Changes in microbial metabolic C- and N- limitations in the rhizosphere and bulk soils along afforestation chronosequence in desertified ecosystems

Temporal variation of microbial nutrient limitation in citrus plantations: insights from soil enzyme stoichiometry

Soil enzyme carbon (C): nitrogen (N): phosphorous (P) stoichiometry and their vector model has been widely used to elucidate the balance between microbial nutrient requirements and soil nutrient availability. However, limited knowledge is available on the dynamics of soil enzyme stoichiometry and microbial nutrient limitation following afforestation, especially in the economic forest. In this study, the effects of citrus plantation on C: N: P stoichiometry were assessed through a comparative study between cropland and citrus plantations with varying durations of afforestation (i.e., 3, 15, 25, and 35 years). It was found that the C, N, and P contents in the soil (SOC, STN, and STP), microbial biomass (MBC, MBN, and MBP), as well as the activities of C-, N-, and P-acquiring enzymes (BG, NAG, and AP), were 1.02 to 2.51 times higher than those in cropland. Additionally, C, N, and P contents in soil and microbial biomass increased consistently with increasing afforestation time. While the activities of C-, N-, and P-acquiring enzymes increased from 3 years to 25 years and then significantly decreased. In addition to NAG: AP, the stoichiometry of C, N, and P in soil (SOC: STN, SOC: STP, and STN: STP) and microbial biomass (MBC: MBN, MBC: MBP, and MBN: MBP), along with BG: NAG, exhibited a decline of 7.69-27.38% compared to cropland. Moreover, the majority of the C: N: P stoichiometry in soil, microbial biomass, and enzymes consistently decreased with increasing afforestation time, except for SOC: STN and NAG: AP, which exhibited an opposite trend. Furthermore, a significant decrease in microbial carbon limitation and an increase in microbial nitrogen limitation were observed with increasing afforestation time. Collectively, the dynamic of microbial nutrient limitation was primarily influenced by the interaction between soil nutrients and edaphic factors. The findings suggest that with the increasing duration of citrus plantation, it is crucial to focus on nitrogen (N) fertilization while maintaining a delicate balance between fertilization strategies and soil acidity levels.

Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao

Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.

Mechanisms of microbial-driven changes in soil ecological stoichiometry around gold mines

In this study, we used soils with different pollution and nutrient levels (non-polluted S1, highly polluted low-nutrient S2, and highly polluted high nutrient S3) around the gold mine tailing ponds, and combined with metabolic limitation modeling and macro-genomics approaches, aiming to investigate the relationship between soil microbial composition and soil eco-chemometrics characteristics under heavy metal stress. The results showed that heavy pollution resulted in reduced SOC, TN, microbial biomass, and with C- and P- acquisition (BG, CBH, ALP) as well as nitrogen limitation of soil microbial metabolism in soils (S2, S3). Further analysis by macrogenomics showed that heavy metal contamination led to an increase in α-microbial diversity and altered the composition of microbial communities in the soil. The cycling of C, N, and P nutrients was altered by affecting the relative abundance of Anaeromyxobacter, Steroidobacter, Bradyrhizobium, Acidobacterium, Limnochorda (predominantly in the Ascomycetes and Acidobacteria phyla), with the most pronounced effect on the composition of microorganisms synthesizing C-acquiring enzymes, and heavy metals and pH were the main influences on ecological stoichiometry. The results of this study are useful for understanding the sustainability of ecological remediation in heavy metal contaminated areas and for developing ecological restoration strategies.

Endophyte inoculation enhanced microbial metabolic function in the rhizosphere benefiting cadmium phytoremediation by Phytolaccaacinosa

