Crop rotation stage has a greater effect than fertilisation on soil microbiome assembly and enzymatic stoichiometry

Regulatory effects of nano-carbon on poplar growth and rhizosphere soil organic carbon accumulation

The positive effects of nano-carbon on plant growth and soil C sequestration within the rhizosphere have been widely recognized. Nevertheless, information is seriously deficient in understanding the underlying mechanisms based on microbial communities and carbon cycle functional genes. Here, metagenomic sequencing was employed to explore different responses of poplar seedling growth and organic carbon fractions to nano-carbon fertilizers at concentrations of 0 ml/kg (CK), 5 ml/kg (NC-5), 10 ml/kg (NC-10) and 20 ml/kg (NC-20). We observed that, after 120 days of nano-carbon fertilizers treatments, the growth indexes (height and biomass) of poplar were significantly increased by 37.83-173.13 %, and C fractions in the rhizosphere soil were significantly increased by 1.64-8.16 % with the NC-5 treatment having a greater impact on organic carbon components than the NC-10 and NC-20 treatments. Compared to CK, the additions of nano-carbon fertilizers significantly increased the content of total nitrogen (TN), nitrate nitrogen (NN), and available potassium (AK) in the rhizosphere soil and decreased the pH, and improved stochastic processes in microbial communities, which elevates the abundance of microbes involved in carbon fixation (e.g., Proteobacteria, Actinobacteria) and carbon-cycling genes. In addition, network complexity and stability of microbes were significantly enhanced by nano-carbon treatments. Structural equation model indicated that microbial community assembly processes directly alter rhizosphere SOC accumulation. Carbon functional genes influenced by microbial structure have positive effects on biomass of poplar and SOC contents. Our observations provide key evidence for evaluating how nano-carbon fertilizers may influence functional changes in C cycle that are mediated by microbial synergy.

Microbiome Migration from Soil to Leaves in Maize and Rice

The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant-microbe interactions for sustainable agriculture.

Understanding the microbiome-crop rotation nexus in karst agricultural systems: insights from Southwestern China

Understanding how soil properties and microbial communities respond to crop rotation is essential for the sustainability of agroecosystems. However, there has been limited research on how crop rotation alters below-ground microbial communities in soils with serious bacterial wilt within the karst agricultural system. This study investigated the effects of continuous planting of corn, tobacco, and tobacco-corn rotation on soil microbial communities in the karst regions of Southwestern China. High-throughput sequencing was used to evaluate the responses of the soil microbial community structure to crop monoculture and rotation patterns. As expected, the tobacco-corn rotation mitigated the negative effects of continuous cropping and reduced soil acidification. The tobacco-corn rotation also significantly altered the composition of microbial communities and promoted plant growth by fostering a higher abundance of beneficial microorganisms. The predominant bacteria genera Sphingomonas and Gaiella and the predominant fungal genera Mortierella and Saitozyma were identified as discriminant biomarkers that are critical to soil ecosystem health. pH, available potassium (AK), and available phosphorus (AP) were the primary soil factors related to the soil microbiome assembly. This study aimed to demonstrate the association between crop rotation and microbiomes, suggesting that altering cultivation patterns could enhance karst agricultural systems.

Introduction of Panax notoginseng into pine forests significantly enhances the diversity, stochastic processes, and network complexity of nitrogen-fixing bacteria in the soil

Introduction

Nitrogen-fixing bacteria (NFB) have a pivotal impact on the nitrogen cycle within agroforestry systems. The organic management of the Panax notoginseng (sanqi)-Pinus armandii agroforestry (SPA) system resulted in nitrogen deficiency because of the lack of application of chemical fertilizers. Therefore, assessing the variability in NFB due to the cultivation of sanqi in the SPA system becomes crucial.

Methods

The seasonal dynamics in the abundance, diversity, and community structure of NFB in the soil of monocropping pine (MP) and SPA systems were assessed using real-time quantitative polymerase chain reaction and high-throughput sequencing technology.

Results and discussion

Sanqi cultivation triggered a decrease in the abundance of NFB but increased α diversity. Additionally, significant differences in the community structure of NFB were noted between the MP and SPA systems. Moreover, the abundance of Bradyrhizobium and Azospirillum increased in the soil after sanqi was cultivated. Furthermore, the cultivation of sanqi broadened the ecological niche breadth of NFB and increased the stochasticity in its community structure assembly (i.e., dispersal limitation). Additionally, the SPA system increased the network complexity but not the stability of NFB. The structural equation model (SEM) revealed that pH directly impacted the network complexity and stability of NFB in the SPA system. Sanqi cultivation positively influences the community characteristics of NFB in the soil in the SPA system. Our study provides new insights into nitrogen cycling and utilization in the SPA system.

