Soil microbial community characteristics under different vegetation types at the national nature reserve of Xiaolongshan Mountains, Northwest China

Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas

IMPORTANCE

The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.

Stability of soil bacteria in undisturbed soil and continuous maize cultivation in Northern Thailand

Rotational shifting cultivation (RSC) in Northern Thailand serves the dual purpose of ensuring food security and meeting economic goals through maize cultivation. However, the research question remains: Does the dynamics of soil bacterial communities differ between maize monoculture and RSC fields with continuous fallow throughout the season? Therefore, the objective of this study was to investigate and compare the variation of soil bacterial communities in maize monoculture and fallow RSC fields. A continuous 5-year fallow field (undisturbed soil; CF-5Y) and a continuous 5-year maize cultivation field (M-5Y) in Mae Chaem District, Chiang Mai Province, Northern Thailand, were selected due to their similarities in microclimate, topography, and the 5-year duration of different field activities. Over the span of a year, we collected soil samples from the surface layer (0-2 cm depth) at both sites. These collections occurred at 3-month intervals, starting from March 2022 (summer season) and followed by June (rainy season), September (rainy season), December (winter season), and March 2023 (summer season). Soil bacterial diversity and composition were analyzed using 16S rRNA gene-based metagenomic analysis. The results found that undisturbed soil over a 5-year period exhibited more stability in the richness and diversity of bacteria across seasons compared with M-5Y. Notably, fertilizer application and tillage practices in M-5Y can enhance both the diversity and richness of soil bacteria. In terms of bacterial abundance, Proteobacteria prevailed in CF-5Y, while Actinobacteria dominated in M-5Y. At the genus level, Candidatus Udaeobacter dominated during the summer and winter seasons in both CF-5Y and M-5Y sites. Interestingly, during the rainy season, the dominant genus shifted to Bacillus in both CF-5Y and M-5Y fields. The soil bacterial community in M-5Y was strongly influenced by organic matter (OM) and organic carbon (OC). In contrast, in CF-5Y, there was no correlation between soil properties and the soil bacterial community, likely due to the lower variation in soil properties across seasons. β-Glucosidase was the dominant enzyme in both CF-5Y and M-5Y sites, and it showed a positive correlation with OM and OC. Further studies should continue to investigate soil bacteria dynamics, considering the changes in land management practices.

Similarities and differences in the microbial structure of surface soils of different vegetation types

Background

Soil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem's material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes.

Methods

In order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively.

Results

Our findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of different vegetation types and the relative abundance of soil microorganisms at both phyla and genus levels. This experiment serves as a crucial step towards unraveling the intricate relationships between plants, soil microbes, and soil, as well as understanding the underlying driving mechanism.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10  cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20  cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

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.

The Effects of Shrub Removal on Soil Microbial Communities in Primary Forest, Secondary Forest and Plantation Forest on Changbai Mountain

Shrub removal is a common management method in forest ecosystems, but comparatively little is known regarding the effects of shrub removal on soil microbial communities among primary forest, secondary forest, and plantation forests in temperate forests, which limits our accurate assessment of sustainable management of understory vegetation removal. Given this, we used a long-term operation experiment across a contrasting mixed broadleaved-Pinus koraiensis forest, Betula platyphylla forest, and Larix gmelinii plantation forest to explore the variations of soil properties and microbial community after 5 years of shrub removal on Changbai Mountain, as well as the contribution of the soil properties and understory plant diversity to the soil microbial community. The results demonstrated that shrub removal could significantly alter soil SWC and TN, TP, and AP contents of the L. gmelinii, as well as N/P of B. platyphylla. Moreover, shrub removal also clearly improved soil bacterial Pielou_e index and Simpson index of mixed broadleaved-P. koraiensis and soil bacterial Simpson index of L. gmelinii, and decreased soil fungal Pielou_e index and Shannon index of L. gmelinii and soil bacterial Pielou_e index and soil fungal Shannon index of B. platyphylla. Identically, shrub removal notably altered the soil bacterial community composition. Soil characteristics and understory plant diversity accounted for 48.02% and 26.88%, and 45.88% and 27.57% of the variance in the bacterial and fungal community composition, respectively. This study aimed to provide an important scientific basis for the restoration and sustainable management of temperate forests in the Changbai Mountain region.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Urbanization alters soil bacterial communities in southern China coastal cities

