to the elevated content of soil Ca2+ and Mg2+ content, facilitated by the high CaO content and Ca/Mg ratio in the bedrock of karst forests. However, the thicker soil layer exhibited higher soil nutrient storage, resulting in greater tree diversity in non-karst forests. These findings suggest that high tree richness may increase root biomass and secretion of root exudates in non-karst regions, thereby enhancing the abundance of AMF and their interspecies interactions. Consequently, the diverse bedrock properties that drive variations in soil properties, nutrients, and plant diversity can impact AMF communities, ultimately promoting plant growth and contributing to vegetation recovery.

Invasive earthworms can change understory plant community traits and reduce plant functional diversity

Among the most important impacts of biological invasions on biodiversity is biotic homogenization, which may further compromise key ecosystem processes. However, the extent to which they homogenize functional diversity and shift dominant ecological strategies of invaded communities remains uncertain. Here, we investigated changes in plant communities in a northern North American forest in response to invasive earthworms, by examining the taxonomic and functional diversity of the plant community and soil ecosystem functions. We found that although plant taxonomic diversity did not change in response to invasive earthworms, they modified the dominance structure of plant functional groups. Invasive earthworms promoted the dominance of fast-growing plants at the expense of slow-growing ones. Moreover, earthworms decreased plant functional diversity, which coincided with changes in abiotic and biotic soil properties. Our study reveals that invasive earthworms erode multiple biodiversity facets of invaded forests, with potential cascading effects on ecosystem functioning.

Strengthen interactions among fungal and protistan taxa by increasing root biomass and soil nutrient in the topsoil than in the soil-rock mixing layer

Soil depth plays a crucial role in shaping the interactions between soil microbes and nutrient availability. However, there is limited understanding of how bacterial, fungal, and protistan communities respond to different soil depths, particularly in the unique geological context and soil properties of karst regions. Organic matter, total nitrogen, and phosphorus, ammonium, nitrate, and plant root biomass, as well as bacterial and fungal abundances, bacterial and protistan diversity were higher in the 0-20 cm soil layer than those in the 20-40 cm and soil-rock mixing layers. In contrast, soil pH was higher in the 20-40 cm and soil-rock mixing layers than that in the 0-20 cm soil layer. The soil exchange of calcium, nitrate, and root biomass were identified as the primary factors regulating microbial assemblages across the depth transect. Moreover, co-occurrence network analysis revealed a greater degree of connectivity between protistan taxa and fungal taxa in the 0-20 cm soil layer than those in the 20-40 cm and soil-rock mixing layers. In contrast, the number of association links between protist-bacteria and bacteria-bacteria was higher in the soil-rock mixing layers compared to the 0-20 cm soil layer. Actinobacteria, Ascomycota, and unclassified protistan taxa were identified as keystones, displaying the highest number of connections with other microbial taxa. Collectively, these results suggested that the increased plant root biomass, coupled with sufficient available nutrient inputs in the upper 0-20 cm soil layer, facilitates strong interactions among fungal and protistan taxa, which play crucial roles in the topsoil. However, as nutrients become less available with increasing depth, competition among bacterial taxa and the predation between bacterial and protistan taxa intensify. Therefore, these findings indicate the interactions among keystone taxa at different soil depths has the potential to generate ecological implications during vegetation restoration in fragile ecosystems.

Plant growth and development of tropical seagrass determined rhizodeposition and its related microbial community

In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.

Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth

Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya's broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL-1 solubilization in vitro. All strains produced organic acids in Pikovskaya's broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g-1 dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g-1 dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.

Combined omics approaches expose metabolite-microbiota correlations in grape berries of three cultivars of Douro wine region

This study hypothesized the existence of cultivar-associated correlations between grape berry metabolites and its microbial residents, in Douro wine region. Integrated metabolomics with metabarcoding showed that the microbial biodiversity is not associated to berry sugar concentration, but closely connected to the profile of amino acids, flavonoids and wax compounds, which drove cultivar differentiation together with the prevalence of pathogenic fungi, yeasts and bacteria, mainly Dothideomycetes and Gammaproteobacteria. Over 7000 metabolite-microbiota correlations with ρ >|0.99| exposed a core of 15 metabolites linked to 11 microbial taxa. Serine, oxalate, cyanidin-3-O-glucoside, petunidin-3-O-glucoside, gallic acid, germanicol, sitosterol and erythrodiol correlated negatively to the abundance of most taxa, including Alternaria, Aureobasidium, Pseudopithomyces, Pseudomonas and Sphingomonas. In contrast, phenylalanine, asparagine, alanine, (epi)gallocatechin and procyanidin gallate mediated positive metabolite-OTU correlations. E. necator and A. carbonarius correlated negatively with stigmasterol and amyrin. Complex fungi-bacteria relationships ruled by Dothideomycetes and Alphaproteobacteria further suggest tight host-microbe interactions at the carposphere.

Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae

Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant-microorganism interactions.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea

BACKGROUND

Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.

RESULTS

Our findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.

CONCLUSIONS

Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.

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.

Ecosystem consequences of invertebrate decline

Human activities cause substantial changes in biodiversity.1,2 Despite ongoing concern about the implications of invertebrate decline,3,4,5,6,7 few empirical studies have examined the ecosystem consequences of invertebrate biomass loss. Here, we test the responses of six ecosystem services informed by 30 above- and belowground ecosystem variables to three levels of aboveground (i.e., vegetation associated) invertebrate community biomass (100%, 36%, and 0% of ambient biomass) in experimental grassland mesocosms in a controlled Ecotron facility. In line with recent reports on invertebrate biomass loss over the last decade, our 36% biomass treatment also represented a decrease in invertebrate abundance (-70%) and richness (-44%). Moreover, we simulated the pronounced change in invertebrate biomass and turnover in community composition across the season. We found that the loss of invertebrate biomass decreases ecosystem multifunctionality, including two critical ecosystem services, aboveground pest control and belowground decomposition, while harvested plant biomass increases, likely because less energy was channeled up the food chain. Moreover, communities and ecosystem functions become decoupled with a lower biomass of invertebrates. Our study shows that invertebrate loss threatens the integrity of grasslands by decoupling ecosystem processes and decreasing ecosystem-service supply.

Interaction between dissolved organic carbon and fungal network governs carbon mineralization in paddy soil under co-incorporation of green manure and biochar

Legume crops in rice cultivation are typically rotated and incorporated into the soil as green manure to improve soil fertility. Biochar has recently been co-incorporated with green manure to simultaneously stimulate soil organic carbon (SOC) mineralization and increase carbon (C) sequestration. However, few studies examine the effects of the co-incorporation of biochar and green manure on C cycling and the underlying microbial mechanisms in paddy fields. In this study, the effects of the co-incorporation of green manure and biochar on C mineralization, dissolved organic carbon (DOC) characteristics, and microbial community structures were investigated. A pot study was conducted with three treatments: inorganic NPK (NPK), inorganic NPK + green manure (GM), and inorganic NPK + green manure + biochar (GMC). Organic amendments significantly increased cumulative C mineralization, with amounts in the order GMC (3,434 mg·kg-1) > GM (2,934 mg·kg-1) > NPK (2,592 mg·kg-1). Fertilizer treatments had similar effects on DOC concentrations, with amounts in the order GMC (279 mg·kg-1) > GM (255 mg·kg-1) > NPK (193 mg·kg-1). According to fluorescence spectra, the highest microbial humic acid-like fraction and biological index were also in GMC. Co-incorporation of green manure and biochar shifted the composition of bacterial and fungal communities but more importantly, increased fungal network complexity and decreased bacterial network complexity. The increase in fungal network complexity with the increase in DOC concentrations and microbially derived components was the dominant factor in promoting C mineralization. Overall, this study reveals the underlying biochemical mechanism, the interaction between DOC and fungal network of C cycling in paddy soil under the co-incorporation of green manure and biochar management, and provides fundamental knowledge for exploring effective approaches to improve soil fertility and health in the future.

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.

Unlocking complex soil systems as carbon sinks: multi-pool management as the key

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation.

A comprehensive review of chlorophenols: Fate, toxicology and its treatment

Chlorophenols represent one of the most abundant families of toxic pollutants emerging from various industrial manufacturing units. The toxicity of these chloroderivatives is proportional to the number and position of chlorine atoms on the benzene ring. In the aquatic environment, these pollutants accumulate in the tissues of living organisms, primarily in fishes, inducing mortality at an early embryonic stage. Contemplating the behaviour of such xenobiotics and their prevalence in different environmental components, it is crucial to understand the methods used to remove/degrade the chlorophenol from contaminated environment. The current review describes the different treatment methods and their mechanism towards the degradation of these pollutants. Both abiotic and biotic methods are investigated for the removal of chlorophenols. Chlorophenols are either degraded through photochemical reactions in the natural environment, or microbes, the most diverse communities on earth, perform various metabolic functions to detoxify the environment. Biological treatment is a slow process because of the more complex and stable structure of pollutants. Advanced Oxidation Processes are effective in degrading such organics with enhanced rate and efficiency. Based on their ability to generate hydroxyl radicals, source of energy, catalyst type, etc., different processes such as sonication, ozonation, photocatalysis, and Fenton's process are discussed for the treatment or remediation efficiency towards the degradation of chlorophenols. The review entails both advantages and limitations of treatment methods. The study also focuses on reclamation of chlorophenol-contaminated sites. Different remediation methods are discussed to restore the degraded ecosystem back in its natural condition.

