Metal-Organic Framework-Enabled Sustainable Agrotechnologies: An Overview of Fundamentals and Agricultural Applications

With aggravated abiotic and biotic stresses from increasing climate change, metal-organic frameworks (MOFs) have emerged as versatile toolboxes for developing environmentally friendly agrotechnologies aligned with agricultural practices and safety. Herein, we have explored MOF-based agrotechnologies, focusing on their intrinsic properties, such as structural and catalytic characteristics. Briefly, MOFs possess a sponge-like porous structure that can be easily stimulated by the external environment, facilitating the controlled release of agrochemicals, thus enabling precise delivery of agrochemicals. Additionally, MOFs offer the ability to remove or degrade certain pollutants by capturing them within their pores, facilitating the development of MOF-based remediation technologies for agricultural environments. Furthermore, the metal-organic hybrid nature of MOFs grants them abundant catalytic activities, encompassing photocatalysis, enzyme-mimicking catalysis, and electrocatalysis, allowing for the integration of MOFs into degradation and sensing agrotechnologies. Finally, the future challenges that MOFs face in agrotechnologies were proposed to promote the development of sustainable agriculture practices.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem

Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.

Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition

The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (-18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Land abandonment transforms soil microbiome stability and functional profiles in apple orchards of the Chinese Losses Plateau

Land abandonment is considered an effective strategy for ecological restoration on a global scale. However, few studies have focused on how environmental heterogeneity associated with the age of land abandonment affects the assembly and potential functions of the soil microbial community. In the present study, we investigated the community assembly of soil bacteria and fungi as well as the stability of soil networks and their potential functions in the chronosequence of abandoned apple orchards. We elucidated that the Shannon diversity of bacteria and the richness of fungi increased as land abandonment progressed. In addition, land abandonment destabilized the microbial network stability but increased network complexity. Soil available nitrogen, total carbon, and moisture are the potentially important factors in shaping the soil microbial assembly. Importantly, we showed that the microbial community diversity and functional diversity presented a synchronization effect in response to the different stages of land abandonment. Furthermore, specific bacterial taxa related to carbon fixation, dissimilatory nitrate reduction, and organic phosphorus mineralization were significantly enriched during the early abandonment stage. Collectively, these results indicate that land abandonment significantly transformed soil microbiome assembly and functional adaptation during the restoration process. These findings provide valuable insights into the influence of ecological restoration on soil microbiome and ecosystem functions in arable areas.

Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0-9) on soil functions and bacterial communities in both topsoils (0-20 cm) and subsoils (20-40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.

The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems

A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.

Grass-legume mixtures maintain forage biomass under microbial diversity loss via gathering Pseudomonas in root zone soil

IMPORTANCE

Grass-legume mixtures are a common practice for establishing artificial grasslands, directly or indirectly contributing to the improvement of yield. In addition, this method helps maintain soil and plant health by reducing the use of chemical fertilizers. The impact of grass-legume mixtures on yield and its underlying microbial mechanisms have been a focus of scientific investigation. However, the benefits of mixtures in the context of soil microbial diversity loss remain a problem worthy of exploration. In this study, we examined different aboveground and belowground diversity combinations to elucidate the mechanisms by which grass-legume mixtures help maintain stable yields in the face of diversity loss. We identified the significantly enriched Pseudomonas genus microbial ASV53, which was gathered through homogeneous selection and served as a keystone in the co-occurrence network. ASV53 showed a strong positive correlation with biomass and the abundance of nitrogen-fixing genes. These findings provide a new theoretical foundation for utilizing grass-legume mixtures to enhance grass yields and address the challenges posed by diversity loss.

Sophora tonkinensis: response and adaptation of physiological characteristics, functional traits, and secondary metabolites to drought stress

The medicinal plant Sophora tonkinensis is a characteristic Chinese shrub of karst areas. The arid climate in karst areas produces high-quality S. tonkinensis; however, the mechanisms of drought tolerance are not clear, which restricts sustainable plantings of S. tonkinensis. This study involved a 20-day drought stress experiment with potted S. tonkinensis and threee soil water regimes: control (CK), mild drought (MDT), and severe drought (SDT). Plant morphology, biomass, physiological indicators, alkaloid content, and other changes under drought stress were monitored. The content of soluble sugars and proteins, and activity of antioxidant enzymes in leaves and roots were higher under drought than CK, indicating that S. tonkinensis is tolerant to osmotic stress in early drought stages. Content of matrine and oxymatrine increased gradually with increasing drought duration in the short term. The epidermis of S. tonkinensis leaves have characteristics of desert plants, including upper epidermal waxy layer, lower epidermal villi, and relatively sunken stomata, suggesting that S. tonkinensis has strong drought tolerance. In conclusion, drought stress changed the cell structure of S. tonkinensis, induced antioxidant enzyme activity and increased its resistance to drought.

