Multiomics reveals Claroideoglomus etunicatum regulates plant hormone signal transduction, photosynthesis and La compartmentalization in maize to promote growth under La stress.

Rare earth elements (REEs) have been widely used in traditional and high-tech fields, and high doses of REEs are considered a risk to the ecosystem. Although the influence of arbuscular mycorrhizal fungi (AMF) in promoting host resistance to heavy metal (HM) stress has been well documented, the molecular mechanism by which AMF symbiosis enhances plant tolerance to REEs is still unclear. A pot experiment was conducted to investigate the molecular mechanism by which the AMF Claroideoglomus etunicatum promotes maize (Zea mays) seedling tolerance to lanthanum (La) stress (100 mg·kg-1 La). C. etunicatum symbiosis significantly improved maize seedling growth, P and La uptake and photosynthesis. Transcriptome, proteome, and metabolome analyses performed alone and together revealed that differentially expressed genes (DEGs) related to auxin /indole-3-acetic acid (AUX/IAA) and the DEGs and differentially expressed proteins (DEPs) related to ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (Nramp6), vacuoles and vesicles were upregulated. In contrast, photosynthesis-related DEGs and DEPs were downregulated, and 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI(3)P) was more abundant under C. etunicatum symbiosis. C. etunicatum symbiosis can promote plant growth by increasing P uptake, regulating plant hormone signal transduction, photosynthesis and glycerophospholipid metabolism pathways and enhancing La transport and compartmentalization in vacuoles and vesicles. The results provide new insights into the promotion of plant REE tolerance by AMF symbiosis and the possibility of utilizing AMF-maize interactions in REE phytoremediation and recycling.

Bio-organic fertilizer promoted phytoremediation using native plant leymus chinensis in heavy Metal(loid)s contaminated saline soil.

Heavy metal(loid)s (HMs) contaminated saline soil appeared around the world, however, remediation regarding these collected from field conditions remains unknown. Native plants cultivation and bio-organic fertilizer (BOF) application were two efficient tools for soil amelioration. Herein, a pot experiment was conducted to examine the feasibility of a native plant (Leymus chinensis) for phytoremediation, and investigate the impacts of lignite based bio-organic fertilizer (LBOF) and manure based bio-organic fertilizer (MBOF) on phytoremediation of the soil contaminated by Pb, Cd, As, Zn, Cu, Ca2+, and SO42-. The results demonstrated the effectiveness of L. chinensis and highlighted the positive impacts of BOF according to the improved plant growth, HMs phytostabilization, salt removal, and soil properties. LBOF and MBOF changed soil microbiome to assist phytoremediation in addition to physiological modulation. Having enhanced fungal and bacterial richness respectively, LBOF and MBOF recruited various plant growth promoting rhizobacteria with different functions, and shifted microbial co-occurrence networks and keystone taxa towards these different but beneficial forms. Structural equation models comprehensively reveled the strategy discrepancy of LBOF and MBOF to regulate the plant biomass, HMs uptake, and soil salt. In summary, L. chinensis coupled with BOF, especially LBOF, was a effective strategy to remediate HMs contaminated saline soil.

Synergistic mechanisms of bioorganic fertilizer and AMF driving rhizosphere bacterial community to improve phytoremediation efficiency of multiple HMs-contaminated saline soil.

The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and promote plant growth, while their synergistic effects on plant growth and rhizosphere microorganism are largely unknown. This study explored the effects of AMF (Rhizophagus intraradices), BOF and BOF + RI assisted phytoremediation on heavy metals contaminated saline soil improvement and revealed the microbial mechanism. For this purpose, a pot trial consisting of four treatments (CK, RI, BOF and BOF + RI) was carried out. The results showed that the biomass, nutrient element contents, the accumulation of heavy metals and Na of Astragalus adsurgens and soil properties were most significantly improved by BOF + RI. BOF + RI significantly impacted rhizosphere microbial diversity, abundance and community composition. Chloroflexi and Patescibacteria at the phylum level and Actinomadura, Iamia, and Desulfosporosinus at the genus level were significantly enriched in BOF + RI. Network analysis revealed that BOF + RI significantly changed the keystone and enhanced complexity and interaction. Most of the keystones had roles in promoting plant growth and stress resistance. This study suggested that phytoremediation assisted by BOF and AMF is an attractive approach to ameliorate heavy metals contaminated saline soil.