Increased soil carbon storage through plant diversity strengthens with time and extends into the subsoil

Soils are important for ecosystem functioning and service provisioning. Soil communities and their functions, in turn, are strongly promoted by plant diversity, and such positive effects strengthen with time. However, plant diversity effects on soil organic matter have mostly been investigated in the topsoil, and there are only very few long-term studies. Thus, it remains unclear if plant diversity effects strengthen with time and to which depth these effects extend. Here, we repeatedly sampled soil to 1 m depth in a long-term grassland biodiversity experiment. We investigated how plant diversity impacted soil organic carbon and nitrogen concentrations and stocks and their stable isotopes ¹³ C and ¹⁵ N, as well as how these effects changed after 5, 10, and 14 years. We found that higher plant diversity increased carbon and nitrogen storage in the topsoil since the establishment of the experiment. Stable isotopes revealed that these increases were associated with new plant-derived inputs, resulting in less processed and less decomposed soil organic matter. In subsoils, mainly the presence of specific plant functional groups drove organic matter dynamics. For example, the presence of deep-rooting tall herbs decreased carbon concentrations, most probably through stimulating soil organic matter decomposition. Moreover, plant diversity effects on soil organic matter became stronger in topsoil over time and reached subsoil layers, while the effects of specific plant functional groups in subsoil progressively diminished over time. Our results indicate that after changing the soil system the pathways of organic matter transfer to the subsoil need time to establish. In our grassland system, organic matter storage in subsoils was driven by the redistribution of already stored soil organic matter from the topsoil to deeper soil layers, for example, via bioturbation or dissolved organic matter. Therefore, managing plant diversity may, thus, have significant implications for subsoil carbon storage and other critical ecosystem services.

The structure of root-associated fungal communities is related to the long-term effects of plant diversity on productivity

Root-associated fungi could play a role in determining both the positive relationship between plant diversity and productivity in experimental grasslands, and its strengthening over time. This hypothesis assumes that specialized pathogenic and mutualistic fungal communities gradually assemble over time, enhancing plant growth more in species-rich than in species-poor plots. To test this hypothesis, we used high-throughput amplicon sequencing to characterize root-associated fungal communities in experimental grasslands of 1 and 15 years of age with varying levels of plant species richness. Specifically, we tested whether the relationship between fungal communities and plant richness and productivity becomes stronger with the age of the experimental plots. Our results showed that fungal diversity increased with plant diversity, but this relationship weakened rather than strengthened over the two time points. Contrastingly, fungal community composition showed increasing associations with plant diversity over time, suggesting a gradual build-up of specific fungal assemblages. Analyses of different fungal guilds showed that these changes were particularly marked in pathogenic fungi, whose shifts in relative abundance are consistent with the pathogen dilution hypothesis in diverse plant communities. Our results suggest that root-associated fungal pathogens play more specific roles in determining the diversity-productivity relationship than other root-associated plant symbionts.

Fungal diversity dominates the response of multifunctionality to the conversion of pure plantations into two-aged mixed plantations

Plantation forests are essential in driving global biogeochemical cycling and mitigating climate change. Biodiversity and environmental factors can shape multiple forest ecosystem functions simultaneously (i.e., multifunctionality). However, their effect on multifunctionality when pure plantations are converted into two-aged plantations remains underexplored. Therefore, we assessed above- and below-ground biodiversity and environmental factors and 11 ecosystem functions in different plantation types in subtropical China. The two-aged mixed plantations exhibited higher multifunctionality than did a pure plantation, primarily due to soil fungal diversity and secondarily due to tree diversity, based on the coefficient of variation for tree diameter at breast height (CV_D) and community-weighted specific leaf area (CWM_SLA). Further analysis revealed saprotrophy as the key soil fungal trophic mode in maintaining multifunctionality. Moreover, structural equation modeling confirmed that soil environmental factors, namely the soil water content and pH, had no direct association with multifunctionality, but were indirectly related to multifunctionality via elevated CV_D and CWM_SLA, respectively. Our results indicate that the tree and soil fungal diversity, as well as soil environmental factors, resulting from the conversion of pure plantations to two-aged mixed plantations, can enhance multifunctionality, and provide a better comprehensive understanding of the driving mechanisms of multifunctionality, leading to the sustainable management of subtropical plantation forest ecosystems.