The Rpf107 gene, a homolog of LOR, is required for the symbiotic nodulation of Robinia pseudoacacia

MAIN CONCLUSION

Rpf107 is involved in the infection process of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The LURP-one related (LOR) protein family plays a pivotal role in mediating plant defense responses against both biotic and abiotic stresses. However, our understanding of its function in the symbiotic interaction between legumes and rhizobia remains limited. Here, Rpf107, a homolog of LOR, was identified in Robinia pseudoacacia (black locust). The subcellular localization of Rpf107 was analyzed, and its function was investigated using RNA interference (RNAi) and overexpression techniques. The subcellular localization assay revealed that Rpf107 was mainly distributed in the plasma membrane and nucleus. Rpf107 silencing prevented rhizobial infection and hampered plant growth. The number of infected cells in the nitrogen fixation zone of the Rpf107-RNAi nodules was also noticeably lower than that in the control nodules. Notably, Rpf107 silencing resulted in bacteroid degradation and the premature aging of nodules. In contrast, the overexpression of Rpf107 delayed the senescence of nodules and prolonged the nitrogen-fixing ability of nodules. These results demonstrate that Rpf107 was involved in the infection of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The findings reveal that a member of the LOR protein family plays a role in leguminous root nodule symbiosis, which is helpful to clarify the functions of plant LOR protein family and fully understand the molecular mechanisms underlying legume-rhizobium symbiosis.

Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass

Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.

Exploring root system architecture and anatomical variability in alfalfa (Medicago sativa L.) seedlings

BACKGROUND

The growth of alfalfa (Medicago sativa L.) is significantly hampered by drought and nutrient deficiencies. The identification of root architectural and anatomical characteristics holds paramount importance for the development of alfalfa genotypes with enhanced adaptation to adverse environmental conditions. In this study, we employed a visual rhizobox system to investigate the variability in root system architecture (including root depth, root length, root tips number, etc.), anatomical features (such as cortical traits, total stele area, number and area of vessel, etc.), as well as nitrogen and phosphorus uptake across 53 alfalfa genotypes during the seedling stage.

RESULTS

Out of the 42 traits measured, 21 root traits, along with nitrogen (N) and phosphorus (P) uptake, displayed higher coefficients of variation (CVs ≥ 0.25) among the tested genotypes. Local root morphological and anatomical traits exhibited more significant variation than global root traits. Twenty-three traits with CVs ≥ 0.25 constituted to six principal components (eigenvalues > 1), collectively accounting for 88.0% of the overall genotypic variation. Traits such as total root length, number of root tips, maximal root depth, and others exhibited positive correlations with shoot dry mass and root dry mass. Additionally, total stele area and xylem vessel area showed positive correlations with N and P uptake.

CONCLUSIONS

These root traits, which have demonstrated associations with biomass and nutrient uptake, may be considered for the breeding of alfalfa genotypes that possess efficient resource absorption and increased adaptability to abiotic stress, following validation during the entire growth period in the field.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Leguminous plants significantly increase soil nitrogen cycling across global climates and ecosystem types

Leguminous plants are an important component of terrestrial ecosystems and significantly increase soil nitrogen (N) cycling and availability, which affects productivity in most ecosystems. Clarifying whether the effects of legumes on N cycling vary with contrasting ecosystem types and climatic regions is crucial for understanding and predicting ecosystem processes, but these effects are currently unknown. By conducting a global meta-analysis, we revealed that legumes increased the soil net N mineralization rate (Rmin ) by 67%, which was greater than the recently reported increase associated with N deposition (25%). This effect was similar for tropical (53%) and temperate regions (81%) but was significantly greater in grasslands (151%) and forests (74%) than in croplands (-3%) and was greater in in situ incubation (101%) or short-term experiments (112%) than in laboratory incubation (55%) or long-term experiments (37%). Legumes significantly influenced the dependence of Rmin on N fertilization and experimental factors. The Rmin was significantly increased by N fertilization in the nonlegume soils, but not in the legume soils. In addition, the effects of mean annual temperature, soil nutrients and experimental duration on Rmin were smaller in the legume soils than in the nonlegume soils. Collectively, our results highlighted the significant positive effects of legumes on soil N cycling, and indicated that the effects of legumes should be elucidated when addressing the response of soils to plants.