Bioorganic fertilizers improve the adaptability and remediation efficiency of Puccinellia distans in multiple heavy metals-contaminated saline soil by regulating the soil microbial community.

Soil salinization and heavy metal (HM) pollution are global environmental problems. Bioorganic fertilizers facilitate phytoremediation, but their roles and microbial mechanisms in natural HM-contaminated saline soils have not been explored. Therefore, greenhouse pot trials were conducted with three treatments: control (CK), manure bioorganic fertilizer (MOF), and lignite bioorganic fertilizer (LOF). The results showed that MOF and LOF significantly increased nutrient uptake, biomass, toxic ion accumulation in Puccinellia distans, soil available nutrients, SOC, and macroaggregates. More biomarkers were enriched in MOF and LOF. Network analysis confirmed that MOF and LOF increased the number of bacterial functional groups and fungal community stability and strengthened their positive association with plants; Bacteria have a more significant effect on phytoremediation. Most biomarkers and keystones play important roles in promoting plant growth and stress resistance in the MOF and LOF treatments. In summary, besides enrichment of soil nutrients, MOF and LOF can also improve the adaptability and phytoremediation efficiency of P. distans by regulating the soil microbial community, with LOF having a greater effect.

Biocontrol features of Pseudomonas syringae B-1 against Botryosphaeria dothidea in apple fruit.

Apple ring rot caused by Botryosphaeria dothidea is an important disease that leads to severe quality deterioration and yield loss at pre-harvest and postharvest stages. Therefore, it is urgent to develop safe and efficient measures to control this disease. The objective of the present study was to investigate the biocontrol features of Pseudomonas syringae B-1 against B. dothidea and explore its mechanism of action utilizing in vitro and in vivo assays. The results showed that P. syringae B-1 strongly reduced the incidence of apple ring rot and lesion diameter by 41.2 and 90.2%, respectively, in comparison to the control fruit. In addition, the control efficiency of strain B-1 against B. dothidea infection depended on its concentration and the interval time. P. syringae B-1 cells showed higher inhibitory activities than its culture filtrates on the mycelial growth and spore germination of B. dothidea. Moreover, P. syringae B-1 treatment alleviated electrolyte leakage, lipid peroxidation, and H2O2 accumulation in B. dothidea-infected apple fruit by increasing antioxidant enzyme activities, including peroxidase, catalase, superoxide dismutase, and ascorbate peroxidase. We also found that strain B-1 treatment enhanced four defense-related enzyme activities and stimulated the accumulation of three disease-resistant substances including phenolics, lignin, and salicylic acid (SA) in apple fruit. In addition, strain B-1 triggered the upregulated expression of defense-related genes such as PR genes (PR1, PR5, GLU, and CHI) and two genes involved in the biosynthesis of SA (SID2 and PAD4) to promote the resistance potential in apple fruit. Hence, our results suggest that P. syringae B-1 is a promising strategy against B. dothidea, mainly through reducing oxidative damage, activating defense-related enzymes, accumulating disease-resistant substances, and triggering the expression of resistance-correlated genes in apple fruit.

Shift in rhizospheric and endophytic microbial communities of dominant plants around Sunit Alkaline Lake.

Alkaline lakes are a special type of extreme saline-alkali ecosystem, and the dominant plants store a large number of microbial resources with salinity-tolerant or growth-promoting properties in the littoral zones. In this study, high-throughput sequencing technology and molecular ecological networks were used to analyze the bacteria and fungi from different rhizocompartments of three dominant plants along the salinity gradient in the littoral zones of Sunit Alkali Lake. The study found that fungal communities were more tolerant of environmental abiotic stress, and salinity was not the main environmental factor affecting the composition of microbial communities. Mantel test analysis revealed that SOC (soil organic carbon) was the primary environmental factor affecting the rhizosphere bacterial community as well as the rhizosphere endophyte bacteria and fungi, while CO32- (carbonate ions) had a greater impact on the rhizosphere fungal communities. In addition, keystones identified through the associated molecular network play an important role in helping plants resist saline-alkali environments. There were significant differences in the metabolic pathways of microorganisms from different rhizocompartments predicted by the PICRUSt2 database, which may help to understand how microorganisms resist environmental stress. This study is of great importance for understanding the salt environments around alkaline lakes and excavating potential microbial resources.

Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships.

Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.

Claroideoglomus etunicatum affects the structural and functional genes of the rhizosphere microbial community to help maize resist Cd and La stresses.

Arbuscular mycorrhizal fungi (AMF) and plant rhizosphere microbes reportedly enhance plant tolerance to abiotic stresses and promote plant growth in contaminated soils. The co-contamination of soil by heavy metals (e.g., Cd) and rare earth elements (e.g., La) represents a severe environmental problem. Although the influence of AMF in the phytoremediation of contaminated soils is well documented, the underlying interactive mechanisms between AMF and rhizosphere microbes are still unclear. We conducted a greenhouse pot experiment to evaluate the effects of AMF (Claroideoglomus etunicatum) on maize growth, nutrient and metal uptake, rhizosphere microbial community, and functional genes in soils with separate and combined applications of Cd and La. The purpose of this experiment was to explore the mechanism of AMF affecting plant growth and metal uptake via interactions with rhizosphere microbes. We found that C. etunicatum (i) significantly enhanced plant nutritional level and biomass and decreased metal concentration in the co-contaminated soil; (ii) significantly altered the structure of maize rhizosphere bacterial and fungal communities; (iii) strongly enriched the abundance of carbohydrate metabolism genes, ammonia and nitrate production genes, IAA (indole-3-acetic acid) and ACC deaminase (1-aminocyclopropane-1-carboxylate) genes, and slightly altered the abundance of P-related functional genes; (iv) regulated the abundance of microbial quorum sensing system and metal membrane transporter genes, thereby improving the stability and adaptability of the rhizosphere microbial community. This study provides evidence of AMF improving plant growth and resistance to Cd and La stresses by regulating plant rhizosphere microbial communities and aids our understanding of the underlying mechanisms.

Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur.

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO4 2-, SOC, HCO3 -, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

[Potential of Arbuscular Mycorrhizal Fungi, Biochar, and Combined Amendment on Sandy Soil Improvement Driven by Microbial Community].