Linking plant diversity-productivity relationships to plant functional traits of dominant species and changes in soil properties in 15-year-old experimental grasslands

Positive plant diversity-productivity relationships are known to be driven by complementary resource use via differences in plant functional traits. Moreover, soil properties related to nutrient availability were shown to change with plant diversity over time; however, it is not well-understood whether and how such plant diversity-dependent soil changes and associated changes in functional traits contribute to positive diversity-productivity relationships in the long run. To test this, we investigated plant communities of different species richness (1, 2, 6, and 9 species) in a 15-year-old grassland biodiversity experiment. We determined community biomass production and biodiversity effects (net biodiversity [NEs], complementarity [CEs], and selection effects [SEs]), as well as community means of plant functional traits and soil properties. First, we tested how these variables changed along the plant diversity gradient and were related to each other. Then, we tested for direct and indirect effects of plant and soil variables influencing community biomass production and biodiversity effects. Community biomass production, NEs, CEs, SEs, plant height, root length density (RLD), and all soil property variables changed with plant diversity and the presence of the dominant grass species Arrhenatherum elatius (increase except for soil pH, which decreased). Plant height and RLD for plant functional traits, and soil pH and organic carbon concentration for soil properties, were the variables with the strongest influence on biomass production and biodiversity effects. Our results suggest that plant species richness and the presence of the dominant species, A. elatius, cause soil organic carbon to increase and soil pH to decrease over time, which increases nutrient availability favoring species with tall growth and dense root systems, resulting in higher biomass production in species-rich communities. Here, we present an additional process that contributes to the strengthening positive diversity-productivity relationship, which may play a role alongside the widespread plant functional trait-based explanation.

Astragalus-cultivated soil was a suitable bed soil for nurturing Angelica sinensis seedlings from the rhizosphere microbiome perspective

Angelica sinensis (Oliv.) Diels is an important Chinese medicinal plant. A. sinensis seedlings are grown on an undisturbed alpine meadow soil to ensure the high-quality seedlings, but these soils are disappearing year after year. Thus, selecting a suitable bed soil for A. sinensis seedlings could ensure their long-term sustainability. Using HiSeq sequencing of 16S and 18S marker genes, we investigated the rhizosphere bacterial and fungal microbiotas of the seedlings grown in wheat, astragalus, potato, and angelica-cultivated soils at a geo-authentic habitat. Co-occurrence network analysis, canonical correspondence analysis, Mantel test, and Envfit test were used to examine the relationship between the microbiotas and the surrounding factors. Astragalus-cultivated soils exhibited the following properties: the highest plant weight, the highest neighborhood connectivity in the bacterial network, the highest ratio of positive/negative relationship in both bacterial and fungal networks, the highest relative abundance of the arbuscular mycorrhizal fungi and the ectomycorrhizal fungi, the lowest relative abundance of Rhizoctonia solani, the suitable soil pH, and the close relationship between the rhizosphere microbiotas and the ecological factors. Moreover, each growth stage has its own major drivers in all crop-cultivated soils. Climate temperature and soil pH at 56 days after planting, precipitation at 98 days, and plant weight as well as microbial biomass C and N at 129 days were the major drivers of the bacterial and fungal microbiotas. Overall, the astragalus-cultivated soil was a suitable bed soil for nurturing A. sinensis seedlings to replace the undisturbed alpine meadow soils.

The soil microbiome: An essential, but neglected, component of regenerative agroecosystems

Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Effect of biochar application rate on changes in soil labile organic carbon fractions and the association between bacterial community assembly and carbon metabolism with time