Pristine and Sulfidized Zinc Oxide Nanoparticles Promote the Release and Decomposition of Organic Carbon in the Legume Rhizosphere

The effects and mechanisms of zinc oxide nanoparticles (ZnO NPs) and their aging products, sulfidized (s-) ZnO NPs, on the carbon cycling in the legume rhizosphere are still unclear. We observed that, after 30 days of cultivation, in the rhizosphere soil of Medicago truncatula, under ZnO NP and s-ZnO NP treatments, the dissolved organic carbon (DOC) concentrations were significantly increased by 1.8- to 2.4-fold compared to Zn²⁺ treatments, although the soil organic matter (SOM) contents did not change significantly. Compared to Zn²⁺ additions, the additions of NPs significantly induced the production of root metabolites such as carboxylic acids and amino acids and also stimulated the growth of microbes involved in the degradations of plant-derived and recalcitrant SOM, such as bacteria genera RB41 and Bryobacter, and fungi genus Conocybe. The bacterial co-occurrence networks indicated that microbes associated with SOM formation and decomposition were significantly increased under NP treatments. The adsorption of NPs by roots, the generation of root metabolites (e.g., carboxylic acid and amino acid), and enrichment of key taxa (e.g., RB41 and Gaiella) were the major mechanisms by which ZnO NPs and s-ZnO NPs drove DOC release and SOM decomposition in the rhizosphere. These results provide new perspectives on the effect of ZnO NPs on agroecosystem functions in soil-plant systems.

Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands

Atmospheric trace gases, such as H₂ and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H₂ and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.

Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy

BACKGROUND

Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.

RESULTS

Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.

CONCLUSIONS

Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.

Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems

Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R² = 0.15, P < 0.001) and rare (R² = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.05, P < 0.05) and nitrogen (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

Fast and slow skeletal myosin binding protein-C and aging

Aging is associated with skeletal muscle strength decline and cardiac diastolic dysfunction. The structural arrangements of the sarcomeric proteins, such as myosin binding protein-C (MyBP-C) are shown to be pivotal in the pathogenesis of diastolic dysfunction. Yet, the role of fast (fMyBP-C) and slow (sMyBP-C) skeletal muscle MyBP-C remains to be elucidated. Herein, we aimed to characterize MyBP-C and its paralogs in the fast tibialis anterior (TA) muscle from adult and old mice. Immunoreactivity preparations showed that the relative abundance of the fMyBP-C paralog was greater in the TA of both adult and old, but no differences were noted between groups. We further found that the expression level of cardiac myosin binding protein-C (cMyBP-C), an important modulator of cardiac output, was lowered by age. Standard SDS-PAGE along with Pro-Q Diamond phosphoprotein staining did not identify age-related changes in phosphorylated MyBP-C proteins from TA and cardiac muscles; however, it revealed that MyBP-C paralogs in fast skeletal and cardiac muscle were highly phosphorylated. Mass spectrometry further identified glycogen phosphorylase, desmin, actin, troponin T, and myosin regulatory light chain 2 as phosphorylated myofilament proteins in both ages. MyBP-C protein-bound carbonyls were determined using anti-DNP immunostaining and found the carbonyl level of fMyBP-C, sMyBP-C, and cMyBP-C to be similar between old and adult animals. In summary, our data showed some differences regarding the MyBP-C paralog expression and identified an age-related reduction of cMyBP-C expression. Future studies are needed to elucidate which are the age-driven post-translational modifications in the MyBP-C paralogs.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation

Soil aggregates are extremely vulnerable to agricultural intensification and are important drivers of soil health, microbial diversity, and biogeochemical cycling. Despite its importance, there is a dearth of studies revealing how fertilization regimes influence diazotrophic community behind soil aggregates, as well as the potential consequences for crop yields. To do this, a two-decade fertilization of wheat-maize intercropping field experiment was conducted in Loess Plateau of China semiarid area under three treatments: no fertilizer, chemical and organic fertilizer. Moreover, we categorized soil aggregates as large macroaggregates (>2 mm), medium macroaggregates (1-2 mm), small macroaggregates (0.25-1 mm), microaggregates (< 0.25 mm) and rhizosphere soils aggregates. We found that soil aggregates exerted a much more influence on the nifH gene abundance than fertilization practices. Particularly, nifH gene abundance has been promoted with increasing the size of soil aggregates fraction without blank soil in the organic fertilization while its abundance presented contrast patterns in the chemical fertilization. Bipartite association networks indicated that different soil aggregates shaped niche differentiation of diazotrophic community behind fertilization regimes. Additionally, we found that organic fertilization strengthens the robustness of diazotrophic communities as well as increases the complexity of microbial networks by harboring keystone taxa. Mantel test results suggested that specific soil factors exerted more selective power on diazotrophic community and nifH gene abundance in the chemical fertilization. Furthermore, β-diversity and nifH gene abundance of diazotrophic communities in the soil microaggregates jointly determine the crop yields. Collectively, our findings emphasize the key role of functional community diversity in sustaining soil cycling process and crop yields under long-term fertilization, and facilitate our understanding of the mechanisms underlying diazotrophic community in response to agricultural intensification, which could pave the way to sustainable agriculture through manipulating the functional taxa.