Sandy soils are considered as a significant transition phase to desertification. The effective recovery of sandy soils is of great significance to mitigate the desertification process. Some studies have shown that arbuscular mycorrhizal (AM) fungi and biochar improved the sandy soil, but there have been very few studies regarding the combined effects of AM fungi and biochar amendments on sandy soil improvement. Additionally, the roles of the bacterial and fungal community during the process of sandy soil improvement remain unclear. A greenhouse pot experiment with four treatments, including a control (CK, no amendment), single AM fungi-assisted amendment (RI), single biochar amendment (BC), and combined amendment (BC_RI, biochar plus AM fungi), was set up. This study investigated the effects of different amendment methods on the Nitrariasi birica mycorrhizal colonization, biomass, nutrient (N, P, K, Ca, and Mg) content, soil organic carbon, soil nutrient (TN, TP, and TK) content, and soil water-stable aggregate composition. High throughput sequencing technology was used to investigate the roles of the bacterial and fungal communities during the process of sandy soil improvement. Combined with multiple analysis methods, the improvement mechanisms of different amendment methods were explored. The aim was to provide basic data and scientific basics for reasonably and effectively improving sandy soils. The results indicated that a significant mycorrhiza colonization was observed in the inoculation (RI and BC_RI) treatments, but there was no substantial difference in the mycorrhiza colonization with the RI and BC_RI. Compared with the CK, the shoot biomass and shoot element (N, K, Ca, and Mg) contents were significantly increased in the RI, and the shoot element (N, P, K, Ca, and Mg) contents were significantly increased in the BC and BC_RI; compared with the RI and BC, the root biomass and the root element (P, K, Ca, and Mg) contents were significantly increased in the BC_RI. Compared with the CK, the soil organic carbon contents were significantly increased in the BC and BC_RI, the soil TN contents were significantly increased by 152.54%, and the soil TP and TK contents were significantly decreased by 12.5% and 18.8%, respectively. The proportion of soil aggregates with particle sizes of 0.25-0.05 mm was the highest in each treatment, and the large particle size (>0.25 mm) soil aggregate was significantly increased in the BC_RI. Compared with the CK, the Sobs and Shannon indices of the bacterial/fungal community were significantly decreased in the RI and BC_RI. There was a difference in the microbial community compositions and abundance in the various treatments. The results of the RDA and network analysis were as follows:the effects of AM fungi, biochar, and combined amendment on the soil environment and microbial community structure were significant; in the different amendment treatments, the relationship of the microbial molecular ecological network was significantly changed, and the composition of the core species varied; compared with the RI, there was a higher network connection degree and a richer core species composition in the BC and BC_RI; moreover, the essential role of Rhizophagus intraradices was weaken and the core roles of the other microorganisms (especially bacterial species) were enhanced under the combined effects of biochar and AM fungi. The SEM results demonstrated that the application of AM fungi and biochar could directly affect the bacteria/fungi community structure, and further affect the plant growth and soil properties. The differences in the microbial community structure (especially the change in the microbial interaction) were the key driving factors that led to the difference in the soil improvement effectiveness. In summary, the effects of the different amendment methods on the improvement effectiveness of sandy soils varied. The microbial community played key roles in the process of sandy soil improvement, and there were potential advantages and applications in accelerating the ecological restoration of sandy soils under the combined AM fungi and biochar amendment.

Evaluation of Microbial Assemblages in Various Saline-Alkaline Soils Driven by Soluble Salt Ion Components.

Land degraded by salinization and alkalization is widely distributed globally and involves a wide range of ecosystem types. However, the knowledge of the indigenous microbial assemblages and their roles in various saline-alkaline soils is limited. This study demonstrated microbial assemblages in various saline-alkaline soils from different regions of Inner Mongolia and revealed the key driving factors to influence microbiome. The correlation network analysis indicates the difference in adaptability of bacterial and fungal communities under stimulation by saline-alkaline stress: fungal community shows higher tolerance, stability, and resilience to various saline-alkaline soils than a bacterial community. The keystone bacteria and fungi that have potential adaptability to various saline-alkaline environments are further identified, and they may confer benefits in restoring saline-alkaline soils by their own effects or assisting plants. For salt-rich soils in different regions, the soluble salt ion components are the major determinant to drive microbial assemblages of different saline-alkaline soils, rather than salinity. Thus, these saline-alkaline soils are clustered into sulfated, chlorinated, and soda-type saline-alkaline soils. Multivariate analysis reveals unique, dominant, and common microbial taxa in three saline-alkaline soils. This result of the conceptual mode indicates that potential roles of unique and dominant microbial taxa on regulating saline-alkaline functions are more vital.

Arbuscular mycorrhizal fungi alter microbiome structure of rhizosphere soil to enhance maize tolerance to La.