Optimizing nitrogen fertilization rate to achieve high yield and high soil quality in paddy ecosystems with straw incorporation

Plastic film mulching is a potentially water-saving cultivation strategy, while straw return coupled with nitrogen (N) fertilization can ensure sustainable soil productivity and increased soil organic matter (SOM) sequestration. Nevertheless, a comprehensive understanding of how soil quality and agronomic productivity respond to long-term N fertilization and straw incorporation practices under non-flooded conditions with plastic film mulching remains elusive. Herein, a 15-year field experiment with straw incorporation practices (straw return and no straw return) under various N fertilization rates (N0, N1, N2, N3, and N4: 0, 45, 90, 135, and 180 kg N ha-1, respectively) was conducted to explore their long-term effects. Compared with N0, N fertilization significantly improved rice yield (52.2-74.0%) and plant N uptake (50.1-96.8%). Effective panicle density was the primary component affecting rice yield under different N conditions. However, N use efficiency was lowest under 180 kg N ha-1. N fertilization primarily impacted rice yield by directly supplying N for rice growth, accounting for 79% of the rice yield variation. The modest enhancement in rice yield resulting from straw return was attributed to its positive effects on soil physicochemical properties. Straw return increased alkali-hydrolyzable nitrogen, Olsen-phosphorus, and NH4OAc-exchangeable potassium by 3.4%, 10.4%, and 38.5%, respectively. N fertilization rates altered the impact of straw return on SOM; SOM increased in N2 and N4 under straw return, whereas no difference was observed between the straw management groups under N0, N1, or N3 fertilization. Moreover, while higher N fertilization rates decreased the soil quality index (SQI), straw return offset this negative effect. Considering rice yield, N use efficiency, and SQI, straw return treatment coupled with N application rate of 135 kg ha-1 was deemed suitable for sustainable rice production with plastic film mulching.

Understanding the influence of plant genetic factors on rhizosphere microbiome assembly in Panax notoginseng

Introduction

Functional rhizosphere microbiomes (FRM) are critical for plant health and yield. However, the ecological succession of FRM and their links to plant genetic factors across the life cycle of perennial plants remain poorly understood.

Methods

This study profiled FRM, including plant-beneficial bacteria (PBB) and fungal plant pathogens (FPP), across different developmental stages of Panax notoginseng.

Results

The biodiversity of both PBB and FPP were significantly higher in rhizosphere compared with farmland soil, and exhibited different succession patterns with plant growth. The relative abundance of PBB, but not FPP, decreased after plant cultivation. There were significantly negative correlations between FPP and PBB, particularly the biocontrol subgroup (ρ = -0.56, p < 0.001). The antagonistic effects of biocontrol bacteria against fungal pathogens were further validated by in vitro assays. The fitting of neutral community model indicated that the deterministic assembly of PBB, especially the biocontrol subgroup, was the strongest at the 3rd-year root growth stage of P. notoginseng. Plant genes involved in protein export, biosynthesis of alkaloids and amino acids were identified as drivers of the deterministic assembly of biocontrol subcommunity by RNA-Seq analysis. Additionally, a total of 13 transcription factors potentially regulating the expression of these biosynthesis genes were identified through co-expression network. In summary, this study unveils the succession patterns of FRM throughout the life cycle of P. notoginseng and the underlying plant genetic mechanisms, providing valuable insights for developing new plant disease management strategies by manipulating microbes.

Is enzymatic stoichiometry a reliable indicator of microbial limitations in carbon, nitrogen, or phosphorus?

The enzymatic stoichiometry approach is based on the assumption that the metabolic and stoichiometric requirements of soil microorganisms are reflected in the production of enzymes targeting specific nutrient resources, making enzyme activities a useful tool for assessing microbial nutrient limitations. In this approach, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG) (occasionally combined with leucine aminopeptidase, LAP), and acid/alkaline phosphatase (AP) are used as proxies for the broader suite of enzymes responsible for catalyzing complex substrates containing carbon (C), nitrogen (N), and phosphorus (P), respectively, because these enzymes catalyze the terminal reactions that release products containing C, N, and P. The fundamental premise of the approach can thus be reformulated as follows: BG:NAG and BG:AP ratios reflect the relative limitations of C versus N and C versus P, respectively, with higher ratios indicating stronger C limitation. Previous meta-analyses have suggested that the enzymatic stoichiometry approach is unreliable, as N and P fertilization often leads to reduction in BG:NAG and BG:AP, respectively, contradicting the predictions of the approach. However, some researchers question the validity of assessing enzymatic stoichiometry after the artificial addition of nutrients via fertilizers. For providing more convincing evidence, this study conducted a meta-analysis to assess the impact of incorporating various C sources, largely representative of those found in natural ecosystems-glucose, cellulose, and plant residues-on the BG:NAG or BG:AP ratios. The results demonstrated that a considerable number of data points exhibited elevated values (i.e., C addition accelerated C limitations), undoubtedly contradicting the fundamental premise of the approach. These findings highlight the unreliability of enzymatic stoichiometry as an indicator of microbial nutrient limitation.