Soil pH determines arsenic-related functional gene and bacterial diversity in natural forests on the Taibai Mountain

Arsenic-related functional genes are ubiquitous in microbes, and their distribution and abundance are influenced by edaphic factors. In arsenic-contaminated soils, soil arsenic content and pH determine the distribution of arsenic metabolizing microorganisms. In the uncontaminated natural ecosystems, however, it remains understudied for the key variable factor in determining the variation of bacterial assembly and mediating the arsenic biogeographical cycles. Here, we selected natural forest soils from southern and northern slopes along the altitudinal gradient of Taibai Mountain, China. The arsenic-related functional genes and soil bacterial community was examined using GeoChip 5.0 and high-throughput sequencing of 16S rRNA genes, respectively. It was found that arsenic-related functional genes were ubiquitous in tested forest soils. The gene arsB has the highest relative abundance, followed by arsC, aoxB, arrA, arsM, and arxA. The arsenic-related functional genes distribution on two slopes were decoupled from their corresponding bacterial community. Though there are higher abundance of bacterial communities on the northern slope than that on the southern slope, for arsenic-related functional genes, the abundance has the contrary trend which showing the more arsenic-related functional genes on the southern slope. In the top ten phyla, Proteobacteria and Actinobacteria were dominant phyla which affected the abundance of arsenic-related functional genes. Redundancy analysis and variance partitioning analysis indicated that soil pH, organic matter and altitude jointly determined the arsenic-related functional genes diversity in the two slopes of Taibai Mountain, and soil pH was a key factor. This indicates that the lower pH may shape more microbes with arsenic metabolic capacity. These findings suggested that soil pH plays a significant role in regulating the distribution of arsenic-related functional microorganisms, even for a forest ecosystem with an altitudinal gradient, and remind us the importance of pH in microbe mediated arsenic transformation.

Macrophage migration inhibitory factor MtMIF3 prevents the premature aging of Medicago truncatula nodules

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine involved in immune response in animals. However, the role of MIFs in plants such as Medicago truncatula, particularly in symbiotic nitrogen fixation, remains unclear. An investigation of M. truncatula-Sinorhizobium meliloti symbiosis revealed that MtMIF3 was mainly expressed in the nitrogen-fixing zone of the nodules. Silencing MtMIF3 using RNA interference (Ri) technology resulted in increased nodule numbers but higher levels of bacteroid degradation in the infected cells of the nitrogen-fixing zone, suggesting that premature aging was induced in MtMIF3-Ri nodules. In agreement with this conclusion, the activities of nitrogenase, superoxide dismutase and catalase were lower than those in controls, but cysteine proteinase activity was increased in nodulated roots at 28 days postinoculation. In contrast, the overexpression of MtMIF3 inhibited nodule senescence. MtMIF3 is localized in the plasma membrane, nucleus, and cytoplasm, where it interacts with methionine sulfoxide reductase B (MsrB), which is also localized in the chloroplasts of tobacco leaf cells. Taken together, these results suggest that MtMIF3 prevents premature nodule aging and protects against oxidation by interacting with MtMsrB.

Determining the contribution of microbiome complexity to the soil nutrient heterogeneity of fertile islands in a desert ecosystem

"Fertile islands" are known as hotspots of soil nutrient spatial heterogeneity in dryland ecosystems. Although soil microorganisms play critical functional roles in nutrient capture and cycling within fertile islands, our understanding of polymicrobial community roles in regulating soil nutrient distribution in fertile islands remains limited. Herein, we aim to clarify the relationships between the complexity of soil microbial (bacterial, archaeal and fungal) communities and the nutrient distribution around fertile islands. Soil samples were collected along vertical profiles at varying depths in three patches under the canopy of Hedysarum scoparium (CENTRE), at the edge (EDGE) of the canopy and outside (OUTSIDE) the canopy in an area of flowing sand. All the three microbiota have showed spatial heterogeneity around the fertile islands. Among them, bacteria had the most significant heterogeneity, and bacterial community assembly was dominated by deterministic processes. Microbial interaction patterns also showed spatial heterogeneity among different patches. More interaction complexity within microbiota was found in the bacteria in the CENTRE patch and in the fungi in the OUTSIDE patch. In addition, the proportions of among-kingdom connections were reduced under the canopies. Bacteria had the highest connectivity and centrality in the polymicrobial networks and were the most important predictor of polymicrobial interaction complexity, which may have contributed to the distribution of soil nutrients. The random forest (RF) model provided evidence that bacterial beta-diversity and the polymicrobial network complexity index can be optimal predictors of the soil multinutrient cycling index. Our study highlighted the responses of bacteria and polymicrobial interactions to fertile islands and their importance in driving soil nutrient heterogeneity. This information will help in managing soil microorganisms to provide dryland ecosystem services.