Biochar aging affects the stability of soil carbon. Analyzing the effect of biochar on soil organic carbon (SOC) forms and their relations with microbial community assembly and carbon metabolism with time is helpful for soil carbon sequestration (by adapting the farm management approach). Four treatments with no, low, medium, and high biochar application rates (0 %, 1 %, 2 %, and 4 % of the total dry weight of topsoil before winter wheat planting, abbreviated as control, LB, MB, and HB, respectively) were conducted in the field. The SOC and particulate organic carbon positively correlated with the biochar application rate. Biochar decreased readily oxidizable carbon (P < 0.05) after 8 months of application compared to the control; however, the difference disappeared with time. Biochar increased dissolved organic carbon (DOC) but had no effect on water- soluble organic carbon (WSOC); DOC and WSOC decreased with time. Furthermore, LB and HB stabilized the bacterial alpha diversities with time. Based on high-throughput sequencing, HB reduced the relative abundance of Actinobacteriota but increased that of Acidobacteria (P < 0.05) after 12 months of biochar application. Time-wise, the bacterial community assembly was determined by deterministic processes that were significantly affected by the available nitrogen, DOC, or WSOC. Compared with the control, biochar decreased bacterial links and improved bacterial metabolism of phenolic acids and polymers with time, as evidenced by Biolog EcoPlates. Structural equation modeling revealed that the contribution of bacterial assembly processes to carbon metabolism changed with time. Microbial carbon metabolism was most positively influenced by differences in the composition of bacterial specialists. These findings reinforced that changes in soil labile organic carbon were time-dependent but not necessarilty affected by the biochar application rate.

Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility

The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.

Cyperus rotundus L. drives arable soil infertile by changing the structure of soil bacteria in the rhizosphere, using a maize field as an example

Rhizosphere microorganisms can greatly affect plant growth, especially the plant growth-promoting rhizobacteria (PGPR), which can improve plant root development and growth because they contain various biological functions including nitrogen fixation, phosphate solubilization, and phytosiderophore production. This study demonstrates that Cyperus rotundus L. is capable of developing and forming complex underground reproductive systems at arbitrary burial depths and cutting modes due to its extremely strong multiplication and regeneration ability. With the densities of C. rotundus increasing, the abundance of PGPR, soil enzymes invertase and urease, the nutrient contents of the field soil, and maize quality were impacted. Notably, more abundance of PGPR-most notably, the nitrogen-fixing microorganisms (NFMs) such as Azospirillum, Burkholderia, Mycobacterium, and Rhizobium-enriches in the rhizosphere of C. rotundus than in that of maize. In addition, the activities of soil enzymes invertase (S_SC) and urease (S_SU) were significantly higher in its rhizosphere than in maize, further proving that more NFMs enrich the C. rotundus rhizosphere. The nutrient contents of the field soil of TN, SOM, and SOC were reduced, indicating that the presence of C. rotundus made the soil infertile. Hence, these pieces of evidence indicate that C. rotundus may drive the field soil infertile as reflected by reduced soil nutrients via altering rhizosphere bacteria community structure.

Drought legacy effects on root morphological traits and plant biomass via soil biota feedback

Drought causes soil feedback effects on plant performance. However, how the linkages between conditioned soil biota and root traits contribute to explain plant-soil feedback (PSF) as a function of drought is unknown. We utilized soil inoculum from a conditioning experiment where grassland species grew under well-watered and drought conditions, and their soil fungi were analyzed. Under well-watered conditions, we grew 21 grassland species with those inocula from either conspecific or heterospecific soils. At harvest, plant biomass and root traits were measured. Negative PSF (higher biomass in heterospecific than in conspecific soils) was predominant, and favored in drought-conditioned soils. Previous drought affected the relationship between root traits and fungal groups. Specific root surface area (SRSA) was higher in heterospecific than in conspecific droughted soils and was linked to an increase in saprotroph richness. Overall, root diameter was higher in conspecific soils and was linked to mutualist and pathogen composition, whereas the decrease of root : shoot in heterospecific soils was linked to pathogenic fungi. Drought legacy affects biomass and root morphological traits via conditioned soil biota, even after the drought conditions have disappeared. This provides new insights into the role that soil biota have modulating PSF responses to drought.

Root phenotypes as modulators of microbial microhabitats

Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.

The in vivo and vitro degradation of sulfonamides in wetland plants reducing phytotoxicity and environmental pollution

Aquatic plants can be used for in situ remediation of water-borne pharmaceutical compounds; however, such information and that of the potential risks of metabolites released into the environment are limited. This study determined the capacity of Canna indica and Acorus calamus used in the remediation of water-borne sulfonamides (SA). The tolerance, removal, accumulation, and biotransformation of various water-borne SAs were investigated in vivo by exposing plants to SA solutions (50 µg/L and 500 µg/L). After 28 days, C. indica removed more SAs (89.3-97.8%) than A. calamus (12.8-84.6%) and non-planted systems (8.0-69.3%). The SA removal results, except from the A. calamus system with 500 µg/L SA, fit the first-order kinetics model. The estimated half-lives of all SAs were 3-40 h and 2-60 h in the C. indica and A. calamus systems, respectively. In vivo biotransformation and rhizosphere degradation were the major phyto-removal mechanisms, constituting 24.9-81.1% and 0.0-37.1% of all SAs in the C. indica and A. calamus systems, respectively. SA acetyl metabolites were detected only in plant tissues supporting evidence for plant metabolic processes without risk into the environment. SA metabolism including oxidation, methylation, and conjugation via acetylation was potentially beneficial to accumulation and tolerate stress of antibiotic. Canna indica was more suitable for cleaning SA. Our findings better clarify the potential and low risks of phytoremediation in antibiotic-contaminated waters.

