Forest succession improves the complexity of soil microbial interaction and ecological stochasticity of community assembly: Evidence from Phoebe bournei-dominated forests in subtropical regions

Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations

Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.

Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.

Decomposing benefits: Examining the impact of beech deadwood on soil properties and microbial diversity

Deadwood is an important element of forest ecosystems that affects many of its components, including the soil environment. Our research is an attempt to determine the role of decaying wood in shaping the properties of forest soils in mountain ecosystems. The aim of our research was to present the influence of beech deadwood on physicochemical properties and microbiological diversity of soils. The research was carried out in the Baba Góra Massif at its northern exposure. The research plots were established in the altitude gradient at 600, 800 and 1000 m above sea level. On each plot, samples were taken from decaying wood, from the soil directly under the decaying log, and a soil sample 1 m from the log as a control. We determined the basic properties of the samples, that is pH, C and N concentration and lignin content. The enzymatic activity and additionally, the taxonomic composition of soil bacterial and fungal communities was determined in the collected samples. Our research indicates the important role of decaying beech wood in shaping the properties of forest soils. We noted a positive effect of decaying wood on the properties of the tested soils. Soils affected by deadwood were characterized by significantly higher pH, C and N concentrations compared to control soils, regardless of their location in the altitude gradient. Additionally, we found that soils affected by decaying wood are characterized by a different composition of microorganisms regardless of their location in the altitude gradient. In control soil the fungal and bacterial alpha diversity were lowest compared with the deadwood and soil under the influence of deadwood. Our results may have practical applications in the management of forest ecosystems. The presented results indicate the possibility of leaving deadwood in order to improve its basic physicochemical properties and increase microbial diversity.

Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Changes in nitrogen and phosphorus availability driven by secondary succession in temperate forests shape soil fungal communities and function

The soil fungal community plays an important role in forest ecosystems and is crucially influenced by forest secondary succession. However, the driving factors of fungal community and function during temperate forest succession and their potential impact on succession processes remain poorly understood. In this study, we investigated the dynamics of the soil fungal community in three temperate forest secondary successional stages (shrublands, coniferous forests, and deciduous broad-leaved forests) using high-throughput DNA sequencing coupled with functional prediction via the FUNGuild database. We found that fungal community richness, α-diversity, and evenness decreased significantly during the succession process. Soil available phosphorus and nitrate nitrogen decreased significantly after initial succession occurred, and redundancy analysis showed that both were significant predictors of soil fungal community structure. Among functional groups, fungal saprotrophs and pathotrophs represented by plant pathogens were significantly enriched in the early-successional stage, while fungal symbiotrophs represented by ectomycorrhiza were significantly increased in the late-successional stage. The abundance of both saprotroph and pathotroph fungal guilds was positively correlated with soil nitrate nitrogen and available phosphorus content. Ectomycorrhizal fungi were negatively correlated with nitrate nitrogen and available phosphorus content and positively correlated with ammonium nitrogen content. These results indicate that the dynamics of fungal community and function reflected the changes in nitrogen and phosphorus availability caused by the secondary succession in temperate forests. The fungal plant pathogen accumulated in the early-successional stage and ectomycorrhizal fungi accumulated in the late-successional stage may have a potential role in promoting forest succession. These findings contribute to a better understanding of the response of soil fungal communities to secondary forest succession and highlight the importance of fungal communities during the successional process.

The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region

Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.

Effect of Fe3+ on the nutrient removal performance and microbial community in a biofilm system

In this study, the influence of Fe3+ on N removal, microbial assembly, and species interactions in a biofilm system was determined. The results showed that maximum efficiencies of ammonia nitrogen (NH4+-N), total nitrogen (TN), phosphorus (P), and chemical oxygen demand (COD) removal were achieved using 10 mg/L Fe3+, reaching values of 100, 78.85, 100, and 95.8%, respectively, whereas at concentrations of 15 and 30 mg/L Fe3+ suppressed the removal of NH4+-N, TN, and COD. In terms of absolute abundance, the expression of bacterial amoA, narG, nirK, and napA was maximal in the presence of 10 mg/L Fe3+ (9.18 × 105, 8.58 × 108, 1.09 × 108, and 1.07 × 109 copies/g dry weight, respectively). Irrespective of Fe3+ concentrations, the P removal efficiency remained at almost 100%. Candidatus_Competibacter (10.26–23.32%) was identified as the most abundant bacterial genus within the system. Determinism (50%) and stochasticity (50%) contributed equally to microbial community assembly. Co-occurrence network analysis revealed that in the presence of Fe3+, 60.94% of OTUs in the biofilm system exhibited positive interactions, whereas 39.06% exhibited negative interactions. Within the OTU-based co-occurrence network, fourteen species were identified as key microbes. The stability of the system was found to be predominantly shaped by microbial cooperation, complemented by competition for resources or niche incompatibility. The results of this study suggested that during chemical P removal in wastewater treatment plants using biofilm methods, the concentration of supplemental Fe3+ should be maintained at 10 mg/L, which would not only contribute to P elimination, but also enhance N and COD removal.