Rhizosphere effects on soil microbial community structure and enzyme activity in a successional subtropical forest

A transition from arbuscular to ectomycorrhizal forests halts soil carbon sequestration during subtropical forest rewilding

Ecological succession and restoration rapidly promote multiple dimensions of ecosystem functions and mitigate global climate change. However, the factors governing the limited capacity to sequester soil organic carbon (SOC) in old forests are poorly understood. Ecological theory predicts that plants and microorganisms jointly evolve into a more mutualistic relationship to accelerate detritus decomposition and nutrient regeneration in old than young forests, likely explaining the changes in C sinks across forest succession or rewilding. To test this hypothesis, we conducted a field experiment of root-mycorrhizal exclusion in successional subtropical forests to investigate plant-decomposer interactions and their effects on SOC sequestration. Our results showed that SOC accrual rate at the 0-10 cm soil layer was 1.26 mg g-1 yr-1 in early-successional arbuscular mycorrhizal (AM) forests, which was higher than that in the late-successional ectomycorrhizal (EcM) forests with non-significant change. A transition from early-successional AM to late-successional EcM forests increase fungal diversity, especially EcM fungi. In the late-successional forests, the presence of ectomycorrhizal hyphae promotes SOC decomposition and nutrient cycle by increasing soil nitrogen and phosphorus degrading enzyme activity as well as saprotrophic microbial richness. Across early- to late-successional forests, mycorrhizal priming effects on SOC decomposition explain a slow-down in the capacity of older forests to sequester soil C. Our findings suggest that a transition from AM to EcM forests supporting greater C decomposition can halt the capacity of forests to provide nature-based global climate change solutions.

Spatial variations of fungal community assembly and soil enzyme activity in rhizosphere of zonal Stipa species in inner Mongolia grassland

Rhizosphere soil fungal and enzyme activities affect the nutrient cycling of terrestrial ecosystems, and rhizosphere fungi are also important participants in the ecological process of vegetation succession, responding to changes in plant communities. Stipa is an excellent forage grass with important ecological and economic value, and has the spatial distribution pattern of floristic geographical substitution. In order to systematically investigate the synergistic response strategies of fungal communities and enzyme activities in the rhizosphere under the vegetation succession. Here we explored the turnover and assembly mechanisms of Stipa rhizosphere fungal communities and the spatial variation of metabolic activity under the succession of seven Stipa communities in northern China grassland under large scale gradients. The results indicated that the composition, abundance and diversity of fungal communities and microbial enzyme activities in rhizosphere soil differed among different Stipa species and were strikingly varied along the Stipa community changes over the geographic gradient. As the geographical distribution of Stipa community changed from east to west in grassland transect, Mortierellomycetes tended to be gradually replaced by Dothideomycetes. The null models showed that the rhizosphere fungal communities were governed primarily by the dispersal limitation of stochastic assembly processes, which showed decreased relative importance from S. grandis to S. gobica. Moreover, the MAT and MAP were the most important factors influencing the changes in the fungal community (richness, β-diversity and composition) and fungal community assembly, while SC and NP also mediated fungal community assembly processes. These findings deepen our understanding of the responses of the microbial functions and fungal community assembly processes in the rhizosphere to vegetation succession.

Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests

In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.

Crotalaria juncea L. enhances the bioremediation of sulfentrazone-contaminated soil and promotes changes in the soil bacterial community