Comparative analysis of crop rotation systems: the impact of ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca) residues on growth of Chinese cabbage (Brassica rapa var. chinensis)

Continuous cropping in greenhouse cultivation often leads to increased pest and disease problems, reducing crop quality and yield. Crop rotation is a common strategy to address these issues. This study compared the growth of Chinese cabbage (Brassica rapa var. chinensis) following rotations with ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca). The Chinese cabbage exhibited normal growth following ginger rotation but showed abnormal growth after sponge gourd rotation. The study investigated the underlying causes by analyzing soil physicochemical properties and rhizosphere microbial communities of Chinese cabbage using 16S rRNA and ITS sequencing. The results revealed that soil from ginger-Chinese cabbage rotation had higher levels of soil organic carbon (SOC) and available phosphorus (AP), but lower total nitrogen (TN) and available potassium (AK). Despite similar alpha-diversity for both bacterial and fungal communities, distinct bacterial and fungal community structures between two rotation cropping systems were observed. This suggests that even if the alpha-diversity does not change, the composition of the microbial community can shift in ways that might influence soil health and plant growth. Furthermore, redundancy analysis revealed a significant correlation between microbial community structures and soil physicochemical properties of two rotation cropping systems. The SOC and TN were revealed to be the most significant of the investigated soil physicochemical parameters with respect to the variation of both bacterial and fungal assemblages, respectively. The identified biomarkers in bacterial community composition further emphasize the potential for specific microbes to influence crop health positively or negatively. We found that the indicator genera of the bacterial community composition of the ginger-Chinese cabbage rotation system were Amycolatopsis (genus), Pseudonocardiales (order), Pseudonocardiaceae (family), and Amycolatopsis mediterranei, which are known as producers of secondary metabolites, such as antibiotics. These findings highlight the importance of crop selection in rotation strategies for optimizing agricultural outcomes.

Eucalyptus and Native Broadleaf Mixed Cultures Boost Soil Multifunctionality by Regulating Soil Fertility and Fungal Community Dynamics

The growing recognition of mixed Eucalyptus and native broadleaf plantations as a means of offsetting the detrimental impacts of pure Eucalyptus plantations on soil fertility and the wider ecological environment is accompanied by a clear and undeniable positive impact on forest ecosystem functions. Nevertheless, the question of how mixed Eucalyptus and native broadleaf plantations enhance soil multifunctionality (SMF) and the mechanisms driving soil fungal communities remains unanswered. In this study, three types of mixed Eucalyptus and native broadleaf plantations were selected and compared with neighboring evergreen broadleaf forests and pure Eucalyptus plantations. SMF was quantified using 20 parameters related to soil nutrient cycling. Partial least squares path modeling (PLS-PM) was employed to identify the key drivers regulating SMF. The findings of this study indicate that mixed Eucalyptus and native broadleaf plantations significantly enhance SMF. Mixed Eucalyptus and native broadleaf plantations led to improvements in soil properties (7.60-52.22%), enzyme activities (10.13-275.51%), and fungal community diversity (1.54-29.5%) to varying degrees compared with pure Eucalyptus plantations. Additionally, the mixed plantations exhibit enhanced connectivity and complexity in fungal co-occurrence networks. The PLS-PM results reveal that soil properties, fungal diversity, and co-occurrence network complexity directly and positively drive changes in SMF. Furthermore, soil properties exert an indirect influence on SMF through their impact on fungal diversity, species composition, and network complexity. The findings of this study highlight the significant role of mixed Eucalyptus and native broadleaf plantations in enhancing SMF through improved soil properties, fungal diversity, and co-occurrence network complexity. This indicates that incorporating native broadleaf species into Eucalyptus plantations can effectively mitigate the negative impacts of monoculture plantations on soil health and ecosystem functionality. In conclusion, our study contributes to the understanding of how mixed plantations influence SMF, offering new insights into the optimization of forest management and ecological restoration strategies in artificial forest ecosystems.