Enzyme kinetics inform about mechanistic changes in tea litter decomposition across gradients in land-use intensity in Central German grasslands

Grassland ecosystems provide important ecosystem services such as nutrient cycling and primary production that are affected by land-use intensity. To assess the effects of land-use intensity, operational and sensitive ecological indicators that integrate effects of grassland management on ecosystem processes such as organic matter turnover are needed. Here, we investigated the suitability of measuring the mass loss of standardized tea litter together with extracellular enzyme kinetics as a proxy of litter decomposition in the topsoil of grasslands along a well-defined land-use intensity gradient (fertilization, mowing, grazing) in Central Germany. Tea bags containing either green tea (high-quality litter) or rooibos tea (low-quality litter) were buried in 5 cm soil depth. Litter mass loss was measured after three (early-stage decomposition) and 12 months (mid-stage decomposition). Based on the fluorescence measurement of the reaction product 4-methylumbelliferone, Michaelis-Menten enzyme kinetics (V_max: potential maximum rate of activity; K_m: substrate affinity) of five hydrolases involved in the carbon (C)-, nitrogen (N)- and phosphorus (P)-cycle (β-glucosidase (BG), cellobiohydrolase (CBH), cellotriohydrolase (CTH), 1,4-β-N-acetylglucosaminidase (NAG), and phosphatase (PH)) were determined in tea litter bags and in the surrounding soil. The land-use intensity index (LUI), summarizing fertilization, mowing, grazing, and in particular the frequency of mowing were identified as important drivers of early-stage tea litter decomposition. Mid-stage decomposition was influenced by grazing intensity. The higher the potential activity of all measured C-, N- and P-targeting enzymes, the higher was the decomposition of both tea litters in the early-phase. During mid-stage decomposition, individual enzyme parameters (V_max of CTH and PH, K_m of CBH) became more important. The tea bag method proved to be a suitable indicator which allows an easy and cost-effective assessment of land-use intensity effects on decay processes in manged grasslands. In combination with enzyme kinetics it is an appealing approach to identify mechanisms driving litter break down.

Variations in rhizosphere soil total phosphorus and bioavailable phosphorus with respect to the stand age in Pinus massoniana Lamb

Phosphorus (P) is a nutrient limiting plant growth in subtropical regions. However, our understanding of how soil P responds to an increase in stand age is rather poor. In particular, little is known about how bioavailable P pools (soluble P, exchangeable P, hydrolyzable P, and ligand P) shift with a change in stand age. Moreover, the P cycle in rhizosphere soil has the most direct and significant influence on plants. The aim of the present study was to determine the concentrations of total P in various rhizosphere soil bioavailable P fractions in 5-, 9-, 19-, 29-, and 35-year-old stands of Pinus massoniana Lamb. According to the results, total P (TP) concentration and N:P ratio in rhizosphere soil first decreased, and then increased with an increase in stand age. Soluble P concentration decreased first, and then increased with an increase in stand age; exchangeable P and ligand P decreased first, and then tended to be stable with an increase in stand age, whereas hydrolyzable P increased first, and then decreased. Structural Equation Model results suggested that ligand P and soluble P were the major factor affecting the TP. In addition, soil microorganisms and acid phosphatase-driven hydrolyzable P play a crucial role in soil bioavailable P cycling. Overall, the results of our study provide a mechanistic understanding of soil bioavailable P cycling under low available P conditions, and a basis for an effective P management strategy for the sustainable development of P. massoniana plantations.