Rhizosphere microbes are essential partners for plant stress tolerance. Recent studies indicate that arbuscular mycorrhizal fungi (AMF) can facilitate the revegetation of soils contaminated by heavy metals though interacting with rhizosphere microbiome. However, it is unclear how AMF affect rhizosphere microbiome to improve the growth of plant under rare earth elements (REEs) stress. AMF (Claroideoglomus etunicatum) was inoculated to maize grown in soils spiked with Lanthanum (0 mg kg-1, La0; 10 mg kg-1, La10; 100 mg kg-1, La100; 500 mg kg-1, La500). Plant biomass, nutrient uptake, REE uptake and rhizosphere bacterial and fungal community were evaluated. The results indicated that La100 and La500 decreased significantly root colonization rates and nutrition uptake (K, P, Ca and Mg content). La500 decreased significantly α-diversity indexes of bacterial and fungal community. AMF enhanced significantly the shoot and root fresh and dry weight of maize in all La treatments (except for the root fresh and dry weight of La0 and La10 treatment). For La100 and La500 treatments, AMF increased significantly nutrition uptake (K, P, Ca and Mg content) in shoot of maize by 27.40-441.77%. For La500 treatment, AMF decreased significantly shoot La concentration by 51.53% in maize, but increased significantly root La concentration by 30.45%. In addition, AMF decreased bacterial and fungal Shannon index in La0 treatment, but increased bacterial Shannon index in La500 treatment. Both AMF and La500 affected significantly the bacterial and fungal community composition, and AMF led to more influence than La. AMF promoted the enrichment of bacteria, including Planomicrobium, Lysobacter, Saccharothrix, Agrococcus, Microbacterium, Streptomyces, Penicillium and other unclassified genus, and fungi (Penicillium) in La500, which showed the function for promoting plant growth and tolerance of heavy metal. The study revealed that AMF can regulate the rhizosphere bacterial and fungal composition and foster certain beneficial microbes to enhance the tolerance of maize under La stress. Phytoremediation assisted by AMF is an attractive approach to ameliorate REEs-contaminated soils.

Effect of arbuscular mycorrhizal symbiosis on ion homeostasis and salt tolerance-related gene expression in halophyte Suaeda salsa under salt treatments.

Halophytes can remove large quantities of salts from saline soils, so their importance in ecology has received increasing attention. Preliminary studies have shown that arbuscular mycorrhizal (AM) fungi can improve the salt tolerance of halophytes. However, few studies have focused on the molecular mechanisms and effects of AM fungi in halophytes under different salt conditions. A pot experiment was carried out to investigate the effects of Funneliformis mosseae inoculation on growth, nutrient uptake, ion homeostasis and the expression of salt tolerance-related genes in Suaeda salsa under 0, 100, 200 and 400 mM NaCl. The results showed that F. mosseae promoted the growth of S. salsa and increased the shoot Ca2+ and Mg2+ concentrations under no-salt condition and high-salt condition. In addition, AM fungi increased the K+ concentration and maintained a high K+/Na+ ratio at 400 mM NaCl, while AM fungi decreased the K+ concentration and reduced the K+/Na+ ratio at 0 mM NaCl. AM fungi downregulated the expression of SsNHX1 in shoots and the expression of SsSOS1 in roots at 400 mM NaCl. These effects may decrease the compartmentation of Na+ into leaf vacuoles and restrict Na+ transport from roots to shoots, leading to an increase in root Na+ concentration. AM symbiosis upregulated the expression of SsSOS1 in shoots and downregulated the expression of SsSOS1 and SsNHX1 in roots at 100 mM NaCl. However, regulation of the genes (SsNHX1, SsSOS, SsVHA-B and SsPIP) was not significantly different with AM symbiosis at 0 mM or 200 mM NaCl. The results revealed that AM symbiosis might induce diverse modulation strategies in S. salsa, depending on external Na+ concentrations. These findings suggest that AM fungi may play significant ecological roles in the phytoremediation of salinized ecosystems.

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands.

Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil, while the subsoil is assumed to have microbial diversity patterns similar to those of the topsoil. Here we compared patterns and drivers of microbial alpha and beta diversity in and between topsoils (0 to 10 cm) and subsoils (30 to 50 cm) of temperate grasslands in Inner Mongolia of China, covering an ∼1,500-km transect along an aridity gradient. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity remains constant or increases with increasing aridity in topsoil and decreases in subsoil, archaeal diversity decreases in topsoil and remains constant in subsoil. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation and contemporary climate but is most strongly influenced by the factor historical temperature anomaly since the Last Glacial Maximum (LGM) and by soil pH in the subsoil. Moreover, the biogeographic patterns of topsoil-subsoil community dissimilarities vary for different microbial groups and are overall most strongly influenced by soil fertility differences between depths for bacteria and by contemporary climate for archaea. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the spatial variation of bacterial diversity. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCE Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furthermore, we find important and direct legacy effects of historical climate change on the microbial diversity of subsoil yet indirect effects on topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with various climate histories.