Sulfentrazone (STZ) is an efficient tool for the pre- and post-emergence control of monocotyledonous and dicotyledonous weeds in fields of crops such as pineapple, coffee, sugarcane, citrus, eucalyptus, tobacco, and soybean. However, this herbicide persists in the soil, causing phytotoxicity in the subsequent crop. Therefore, it is important to use efficient strategies for the remediation of STZ-contaminated areas. The aim of this study was to evaluate the effects of Crotalaria juncea L. on the remediation of STZ-contaminated soil and on the microbial activity and bacterial community structure therein. The study was conducted in three stages: (i) cultivation of C. juncea in soil contaminated with 200, 400, and 800 g ha-1 STZ; (ii) determination of the soil microbial activity (basal respiration, microbial biomass carbon, and bacterial community structure); and (iii) cultivation of a bioindicator species and determination of the residual fraction of STZ. The soil microbial activity was impacted by the soil type and STZ dose. Soil previously cultivated with C. juncea (rhizospheric soil) displayed higher CO2 and lower qCO2 values than non-rhizospheric soil (no previous C. juncea cultivation). Increasing doses of STZ reduced the activity and lowered the diversity indices of the soil microorganisms. The bacterial community structure was segregated between the rhizospheric and non-rhizospheric soils. Regardless of soil type, the bioindicator of remediation (Pennisetum glaucum R.Br.) grew only at the STZ dose of 200 g ha-1, and the plant intoxication level was also lower in rhizospheric soil treated with this herbicide dose. All P. glaucum plants died in the soils treated with 400 and 800 g ha-1 STZ. Previous cultivation of C. juncea in soils contaminated with 200, 400, and 800 g ha-1 STZ reduced the residual fraction of the herbicide by 4.8%, 12.5%, and 17.4%, respectively, compared with that in the non-rhizospheric soils. In conclusion, previous cultivation with C. juncea promoted increases in the soil bacterial activity and diversity indices, mitigated the deleterious effects of STZ on the bioindicator crop, and reduced the residual fraction of the herbicide in the soil.

Variations in the soil micro-food web structure and its relationship with soil C and N mineralization during secondary succession of subalpine forests

The soil micro-food web is an important network of belowground trophic relationships and it participates directly and indirectly in soil ecological processes. In recent decades, the roles of the soil micro-food web in regulating ecosystem functions in grasslands and agroecosystems have received much attention. However, the variations in the soil micro-food web structure and its relationship with ecosystem functions during forest secondary succession remain unclear. In this study, we investigated how forest secondary succession affected the soil micro-food web (including soil microbes and nematodes) and soil carbon and nitrogen mineralization across a successional sequence of "grasslands - shrublands - broadleaf forests - coniferous forests" in a subalpine region of southwestern China. With forest successional development, the total soil microbial biomass and the biomass of each microbial group generally increased. The significant influences of forest succession on soil nematodes were mainly reflected in several trophic groups with high colonizer-persister values (particularly bacterivore3, herbivore5 and omnivore-predator5) that are sensitive to environmental disturbance. The increases in the connectance and nematode genus richness, diversity, and maturity index indicated an increasingly stable and complex soil micro-food web with forest succession, which was closely related to soil nutrients, particularly the soil carbon contents. Additionally, we found that the soil carbon and nitrogen mineralization rates also exhibited generally increasing trends during forest succession, which had significant positive correlations with the soil micro-food web composition and structure. The path analysis results indicated that the variances in ecosystem functions induced by forest succession were significantly determined by soil nutrients and soil microbial and nematode communities. Overall, these results suggested that forest succession enriched and stabilized the soil micro-food web and promoted ecosystem functions via the increase in soil nutrients, and the soil micro-food web played an important role in regulating ecosystem functions during forest succession.

Soil nutrients, enzyme activities, and bacterial communities in varied plant communities in karst rocky desertification regions in Wushan County, Southwest China

Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made a connection between soil and plants, have been an important role in regulating the succession and restoration of karst vegetation. However, it is still unclear how soil bacterial communities and soil properties respond to natural vegetation restoration processes in karst areas. To address this gap, we investigated the soil nutrients, enzyme activity, and soil bacterial community among various plant communities, including farmland (FL), land with herbs only (SSI), herb-and-shrub land (SSII), woody thickets (SSIII), coniferous forest (SSIV), coniferous and broad-leaved mixed forest (SSV), and evergreen broad-leaved forest (SSVI). Our results found that SSII had the highest levels of soil organic matter, total nitrogen, available phosphorus, available nitrogen, sucrase, and β-glucosidase among all the plant communities. These results indicated that herb-and-shrub land have contributed to the rapid restoration of vegetation in KRD regions. FL exhibited the lowest levels of soil nutrients and enzyme activities, while showing the highest bacterial richness and diversity among all the plant communities. This suggested that appropriate human intervention can increase bacterial diversity and richness in the area. The predominant bacterial phylum also varied among the different plant communities, with Actinobacteria being the most abundant in SSI, SSII, SSIII, and SSIV, while Proteobacteria were the most abundant in SSV and SSVI. Furthermore, PCoA analysis demonstrated significant changes in the soil bacterial community structure, with SSI, SSII, SSIII, and SSIV had shared similar structures, while SSV and SSVI had comparable structures. As for soil characteristics, total phosphorus (TP) and total potassium (TK) were the primary factors affecting the soil bacterial community. SSV and SSVI had the most complex bacterial networks and were more stable than other groups. The genera Ktedonobacter, norank_f_Anaerolineaceae, and Vicinamibacter had the highest betweenness centrality scores and were identified as keystone genera in the co-occurrence network in KRD areas. In summary, our results have demonstrated that herb-and-shrub can promote community succession and increase soil nutrient levels in KRD regions.

The effect of salinity on soil chemical characteristics, enzyme activity and bacterial community composition in rice rhizospheres in Northeastern Thailand

Saline soil is one of the major problems limiting rice productivity in the Northeastern area of Thailand. Thus, the aims of this study were to determine soil physicochemical analysis and soil enzyme activities, and bacterial communities in the rhizosphere of 'RD 6' rice grown in salt-affected rice fields. The Ban Thum sample showed the highest electrical conductivity (EC; greater than 6 dS m^-1) and total Na, while the EC in other fields were at non- or slightly saline levels. The principal component analysis revealed that soil chemical characteristics and soil enzymes activities explained 73.4% of total variation. Soil enzyme activities including dehydrogenase and fluorescein diacetate (FDA) hydrolysis, and soil characteristics including organic matter (OM) and organic carbon (OC) were significantly negatively correlated to EC. This indicated that these soil properties were adversely impacted by salts. Interestingly, activities of all hydrolytic enzymes were not affected by soil salinity. Bacteria that were able to colonize the rhizosphere soils were Achromobacter cholinophagum, Rhizobium tarimense, and unculturable bacteria. In this regard, study on the relationship of soil chemical characteristics and soil enzyme activities together with bacterial communities provided promising data for assessing rice field soil quality in the future.

Litter Inputs Control the Pattern of Soil Aggregate-Associated Organic Carbon and Enzyme Activities in Three Typical Subtropical Forests

Soil extracellular enzyme activities among aggregate fractions are critical to short-term microbial activity and long–term carbon dynamics in forest ecosystems, but little is known regarding the effects of forest types on the soil enzyme activities in different soil aggregate fractions. Three typical subtropical forest types (Broadleaved forest, Moso bamboo forest and Chinese fir forest) were selected, and undisturbed soil samples (0–15 cm) were collected. We investigated the effects of forest types on aggregate stability (mean weight diameter, geometric mean diameter and fractal dimension), aggregate–associated organic carbon (OC) and the functionality of five enzymes (cellobiohydrolase, β-glucosidase, β-xylosidase, N–acetylglucosaminidase, leucine aminopeptidase) of different aggregate fractions (>2 mm, 0.25–2 mm, 0.053–0.25 mm and <0.053 mm). The results showed that the proportion of macro-aggregates, aggregate stability and macro–aggregates associated–carbon content and storage were higher in broadleaved and Moso bamboo forests than in Chinese fir forests, indicating that forest types influence the distribution of total soil OC among aggregate fraction classes and would delay the loss of OC in broadleaved and Moso bamboo forests. We also found that the extracellular enzymes were higher in aggregates of broadleaved forests and Moso bamboo forests. SEM (structural equation model) analysis also supported significantly positive relationships between litter quantity and aggregate enzyme activity, and indirect impact of litter quantity and litter C/N ratio together with soil organic carbon (SOC) and soil aggregate organic C content (SAOCC) on aggregate enzyme activity. The results of this study indicate that forest types showed large impact on aggregate-associated OC and enzyme activities, and the litter input of different forest types is the main control on enzyme activity among different aggregate fractions, and thus may play an important role in adjusting the sink capacity and stability of SOC.