Root attributes dominate the community assembly of soil fungal functional guilds across arid inland river basin

Plant attributes are increasingly acknowledged as key drivers shaping soil fungal communities, but considerable uncertainty exists over fungal community assembly mechanisms and their plant drivers based only on inferences from plant aboveground attributes. To date, empirical evidences of how root attributes are integrated into microbiome-plant linkages remain limited. Using 162 soil samples from a typical arid inland river basin in China, we assessed the drivers that regulate the distribution patterns and assembly processes of total, mycorrhizal, saprotrophic and pathotrophic fungi in surface (0-15 cm) and subsurface soils (15-30 cm). Total fungi and fungal functional guilds exhibited similar distribution patterns in arid inland river basins. Null-model and variance partitioning analysis revealed that the heterogeneous selection induced by root attributes, rather than dispersal limitation, predominated the fungal community assembly. Multiple regressions on matrices further demonstrated that specific root length were the most important predictors of fungal community assembly, which mediated the balance of assembly processes of soil fungal communities. Heterogeneous selection decreased for total, mycorrhizal and saprotrophic fungi, but increased for pathotrophic fungi with increasing specific root length. Additionally, fine-root biomass exerted important effects on fungal assembly processes in subsurface soil but not in surface soil, suggesting root attributes differently affected fungal community assembly between surface and subsurface soil. Collectively, our study highlights the importance of considering root attributes in differentiating the balance of stochastic and deterministic processes in microbial community assembly.

Roots and other residues from leys with or without red clover: Quality and effects on N2O emission factors in a partly frozen soil following autumn ploughing

Revised IPCC guidelines assume that a constant share of N in decomposing crop residues is directly emitted as N₂O (emission factor: EF_N2O), and calculate the amount of nitrogen (N) in non-removable residues of temporary grasslands proportionally to the average annual herbage yield. However, EF_N2O depends on the intrinsic quality of the residues and their interactions with environmental conditions. Only a few field studies on N₂O emissions from grassland renewal are available, and none have simultaneously quantified the N amount and quality of non-removable residues (roots and stubble). To gain insight into the effect of non-removable residue quality on EF_N2O, we studied the amount and quality of roots and stubble and their effect on EF_N2O following the ploughing of three-year-old swards. The measured amount of N in non-removable residues was approximately 20, 25, and 31 kg N per 1 Mg average annual dry matter yield in grass, red clover-grass, and red clover, and 70-83% of it was below ground. However, the EF_N2O of non-removable residues measured over 252 days was lower (0.24%, SE = 14% for grass and red clover-grass) than the IPCC default value (0.6%, CV: 50%) for wet regions, although within the uncertainty margin, and was significantly lower than the EF_N2O of incorporated herbage, which was related to differences in EF_CO2. We advocate for more specific studies that separate the effects of belowground and aboveground residues (AGR), considering the possibility of simplifying the accounting of N₂O emissions from belowground residues while improving that of non-removable AGR from temporary grasslands and other green crops. We observed the accumulation of N₂O in the frozen soil under snow, which was released during diurnal percolation of meltwater. N₂O emissions from frozen soil accounted for 30% or more of the total emissions.

Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.

Land-use change shifts and magnifies seasonal variations of the decomposer system in lowland tropical landscapes

Deforestation and agricultural expansion in the tropics affect local and regional climatic conditions, leading to synergistic negative impacts on land ecosystems. Climatic changes manifest in increased inter- and intraseasonal variations and frequency of extreme climatic events (i.e., droughts and floods), which have evident consequences for aboveground biodiversity. However, until today, there have been no studies on how land use affects seasonal variations below ground in tropical ecosystems, which may be more buffered against climatic variation. Here, we analyzed seasonal variations in soil parameters, basal respiration, microbial communities, and abundances of soil invertebrates along with microclimatic conditions in rainforest and monocultures of oil palm and rubber in Sumatra, Indonesia. About 75% (20 out of 26) of the measured litter and soil, microbial, and animal parameters varied with season, with seasonal changes in 50% of the parameters depending on land use. Land use affected seasonal variations in microbial indicators associated with carbon availability and cycling rate. The magnitude of seasonal variations in microbial parameters in the soil of monocultures was almost 40% higher than in the soil of rainforest. Measured parameters were associated with short-term climatic conditions (3-day period air humidity) in plantations, but not in rainforest, confirming a reduced soil buffering ability in plantations. Overall, our findings suggest that land use temporally shifts and increases the magnitude of seasonal variations of the belowground ecosystem compartment, with microbial communities responding most strongly. The increased seasonal variations in soil biota in plantations likely translate into more pronounced fluctuations in essential ecosystem functions such as nutrient cycling and carbon sequestration, and these ramifications ultimately may compromise the stability of tropical ecosystems in the long term. As the observed seasonal dynamics is likely to increase with both local and global climate change, these shifts need closer attention for the long-term sustainable management of plantation systems in the tropics.