Responses of bacterial communities to microplastics: More sensitive in less fertile soils

Recently, the potential impact of microplastics (MPs) on bacterial communities has risen enormously attention due to the increasing amount of plastic waste generated nowadays. However, there is a lack of clarity due to limited studies on the responses of bacterial communities to MPs exposures in various soil ecosystems. Here, we conducted a soil microcosm experiment to analyze the potential impact of MPs on bacterial communities in farmland soil, forest soil, and sandy soil. The changes in alpha/beta diversity and co-occurrence network of bacterial communities were more significant in farmland soil amended with PS MPs (5 g kg^-1), forest soil amended with PP MPs (5 g kg^-1), and sandy soil amended with PP MPs (1 g kg^-1). Particularly, the bacterial communities in sandy soil with the least soil organic carbon content were disturbed most significantly compared to other treatments. LEfSe analysis revealed that specific bacterial taxa such as phylum Proteobacteria, Actinobacteria, Firmicutes, and genus Sphingomonas, Candidatus Udaeobacter, Gemmatimonas, were sensitive to MPs exposures. Functional annotation showed that perturbation of bacterial communities was related to organic carbon decomposition, nitrogen fixation, nitrate reduction/respiration, etc. In sum, MPs may potentially affect bacterial community structure and functions relevant to carbon/nitrogen cycles at long-term realistic field exposure.

Pristine and sulfidized zinc oxide nanoparticles alter bacterial communities and metabolite profiles in soybean rhizocompartments

A better understanding of bacterial communities and metabolomic responses to pristine zinc oxide manufacture nanoparticles (ZnO MNPs) and its sulfidized product (s-ZnO MNPs), as well as their corresponding Zn ions in rhizocompartments, critical in the plant-microbe interactions, could contribute to the sustainable development of nano-enabled agriculture. In this study, soybean (Glycine max) were cultivated in soils amended with three Zn forms, namely ZnSO₄·7H₂O, ZnO MNPs and s-ZnO MNPs at 0, 100 and 500 mg·kg^-1 for 70 days. Three Zn forms exposures profoundly decreased the bacterial alpha diversity in roots and nodules. High dose (500 mg·kg^-1) groups had a stronger impact on the bacterial beta diversity than low dose (100 mg·kg^-1) groups. In the rhizosphere soil and roots, 500 mg·kg^-1 of ZnSO₄ and s-ZnO MNPs treatments showed the largest shifts in bacterial community structure, respectively. In addition, several significant changed bacterial taxa and metabolites were found at the high dose groups, which were associated with carbon and nitrogen metabolism. PLS-DA plot showed good discrimination in metabolomic profiles of rhizosphere soil and roots between three Zn forms treatments and control. Most metabolic pathways perturbed were closely linked to oxidative stress. Overall, our study indicates either dissolved or nano-particulate Zn exposure at high dose can drastically affected bacterial communities and metabolite profiles in soybean rhizocompartments.

Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

Agricultural ecosystems are facing increasing environmental changes. Revealing ecological stability of belowground organisms is key to developing management strategies that maintain agricultural ecosystem services in a changing world. Here, we collected soils from adjacent pairs of maize and rice fields along large spatial scale across Eastern and Southeast China to investigate the importance of core microbiota as a predictor of resistance of soil microbiome (e.g. bacteria, fungi and protist) to climate changes and nutrient fertilization, and their effect on multiple ecosystem functions, representing key services for crop growth and health in agro-ecosystems. Soil microbiome in maize soils exhibited stronger resistance than that in rice soils, by considering multiple aspects of the resistance index, for example, community, phylogenetic conservation and network complexity. Community resistance of soil microbiome showed a geographic pattern, with higher resistance at lower latitudes, suggesting their stronger resistance in warmer regions. Particularly, we highlighted the role of core phylotypes in enhancing the community resistance of soil microbiome, which was essential for the maintenance of multifunctionality in agricultural ecosystems. Our results represent a significant advance in linking core phylotypes to community resistance and ecosystem functions, and therefore forecasting agro-ecosystems dynamics in response to ongoing environmental changes. These suggest that core phylotypes should be considered a key factor in enhancing agricultural sustainability and crop productivity under global change scenarios.

Lighting Up Agricultural Sustainability in the New Era through Nanozymology: An Overview of Classifications and Their Agricultural Applications

With the concept of sustainable agriculture receiving increasing attention from humankind, nanozymes, nanomaterials with enzyme-like activity but higher environmental endurance and longer-term stability than natural enzymes, have enabled agricultural technologies to be reformative, economic, and portable. Benefiting from their multiple catalytic activities and renewable nanocharacteristics, nanozymes can shine in agricultural scenarios using enzyme engineering and nanoscience, acting as sustainable toolboxes to improve agricultural production and reduce the risk to agricultural systems. Herein, we comprehensively discuss the classifications of nanozymes applied in current agriculture, including peroxidase-like, oxidase-like, catalase-like, superoxide dismutase-like, and laccase-like nanozymes, as well as their biocatalytic mechanisms. Especially, different applications of nanozymes in agriculture are deeply reviewed, covering crop protection and nutrition, agroenvironmental remediation and monitoring, and agroproduct quality monitoring. Finally, the challenges faced by nanozymes in agricultural applications are proposed, and we expect that our review can further enhance agricultural sustainability through nanozymology.