Microplastic-contamination can reshape plant community by affecting soil properties

Microplastics, as emerging contaminants, pose a serious threat to terrestrial ecosystems, yet their impact on plant communities remains largely unexplored. This study utilized the soil seed bank to establish naturally germinated plant communities and investigated the effects of polyethylene (PE) and polypropylene (PP) on community characteristics. Additionally, the study aimed to elucidate the mechanisms by which variations in soil properties influenced plant community. The results indicated that microplastics led to a significant increase in soil available potassium (AK), likely due to alterations in soil microorganism proliferation. Furthermore, microplastics caused a decrease in soil salinity, total phosphorus (TP), and ammonium nitrogen (AN). Additionally, plant community composition shifted, resulting in reduced stability and niche breadth of dominant species. Microplastics also impacted niche overlap and interspecific associations among dominant species, possibly due to the reduced accessibility of resources for dominant species. Salinity, AK, and TP were identified as major drivers of changes in niche breadth, niche overlap, and community stability, with TP exerting the strongest impact on plant community composition. These findings provide valuable insights for the restoration of plant communities in coastal saline-alkali wetland contaminated by microplastics.

Soil bacterial diversity and community structure of Suaeda glauca vegetation in the Hetao Irrigation District, Inner Mongolia, China

Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the saline-alkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO4 2-, K+ and Mg2+ concentrations. The electrical conductivity (EC), soluble ions (Na+, CO3 2- + HCO3 -, K+, Ca2+, Mg2+, and SO4 2+), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes.

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease

BACKGROUND

Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.

RESULTS

In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).

CONCLUSIONS

Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.

Improvement and the relationship between chemical properties and microbial communities in secondary salinization of soils induced by rotating vegetables

Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.

Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process

Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.

Effect of biodegradable PBAT microplastics on the C and N accumulation of functional organic pools in tropical latosol

Microplastics (MPs) pollution is becoming an emerging global stressor for soil ecosystems. However, studies on the impacts of biodegradable MPs on soil C sequestration have been mainly based on bulk C quantity, without considering the storage form of C, its persistency and N demand. To address this issue, the common poly (butylene adipate-co-terephthalate) (PBAT) was used as the model, and its effects on soil functional organic pools, including mineral-associated (MAOM), particulate (POM) and dissolved organic matter (DOM), were investigated from the novel coupled perspective of C and N stocks. After adding PBAT-MPs, the contents of soil POM-C, DOM-C, and MAOM-C were increased by 546.9 %-697.8 %, 54.2 %-90.3 %, and 13.7 %-18.9 %, respectively. Accordingly, the total C increased by 116.0 %-191.1 %. Structural equation modeling showed that soil C pools were regulated by PBAT input and microbial metabolism associated with C and N enzymes. Specifically, PBAT debris could be disguised as soil C to promote POM formation, which was the main pathway for C accumulation. Inversely, the MAOM-C and DOM-C formation was attributed to the PBAT microbial product and the selective consumption in DOM-N. Random forest model confirmed that N-activated (e.g., Nitrospirae) and PBAT-degrading bacteria (e.g., Gemmatinadetes) were important taxa for soil C accumulation, and the key enzymes were rhizopus oryzae lipas, invertase, and ammonia monooxygenase. The soil N accumulation was mainly related to the oligotrophic taxa (e.g., Chloroflexi and Ascomycota) associated with aggregate formation, decreasing the DOM-N by 46.9 %-84.3 %, but did not significantly change the total N storage and other N pools. Collectively, the findings highlight the urgency to control the nutrient imbalance risk of labile N loss and recalcitrant C enrichment in POM to avoid the depressed turnover rate of organic matter in MPs-polluted soil.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation

Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.