Changes in Soil Organic Carbon Fractions and Fungal Communities, Subsequent to Different Management Practices in Moso Bamboo Plantations

Moso bamboo (Phyllostachys pubescens) has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C accumulation and fungi communities related to different management practices. Here, we investigated changes in the soil organic carbon (SOC) fractions and fungal communities of a Moso bamboo plantation under three different management practices (M0: undisturbed; M1: extensively managed; and M2: intensively managed). Compared with M0, SOC levels were reduced by 41.2% and 71.5% in M1 and M2, respectively; furthermore, four SOC fractions (C1: very labile; C2: labile; C3: less labile; and C4: nonlabile) and the carbon management index (CMI) were also significantly reduced by plantation management. These practices further altered fungal communities, for example, by increasing Basidiomycota and Mortierellomycota, and by decreasing Ascomycota and Rozellomycota. Pyrenochaeta, Mortierella, Saitozyma, and Cladophialophora were identified as keystone taxa. Soil fungal communities were significantly related to the pH, NH₄-N, AP, C3, and the C4 fractions of SOC. Random forest modeling identified soil C3 and Mortierella as the most important predictors of the CMI. Our results suggest that reducing human interference would be beneficial for fungal community improvement and C sequestration in Moso bamboo plantations.

Biotic Interactions as Mediators of Context-Dependent Biodiversity-Ecosystem Functioning Relationships

Biodiversity drives the maintenance and stability of ecosystem functioning as well as many of nature’s benefits to people, yet people cause substantial biodiversity change. Despite broad consensus about a positive relationship between biodiversity and ecosystem functioning (BEF), the underlying mechanisms and their context-dependencies are not well understood. This proposal, submitted to the European Research Council (ERC), aims at filling this knowledge gap by providing a novel conceptual framework for integrating biotic interactions across guilds of organisms, i.e. plants and mycorrhizal fungi, to explain the ecosystem consequences of biodiversity change. The overarching hypothesis is that EF increases when more tree species associate with functionally dissimilar mycorrhizal fungi. Taking a whole-ecosystem perspective, we propose to explore the role of tree-mycorrhiza interactions in driving BEF across environmental contexts and how this relates to nutrient dynamics. Given the significant role that mycorrhizae play in soil nutrient and water uptake, BEF relationships will be investigated under normal and drought conditions. Resulting ecosystem consequences will be explored by studying main energy channels and ecosystem multifunctionality using food web energy fluxes and by assessing carbon storage. Synthesising drivers of biotic interactions will allow us to understand context-dependent BEF relationships. This interdisciplinary and integrative project spans the whole gradient from local-scale process assessments to global relationships by building on unique experimental infrastructures like the MyDiv Experiment, iDiv Ecotron and the global network TreeDivNet, to link ecological mechanisms to reforestation initiatives. This innovative combination of basic scientific research with real-world interventions links trait-based community ecology, global change research and ecosystem ecology, pioneering a new generation of BEF research and represents a significant step towards implementing BEF theory for human needs.

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.

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.

The Edaphic and Vegetational Properties Controlling Soil Aggregate Stability Vary with Plant Communities in an Arid Desert Region of Northwest China

The stability of soil aggregates is the basis for supporting ecosystem functions and related services provided by the soil. In order to explore the mechanism of the influence of soil and vegetation properties on the stability of soil aggregates in desert communities, the particle size distribution and aggregate in different communities were compared, and the contribution of soil physical and chemical properties (soil salinity, soil water content, soil pH, soil organic carbon, soil total phosphorus, soil total nitrogen, etc.) and vegetation properties (species richness, phylogenetic richness, plant height and coverage, etc.) to the stability of soil aggregates was determined by using a structural equation model. The results show the following: Soil water content, organic carbon, and salt in river bank plant communities have significant direct positive effects on the mean weight diameter of soil, with path coefficients of 0.50, 0.11, and 0.24, respectively (p < 0.01). Water also indirectly affects soil stability by affecting plant height, soil salt, and soil organic carbon; species richness and vegetation coverage have significant direct positive effects on the soil stability index, with path coefficients of 0.13 and 0.11, respectively (p < 0.01). In the desert marginal plant community, the plant coverage and species richness have significant positive effects on soil stability, with path coefficients of 0.43 (p < 0.001) and 0.35 (p < 0.001), respectively. Phylogenetic richness has a significant direct negative effect on soil stability (p < 0.05), with an effect value of −0.27. Phylogenetic richness indirectly affects soil stability by adjusting the coverage, with an indirect effect value of 0.23. Moisture, ammonium nitrogen, and nitrate nitrogen have significant direct positive effects on soil stability, with effect values of 0.12, 0.09, and 0.15, respectively. Our research shows that the process of soil stabilization is mainly controlled by soil factors and vegetation characteristics, but its importance varies with different community types.