Effect of nanohydroxyapatite/biochar/sodium humate composite on phosphorus availability and microbial community in sandy soils

Phosphorus (P) is essential for crop growth as an indispensable nutrient; however, there has been growing concern over the low use efficiency of P used in current fertilizers. We synthesized and characterized a potential P fertilizer nanohydroxyapatite/biochar/sodium humate (nHAP/BC/HANa) composite. To study the impact of the composite on soil chemical properties and microbial community in sandy soils, we set up four treatments as follows: (1) biochar (BC), (2) nanohydroxyapatite (nHAP), (3) nHAP/BC/HANa composite, and (4) sodium humate (HANa) was added separately into soils amended with nHAP/BC (nHAP/BC + HANa) to compare its performance with that of the nHAP/BC/HANa composite. A key finding was that the nHAP/BC/HANa composite not only significantly increased the soil available P content and alkaline phosphatase activity but also the increased organic matter content compared to the control. Additionally, leaching losses of P in soils amended with the nHAP/BC/HANa composite were lower than those in soils amended with the nHAP/BC + HANa, which suggested that the nHAP/BC/HANa composite had great potential to decrease P loss in sandy soils. Moreover, bacterial communities were more sensitive than fungal communities to all treatments. The bacterial communities showed the most significant changes in the nHAP/BC/HANa treatments. Results from Mantel tests further indicated that the strongest correlation between bacterial communities and soil properties occurring in the nHAP/BC/HANa treatments. Random forest analysis was conducted to identify the dominant microbial taxa, such as Proteobacteria, Acidobacteria, and Gemmatimonadetes, for predicting changes in soil properties. There was an asymptotical transition in bacterial community assembly processes from stochastic to deterministic in the nHAP/BC/HANa treatments. In conclusion, we demonstrated that nHAP/BC/HANa composite had the remarkable contribution to soil P availability in sandy soils, and simultaneously promoted the bacterial functions potential for P cycling, which present valuable insights to the development of potential P fertilizer.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of ¹⁵N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region

Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern, and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates.

Arthrobacter rhizosphaerae sp. nov., isolated from wheat rhizosphere

Gram-stain-positive, aerobic, non-spore-forming strains CCNWLXL 1-35^T, CCNWLXL 12-2 and CCNWLXL 21-a, were isolated from wheat rhizosphere from Yangling, Shaanxi Province, China. Comparison of the 16S rRNA gene sequences showed that they belonged to the genus Arthrobacter and were closely related to Arthrobacter globiformis NBRC 12137^T (97.95% similarity). Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed these strains constituted a single species. The major fatty acids was anteiso-C_15:0. The polar lipids consist of diphosphatidylglycerol, phsophatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and glycolipid. The predominant menaquinone was MK-9. The peptidoglycan type was A4α. Thus, these strains were classified as representing a novel species in the genus Arthrobacter, for which the name Arthrobacter rhizosphaerae sp. nov. is proposed. The type strain is CCNWLXL 1-35^T (=JCM 34638^T, =CCTCC AB 2021087^T) and additional strains are CCNWLXL 12-2 (=JCM 35018, =CCTCC AB 2021546), CCNWLXL 21-a (=JCM 35019, =CCTCC AB 2021545).

Halophytes increase rhizosphere microbial diversity, network complexity and function in inland saline ecosystem

Salinization is an important global environmental problem influencing sustainable development of terrestrial ecosystems. Salt-tolerant halophytes are often used as a promising approach to remedy the saline soils. Yet, how rhizosphere microbes' association and functions vary with halophytes in saline ecosystems remains unclear, restricting our ability to assess the role of halophytes in remedying saline ecosystems. Herein, we examined bacterial and fungal diversities, compositions, and co-occurrence networks in the rhizospheres of six halophytes and bulk soils in a semiarid inland saline ecosystem, and related these parameters to microbial functions. The microbiomes were more diverse and complex and microbial activity and residues were higher in rhizospheres than bulk soils. The connections of taxa in the rhizosphere microbial communities increased with fungi-fungi and bacteria-fungi connections and fungal diversity. The proportion of the fungi-related central connections were larger in rhizospheres (13-73%) than bulk soils (3%). Moreover, microbial activity and residues were significantly correlated with microbial composition and co-occurrence network complexity. These results indicated that enhanced association between fungi and bacteria increased microbial co-occurring network complexity in halophytes rhizosphere, which contributed to the higher microbial functions (microbial activities and residue) in this inland saline ecosystem.