Microbial metabolic activities in rhizosphere soil play a critical role in plant nutrient utilization and metal availability. However, its specific characteristics and influence on endophyte assisted phytoremediation remains unclear. In this study, an endophyte strain Bacillus paramycoides (B. paramycoides) was inoculated in the rhizosphere of Phytolacca acinosa (P. acinosa), and microbial metabolic characteristics of rhizosphere soils were analyzed using Biolog system to investigate how they influence phytoremediation performance of different types of cadmium contaminated soil. The results indicated that endophyte B. paramycoides inoculation enhanced bioavailable Cd percentage by 9-32%, resulting in the increased Cd uptake (32-40%) by P. acinosa. With endophyte inoculation, the utilization of carbon sources was significantly promoted by 4-43% and the microbial metabolic functional diversity increased by 0.4-36.8%. Especially, B. paramycoides enhanced the utilization of recalcitrant substrates carboxyl acids, phenolic compounds and polymers by 48.3-225.6%, 42.4-65.8% and 15.6-25.1%, respectively. Further, the microbial metabolic activities were significant correlated with rhizosphere soil microecology properties and impact phytoremediation performance. This study provided new insight into the microbial processes during endophyte assisted phytoremediation.

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.

Microbial metabolic limitation and carbon use feedback in lead contaminated agricultural soils

Potentially toxic elements (PTEs) pollution causes a great threat to microbial metabolism, which plays a vital role in studying soil nutrient cycling and predicting carbon (C) storage in agroecosystems. However, the responses of microbial metabolism characteristic to heavy metal contamination and the mechanisms through which microbial metabolism mediate nutrient cycling and C dynamics in contaminated soil remain elusive. Here, we performed an incubation experiment over 80 days to investigate the variations in microbial metabolic limitation under various Pb levels (0, 100, 500, 800, 1500, 2000, and 3000 mg Pb kg^-1 dry soil) in cropland soil using extracellular enzymatic stoichiometry, and to reveal the impact of Pb stress on soil C storage by associating with microbial metabolic quotients (qCO₂) and C use efficiency (CUE). The results showed microbial relative C limitation and phosphorus (P) limitation were observed in Pb-contaminated soils. Pb addition enhanced the microbial relative C limitation by approximately 7.3%, while decreasing the P limitation by approximately 12.3%. Furthermore, Pb addition led to higher qCO₂ (from 8.75 to 108 μg C kg^-1 MBC^-1 d^-1) duo to the increase of microbial relative C limitation, suggesting that the more CO₂ was released of per unit of microbial biomass C. The increase of microbial relative C limitation reduced CUE (from 0.35 to 0.10) because of the change in microbial metabolism from growth to respiration maintenance under Pb stress. Consequently, the CUE and qCO₂ together determined the loss of soil C. Our study reveals that microbial relative C limitation is the dominant driver of soil C loss and provides important knowledge of microbial metabolic limitation regulating soil C turnover in PTEs-contaminated agricultural soils.

Microbial metabolic limitation of rhizosphere under heavy metal stress: Evidence from soil ecoenzymatic stoichiometry

Slow nutrient turnover and destructed soil function were the main factors causing low efficiency in phytoremediation of heavy metal (HM)-contaminated soil. Soil ecoenzymatic stoichiometry can reflect the ability of soil microorganisms to acquire energy and nutrients, and drive nutrient cycling and carbon (C) decomposition in HM-contaminated soil. Therefore, for the first time, we used the enzymatic stoichiometry modeling to examine the microbial nutrient limitation in rhizospheric and bulk soil of different plants (Medicago sativa, Halogeton arachnoideus and Agropyron cristatum) near the Baiyin Copper Mine. Results showed that the main pollutants in this area were Cu, Zn, Cd, and Pb, while Cd and Zn have the greatest contribution according to the analysis of pollution load index (PLI). The activities of soil C-, nitrogen (N)-, and phosphorus (P)-acquiring enzymes in the rhizosphere of plants were significantly greater than that in bulk soil. Moreover, microbial C and P limitations were observed in all plant treatments, while the lower limitation was generally in the rhizosphere compared to bulk soil. The HM stress significantly increased microbial C limitation and decreased microbial P limitation, especially in the rhizospheric soil. The partial least squares path modeling (PLS-PM) further indicated that HM concentration has the greatest effects on microbial P limitation (-0.64). In addition, the highest enzyme activities and the lowest P limitation were observed in the rhizospheric and bulk soil of M. sativa, thereby implying that soil microbial communities under the remediation of M. sativa were steadier and more efficient in terms of their metabolism. These findings are important for the elucidation of the nutrient cycling and microbial metabolism of rhizosphere under phytoremediation, and provide guidance for the restoration of HM-contaminated soil.