Urbanization carries essential influences to ecosystem of soil bacteria in coastal cities. Comprehending the patterns and drivers of bacterial diversity are essential to understanding how soil ecosystems respond to environmental change. This study aimed to explore how soil bacterial community (SBC) response to distinct urbanization of coastal cities on composition, assembly process and potential function in Guangdong province, south China. 72 samples from 24 sample sites within 3 cities were included in the study. Soil chemical properties were analyzed, and the bacterial community were investigated by high-throughout sequencing. Proteobacteria and Acidobacteria were the main phyla. Assembly processes remained in stochastic processes and co-occurrence network of SBC kept stable, while urbanization altered SBC by influencing the dominant phyla. The indicators of communities in coastal city soils were the genera gamma_proteobacterium and beta_proteobacterium. Urbanized extent was the non-negligible factor which affected soil bacterial community, despite the total carbon was still the most vital. The impact of urbanization on bacterial communities might follow a non-linear pattern. Faprotax function prediction showed different urbanized coastal city soils share similar metabolic potential. Our study improved our understanding of the response of soil bacterial communities to urbanization in subtropical coastal cities and offered a useful strategy to monitor the ecology risk toward the soil under urbanization.

Soil microbial stoichiometry and community structure responses to long-term natural forest conversion to plantations in a subtropical region

Soil microbial stoichiometry reflects carbon (C) and nutrient (e.g., nitrogen (N) and phosphorus (P)) elemental balances under land-use change (LUC). However, how soil microbial community (SMC) structure and stoichiometry respond to long-term LUC in forests is still unclear. Here, we investigated three 36-year-old typical plantations, Cryptomeria fortunei, Metasequoia glyptostroboides, and Cunninghamia lanceolata, and the natural forest to assess their soil microbial stoichiometry and SMC structure. Three plots (30×30 m²) were randomly set in each forest site. In each plot of every forest site, soil samples of three depths (0-10, 10-30, and 30-60 cm) were collected. Dissolved organic C, N, and P (abbreviated as DOC, DON, and DOP, respectively) and environmental factors were measured. We also detected microbial biomass C, N, and P as well as SMC structure. The results showed that the soil microbial C:N:P stoichiometry had a strong or strict homeostasis regardless of soil depth and exhibited decoupling from the SMC structure at each depth. The SMC structure across forest types was mainly driven by mean annual soil temperature (MAST) and DOC at 0-10 cm depth, by soil water content and MAST at 10-30 cm depth, and by DOC to DOP ratio at 30-60 cm depth. Thus, SMC structure could be jointly regulated by available resources and environment. These results suggest that the C dynamics in forests tend to gain resilience or re-equilibrium over more than three decades after forest conversion. These findings highlight the importance of reforested plantations forest management for sustaining soil C over a long term.

Linking soil organic carbon stock to microbial stoichiometry, carbon sequestration and microenvironment under long-term forest conversion

Forest conversion can drastically impact carbon (C) and nutrient processes and microbial stoichiometry, which will modify soil organic C (SOC) stock. However, SOC stock dynamics and its underlying mechanisms induced by long-term forest conversion remain unclear. Three well-protected plantations converted from natural forests for 36 years were compared, i.e., Cryptomeria fortunei (CF), Metasequoia glyptostroboides (MG) and Cunninghamia lanceolata (CL), with a natural forest (NF) as a control. SOC stock size and stability across three soil depths (0-10, 10-30 and 30-60 cm) were examined with aggregate-based method. Forest floors and fine roots were treated as C and nutrient inputs while soil respiration (Rs) was treated as C output. Soil microbial biomass C, nitrogen and phosphorus were measured to calculate microbial stoichiometry, as well as microenvironment and soil physicochemical properties. The relationships between SOC stock (size and stability) and these factors were explored using structural equation model. The results showed that microbial stoichiometry had strong or strict homeostasis at each soil depth. At 0-10 cm soil deep, SOC stock size varied with tree species (following the rank of CL > NF ≈ CF > MG) but its stability increased in all forest conversion types, regulated by forest floor quantity and quality associated with Rs; at 10-30 cm soil deep, the SOC stock sizes decreased in CF and MG, but SOC stock stability increased in MG, jointly driven by fine root quality and microenvironment; at 30-60 cm soil deep, SOC stock size decreased but its stability increased in MG, whereas both its size and stability had few changes in CF or CL, modified by soil physicochemical property associated with microbial stoichiometry and Rs. Overall, the effects of microbial stoichiometry and microenvironment on SOC stock were not pronounced. Thus, SOC stock size changed with soil depth and tree species but its stability tended to be steady at all depths varying with tree species. These results suggest that SOC stock size and stability are mainly determined by self-regulation process of forest ecosystems over more than three-decade after forest conversion, which will help us more accurately assess C sequestration strategies regarding long-term forest conversion.