Regulation of soil micro-foodwebs to root secondary metabolites in cultivated and wild licorice plants

The diversity of soil eukaryotes and micro-foodwebs are only partially understood. Moreover, how they affect secondary metabolites in plant roots under distinct soil environment is not well elucidated. By combining multiple statistical analyses and network constructions, variations in soil eukaryotic diversity, community assembly processes and potential associations of holistic microbiotas were investigated in the bulk and rhizosphere soils of cultivated and wild licorice, and their regulatory patterns for root secondary metabolites were elucidated. The protistan communities displayed lower alpha diversity, more varied beta diversity patterns, and higher stochastic processes, as compared with fungal communities. Soil fungi individually played a more essential role than soil protists in the regulation of root secondary metabolites. Furthermore, rhizosphere soil was associated with more complicated networks than bulk soil; and wild licorice was associated with more complicated networks than cultivated licorice. Specific responsive modules resulting from networks were essential for the regulation of root secondary metabolites and were mostly affected by edaphic properties. Moreover, these modules directly or indirectly regulated the root secondary metabolites to varying degrees in the presence of soil protists. This indicated that the secondary metabolites were affected by associations between protistan, fungal and bacterial groups, and not merely by individual types of microorganisms in agricultural ecosystems. This study provides insight into the responses of root secondary metabolites to different groups of soil eukaryotic diversity and micro-foodwebs. The results have implications for comprehensively understanding the characteristics of the separate and combined roles of microbiotas for environmental management of licorice plantation ecosystem.

Rhizobial HmuSpSym as a heme-binding factor is required for optimal symbiosis between Mesorhizobium amorphae CCNWGS0123 and Robinia pseudoacacia

Nitrogen-fixing root nodules are formed by symbiotic association of legume hosts with rhizobia in nitrogen-deprived soils. Successful symbiosis is regulated by signals from both legume hosts and their rhizobial partners. HmuS is a heme degrading factor widely distributed in bacteria, but little is known about the role of rhizobial hmuS in symbiosis with legumes. Here, we found that inactivation of hmuS_pSym in the symbiotic plasmid of Mesorhizobium amorphae CCNWGS0123 disrupted rhizobial infection, primordium formation, and nitrogen fixation in symbiosis with Robinia pseudoacacia. Although there was no difference in bacteroids differentiation, infected plant cells were shrunken and bacteroids were disintegrated in nodules of plants infected by the ΔhmuS_pSym mutant strain. The balance of defence reaction was also impaired in ΔhmuS_pSym strain-infected root nodules. hmuS_pSym was strongly expressed in the nitrogen-fixation zone of mature nodules. Furthermore, the HmuS_pSym protein could bind to heme but not degrade it. Inactivation of hmuS_pSym led to significantly decreased expression levels of oxygen-sensing related genes in nodules. In summary, hmuS_pSym of M. amorphae CCNWGS0123 plays an essential role in nodule development and maintenance of bacteroid survival within R. pseudoacacia cells, possibly through heme-binding in symbiosis.

Agricultural Management Drive Bacterial Community Assembly in Different Compartments of Soybean Soil-Plant Continuum

Flowering stage of soybean is an important agronomic trait, which is important for soybean yield, quality and adaptability, and is the external expression of integrating external environmental factors and endogenous signals of the plant itself. Cropping system can change soil properties and fertility, which in turn determine plant growth and yield. The microbial community is the key regulator of plant health and production performance. Currently, there is limited understanding of the effects of cropping systems on microbial community composition, ecological processes controlling community assembly in different soil-plant continuum compartments of soybean. Here, we hope to clarify the structure and assembly process of different soybean compartments bacterial community at flowering stage through our work. The results showed that intercropping decreased the species diversity of rhizosphere and phyllosphere, and phylloaphere microbes mainly came from rhizosphere. FAPROTAX function prediction showed that indicator species sensitive to intercropping and crop rotation were involved in nitrogen/phosphorus cycle and degradation process, respectively. In addition, compared to the continuous cropping, intercropping increased the stochastic assembly processes of bacterial communities in plant-associated compartments, while crop rotation increased the complexity and stability of the rhizosphere network and the deterministic assembly process. Our study highlights the importance of intercropping and crop rotation, as well as rhizosphere and phyllosphere compartments for future crop management and sustainable agricultural regulation of crop microbial communities.

Distinct response patterns of bacterial communities in Ag- and ZnO-rGO nanocomposite-amended silt loam soils

The widespread application of metal-based nanoparticle (MNPs)/reduced graphene oxide (rGO) composites inevitably leads to their release into soils. However, we lack a detailed understanding of the bacterial community response to MNPs-rGO exposure in farmland soils. Here, we conducted a soil microcosm experiment to analyze the potential impact of MNPs-rGO on bacterial communities in two field soils via high-throughput sequencing. The change in alpha diversity of bacterial communities was more susceptible to Ag-rGO and ZnO-rGO treatments than CuO-rGO. In both soils, MNPs-rGO significantly changed the bacterial community structure even at a low dose (1 mg kg^-1). The bacterial community structure was most strongly affected by Ag-rGO at 30 days, but the greatest changes occurred in ZnO-rGO at 60 days. The differences in soil properties could shape bacterial communities to MNPs-rGO exposure. Distance-based redundancy analysis and functional annotation of prokaryotic taxa showed that some bacterial species associated with nitrogen cycling were greatly influenced by Ag-rGO and ZnO-rGO exposure. In sum, Ag-rGO and ZnO-rGO may potentially affect bacterial communities and nitrogen turnover under long-term realistic field exposure. These findings present a perspective on the response of bacterial communities to MNPs-rGO and provide a fundamental basis for estimating the ecological behavior of MNPs-rGO.