Linkages of microbial community structure and root exudates: Evidence from microbial nitrogen limitation in soils of crop families

Rhizosphere microorganisms are critical for crop nutrient cycling and soil ecological functions in agroecosystem soils; however, there is limited information regarding the role of root exudates in determining soil microbial communities and functions in plant-soil systems, especially for microbial nutrient limitations. In the present study, rhizosphere soil samples were collected from the main food crop families, including maize, soybean, potato, and buckwheat, representing the cereals, Leguminosae, Solanaceae, and Polygonaceae families, in the northern Loess Plateau, China, to investigate soil microbial co-occurrences and assembly processes and the relationship between soil microbes and root exudates. The results showed that the crop families greatly regulated the soil microbial community composition and assembly, and all microorganisms of the four species were subjected to N limitation via the vector analysis. The topological properties of the soil microbial networks varied with the crop family, demonstrating that the ecological relationships of bacterial taxa are more complex than those of fungi. Stochastic processes were more important in stimulating assembly across the four crop families; the non-dominated process governed >60 % of the critical ecological turnover in community assembly, whereas dispersal limitation was the key factor influencing fungal community assembly. Furthermore, the metabolic profiles of root exudates in response to microbial N limitation varied by family. Microbial function and metabolic limitations were strongly associated with variations in root exudates, especially amino acids and organic acids, which were directly facilitated by crop families. Our results highlight the key roles of root exudates in stimulating microbial community structure and ecological functions from the perspective of microbial nutrient limitation and improve our understanding of plant-microbe interactions in agricultural ecosystems.

The relationship between shifts in the rhizosphere microbial community and root rot disease in a continuous cropping American ginseng system

The root rot disease causes a great economic loss, and the disease severity usually increases as ginseng ages. However, it is still unclear whether the disease severity is related to changes in microorganisms during the entire growing stage of American ginseng. The present study examined the microbial community in the rhizosphere and the chemical properties of the soil in 1-4-year-old ginseng plants grown in different seasons at two different sites. Additionally, the study investigated ginseng plants' root rot disease index (DI). The results showed that the DI of ginseng increased 2.2 times in one sampling site and 4.7 times in another during the 4 years. With respect to the microbial community, the bacterial diversity increased with the seasons in the first, third, and fourth years but remained steady in the second year. The seasonal changing of relative abundances of bacteria and fungi showed the same trend in the first, third, and fourth years but not in the second year. Linear models revealed that the relative abundances of Blastococcus, Symbiobacterium, Goffeauzyma, Entoloma, Staphylotrichum, Gymnomyces, Hirsutella, Penicillium and Suillus spp. were negatively correlated with DI, while the relative abundance of Pandoraea, Rhizomicrobium, Hebeloma, Elaphomyces, Pseudeurotium, Fusarium, Geomyces, Polyscytalum, Remersonia, Rhizopus, Acremonium, Paraphaeosphaeria, Mortierella, and Metarhizium spp. were positively correlated with DI (P < 0.05). The Mantel test showed that soil chemical properties, including available nitrogen, phosphorus, potassium, calcium, magnesium, organic matter, and pH, were significantly correlated to microbial composition. The contents of available potassium and nitrogen were positively correlated with DI, while pH and organic matter were negatively correlated with DI. In summary, we can deduce that the second year is the key period for the shift of the American ginseng rhizosphere microbial community. Disease aggravation after the third year is related to the deterioration of the rhizosphere microecosystem.

The shift of soil microbial community induced by cropping sequence affect soil properties and crop yield

Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-producing regions of northeastern China. To evaluate the effects of different cropping sequences under conventional fertilization practices on soil properties, microbial communities, and crop yield, six types of plant cropping systems were performed, including soybean monoculture, wheat-soybean rotation, wheat-maize-soybean rotation, soybean-maize-maize rotation, maize-soybean-soybean rotation and maize monoculture. Our results showed that compared with the single cropping system, soybean and maize crop rotation in different combinations or sequences can increase soil total organic carbon and nutrients, and promote soybean and maize yield, especially using soybean-maize-maize and maize-soybean-soybean planting system. The 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing showed that different cropping systems had different effects on bacterial and fungal communities. The bacterial and fungal communities of soybean monoculture were less diverse when compared to the other crop rotation planting system. Among the different cropping sequences, the number of observed bacterial species was greater in soybean-maize-maize planting setup and fungal species in maize-soybean-soybean planting setup. Some dominant and functional bacterial and fungal taxa in the rotation soils were observed. Network-based analysis suggests that bacterial phyla Acidobacteria and Actinobacteria while fungal phylum Ascomycota showed a positive correlation with other microbial communities. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) result showed the presence of various metabolic pathways. Besides, the soybean-maize-maize significantly increased the proportion of some beneficial microorganisms in the soil and reduced the soil-borne animal and plant pathogens. These results warrant further investigation into the mechanisms driving responses of beneficial microbial communities and their capacity on improving soil fertility during legume cropping. The present study extends our understanding of how different crop rotations effect soil parameters, microbial diversity, and metabolic functions, and reveals the importance of crop rotation sequences. These findings could be used to guide decision-making from the microbial perspective for annual crop planting and soil management approaches.