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.

Land-Use Change Enhanced SOC Mineralization but Did Not Significantly Affect Its Storage in the Surface Layer

To achieve carbon (C) neutrality and mitigate climate change, it is crucial to understand how converting natural forests to agricultural plantations influences soil organic C (SOC) mineralization. In this study, we investigated the impact of converting evergreen broadleaf forests (EBF) to extensively managed Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) plantations (MBP) in subtropical China on SOC mineralization rate; the concentrations of labile SOC fractions such as dissolved organic C (DOC), microbial biomass C (MBC), and readily oxidizable C (ROC); the activities of C-degrading enzymes (cellobiohydrolase and phenol oxidase); and the abundance of C-degrading enzyme-encoding genes (cbhI and lcc). Three paired soil samples were taken from the surface layer (0–20 cm) of adjacent EBF-MBP sites in Anji County, Zhejiang province. Results showed that converting EBF to MBP significantly increased the SOC mineralization rate as well as soil pH, MBC, cellobiohydrolase, and phenol oxidase activities, and cbhI gene abundance, but did not change other soil properties described above. In addition, structural equation modelling (SEM) showed that the conversion increased SOC mineralization rate through increasing soil pH, cbhI gene abundance, MBC, and cellobiohydrolase and phenol oxidase activities. Our novel finding that converting EBF to extensively managed MBP enhanced SOC mineralization via increasing the activities of C-degrading enzymes suggests that C-degrading enzymes were a key factor regulating SOC mineralization in the extensively managed subtropical bamboo plantations.

Ecoenzymatic stoichiometry and microbial nutrient limitations in rhizosphere soil along the Hailuogou Glacier forefield chronosequence

Mountain glaciers retreat at an increased rate under global warming, resulting in exposed barren surfaces for primary succession. Soil microbes are an important driver of ecosystem processes. Although variations in soil microbes after deglaciation have been studied extensively, the roles of rhizosphere soil microbes in the biogeochemistry cycle during primary succession are less understood. In this study, Populus purdomii was present throughout the 123-year chronosequence as a representative tree species. We therefore investigated variations in the rhizosphere enzyme activity, microbial community structure, and ecoenzymatic stoichiometry of P. purdomii along Hailuogou Glacier chronosequences. The objective was to determinechanges in rhizosphere enzyme activities and microbial communities, as well as the effects of nutrient limitation on rhizosphere microbes. According to the results, the enzyme activities and microbial group biomass in rhizosphere soil all showed a bimodal trend and were highest at the 43rd or 123rd year, and enzyme activity varied with succession time but not microbial community structure. The rhizosphere soil bacterial community was the dominant community during the 123-year chronosequence. Ecoenzymatic stoichiometry indicated nitrogen restrictions on microbial activity throughout primary succession, with early succession stages (5-15 years) showing greater carbon restriction than late succession stages. Moreover, redundancy and correlation analyses demonstrated that soil microbial phospholipid fatty acid biomass was an important factor for increases in enzyme activities and that enzyme activities in turn played important roles in carbon, nitrogen and phosphorus cycling in rhizosphere soil. Additionally, rhizosphere soil microbial development significantly affected soil organic carbon, total nitrogen and dissolved organic carbon accumulation. Overall, our study links the rhizosphere microbial community and activity to successional chronosequences, providing a deeper understanding of the dynamics of ecosystem succession.

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum

Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 10⁴ cells g^-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96–193.97 μg IAA mg protein^-1), 72 strains (71.3%) solubilized FePO₄ (0.40–56.00 mg l^-1), 44 strains (43.5%) solubilized AlPO₄ (0.62–17.05 mg l^-1), and 44 strains produced siderophores (1.06–3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.