Core microbiota drive functional stability of soil microbiome in reforestation ecosystems

Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.

Microbial traits determine soil C emission in response to fresh carbon inputs in forests across biomes

Soil priming is a microbial-driven process, which determines key soil-climate feedbacks in response to fresh carbon inputs. Despite its importance, the microbial traits behind this process are largely undetermined. Knowledge of the role of these traits is integral to advance our understanding of how soil microbes regulate carbon (C) emissions in forests, which support the largest soil carbon stocks globally. Using metagenomic sequencing and ¹³ C-glucose, we provide unprecedented evidence that microbial traits explain a unique portion of the variation in soil priming across forest biomes from tropical to cold temperature regions. We show that microbial functional profiles associated with the degradation of labile C, especially rapid simple sugar metabolism, drive soil priming in different forests. Genes involved in the degradation of lignin and aromatic compounds were negatively associated with priming effects in temperate forests, whereas the highest level of soil priming was associated with β-glucosidase genes in tropical/subtropical forests. Moreover, we reconstructed, for the first time, 42 whole bacterial genomes associated with the soil priming effect and found that these organisms support important gene machinery involved in priming effect. Collectively, our work demonstrates the importance of microbial traits to explain soil priming across forest biomes and suggests that rapid carbon metabolism is responsible for priming effects in forests. This knowledge is important because it advances our understanding on the microbial mechanisms mediating soil-climate feedbacks at a continental scale.

Multiple Metabolic Phenotypes as Screening Criteria Are Correlated With the Plant Growth-Promoting Ability of Rhizobacterial Isolates

Efficient screening method is the prerequisite for getting plant growth-promoting (PGP) rhizobacteria (PGPR) which may play an important role in sustainable agriculture from the natural environment. Many current traditional preliminary screening criteria based on knowledge of PGP mechanisms do not always work well due to complex plant-microbe interactions and may lead to the low screening efficiency. More new screening criteria should be evaluated to establish a more effective screening system. However, the studies focused on this issue were not enough, and few new screening criteria had been proposed. The aim of this study was to analyze the correlation between the metabolic phenotypes of rhizobacterial isolates and their PGP ability. The feasibility of using these phenotypes as preliminary screening criteria for PGPR was also evaluated. Twenty-one rhizobacterial isolates were screened for their PGP ability, traditional PGP traits, and multiple metabolic phenotypes that are not directly related to PGP mechanisms, but are possibly related to rhizosphere colonization. Correlations between the PGP traits or metabolic phenotypes and increases in plant agronomic parameters were analyzed to find the indicators that are most closely related to PGP ability. The utilization of 11 nutrient substrates commonly found in root exudates, such as D-salicin, β-methyl-D-glucoside, and D-cellobiose, was significantly positively correlated with the PGP ability of the rhizobacterial isolates. The utilization of one amino acid and two organic acids, namely L-aspartic acid, α-keto-glutaric acid, and formic acid, was negatively correlated with PGP ability. There were no significant correlations between four PGP traits tested in this study and the PGP ability. The ability of rhizobacterial isolates to metabolize nutrient substrates that are identical or similar to root exudate components may act as better criteria than PGP traits for the primary screening of PGPR, because rhizosphere colonization is a prerequisite for PGPR to affect plants.

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity-ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.

Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

Regulation of root secondary metabolites by partial root-associated microbiotas under the shaping of licorice ecotypic differentiation in northwest China

Interactions between plant hosts and their microbiotas are becoming increasingly evident, while the effects of plant communities on microbial communities in different geographic environments are poorly understood. Here, the differentiation of licorice plant ecotypes and the distribution of root-associated microbiotas were investigated across five sampling sites in northwest China. The interactions between the environment, plant and microbial communities, and their effects on licorice root secondary metabolites, were elucidated. The plant community was clearly differentiated into distinct ecotypes based on genotyping-by-sequencing and was primarily driven by geographic distance and available soil nitrogen. The bulk soil and root-associated microbiotas (rhizosphere soil and root endosphere) partially correlated with plant community, but all were significantly discriminated by plant clade. Moreover, these microbiotas were explained to different extents by distinct combinations of environment, geography, and plant community. Similarly, three structural equation models showed that licorice root secondary metabolites were complicatedly modulated by multiple abiotic and biotic factors, and were mostly explained by these factors in the rhizosphere model. Collectively, the results provide novel insights into the role of environment-plant-microbiota interactions in regulating root secondary metabolites. That should be accounted for when selecting appropriate licorice planting sites and management measures.