Sustainable management of surface substrate layer based on soil microbial diversity during wheat growth season

Compositional and structural changes in soil microbial communities in response to straw mulching and plant revegetation in an abandoned artificial pasture in Northeast China

Pinus tabulaeformis plantations have been established around northern China to restore degraded land and provide timber or fuelwood. In recent years, widely distributed monoculture P. tabulaeformis forests have been transformed into mixed forests due to various ecological problems. However, the current research on the influence of near-natural transformation of P. tabulaeformis on soil microbial diversity and community composition remains limited. Therefore, we examined the effect of forest conversion from monoculture Pinus tabuliformis (PT) to P. tabuliformis-Armeniaca vulgaris (PTAU), P. tabuliformis - Robinia pseudoacacia (PTRP), P. tabuliformis - Vitex negundo L. var. heterophylla (PTVN) forests on soil microbial community diversity and composition. The results indicated that compared to PT, PTAU, PTVN, and PTRP could enhance the soil pH, TC, TN, AN, and AK in different degrees, the most obvious in PTAU. Near-natural transformation of P. tabuliformis could improve soil bacterial Pielou_e index, and Simpson index, as well as soil fungal Chao1 index. Proteobacteria and Ascomycota were the dominant soil microbial community at the phylum level. What’s more, both soil bacterial and fungal community among PT, PTAU, PTRP and PTVN showed clear different, and PTAU obviously altered the soil microbial community structure. Proteobacteria was the predominant group in PT, while, Gemmatimonadetes enriched in PTVN. Ascomycota was the predominant group in PTAU, while, Basidiomycota was the predominant group in PTRP. Near-natural transformation of P. tabuliformis could change soil microbial community via altering soil characteristics. In brief, our research results revealed the influence of tree composition and soil nutrient availability on soil microbial diversity and composition, and provided management guidance for introduction soil microbial community in forest protection and management.

Knowledge regarding changes in soil microbial communities with forest succession is vital to understand soil microbial community shifts under global change scenarios. The composition and diversity of soil microbial communities across a subalpine forest successional series were therefore investigated in the Wanglang National Nature Reserve on the eastern Qinghai-Tibet Plateau, China. The calculated diversity indices of soil bacteria (8.598 to 9.791 for Shannon-Wiener, 0.997 to 0.974 for Simpson, 4131 to 4974 for abundance-based coverage estimator (ACE) and 3007 to 3511 for Species richness indices), and ACE (1323 to 921) and Species richness (1251 to 879) indices of soil fungi decreased from initial to terminal succession stages, but Shannon-Wiener and Simpson of soil fungi indices varied slightly with forest succession. Meanwhile, the composition and structure of soil microbial communities varied markedly with forest succession. The relative abundance of the dominant bacterial phyla (Acidobacteria, Firmicutes and Actinobacteria) and fungal taxa (Mortierellomycota, Rozellomycota and unassigned phylum clade GS01) varied considerably with forest succession. However, regardless of successional stage, Proteobacteria and Acidobacteria dominated soil bacterial communities and Ascomycota and Basidiomycota dominated soil fungal communities. Moreover, the changes in soil microbial diversity with forest succession were significantly affected by soil pH, soil organic carbon, soil temperature, altitude, and non-woody debris stock. Importantly, soil pH was the dominant driver of soil microbial community shift with forest succession. In conclusion, the forests at different succession stages not only conserve same microbial populations, but also nurse unique microbial diversity across the forest succession series; and the biodiversity of soil bacterial and fungal communities has differential responses to forest succession.

To understand the distribution of the soil microbial community in natural walnut orchards at different altitude gradients (3000–3500 m) and to reveal the mechanism of the soil microbial activity in natural walnut orchards adapting to high-altitude environments, soil samples from four groups of natural walnut orchards in Gyaca County, southeast Tibet, were studied. Illumina MiSeq sequencing technology was used to analyze the community composition and diversity of soil bacteria and fungi and their responses to the altitudes. The alpha diversity results showed that the vertical distribution pattern of the fungal community was more obvious than that of the bacterial community and the bacterial community diversity first increased (~3364 m) and then decreased with altitude. The number of amplicon sequence variants (ASVs) in the soil bacterial community was significantly higher than that in the fungal community, but soil bacterial and fungal communities in walnut orchards at different altitudes exhibited both inheritance and uniqueness. At the phylum level, the dominant bacterial phyla at different altitudes were Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi (relative abundances > 10.0% in each treatment). With the increase in altitude, the relative abundance of Actinobacteria increased gradually while that of Acidobacteria and Proteobacteria decreased gradually. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (relative abundances >5.0% in each treatment). With the increase in altitude, the relative abundance of Ascomycota increased significantly. At the genus level, the number of dominant bacteria and fungi in the soil decreased gradually with increased altitude and showed anisotropic distribution characteristics. The relative abundances of Actinobacteria among the bacterial phyla—and Olpidiomycota and Zoopagomycota among the fungal phyla—were positively correlated with the altitude (p < 0.05). Most dominant bacterial and fungal phyla were highly significantly (p < 0.01) or significantly (p < 0.05) negatively correlated with the altitude. Soil nitrogen and phosphorus availabilities are the main limiting factors of microbial community diversity. Therefore, altitude caused changes in soil physicochemical properties which directly or indirectly affected the composition and diversity of soil bacterial and fungal communities, and our study provides a theoretical basis for the altitudinal pattern and succession changes in soil microbial communities in the natural walnut orchards of southeast Tibet.

Changes in soil abiotic and biotic properties can be powerful drivers of feedback between plants and soil microbial communities. However, the specific mechanisms by which seasonal changes in environmental factors shape soil microbial communities are not well understood. Here, we collected soil samples from three sites along an elevational gradient (200–1200 m) in subtropical forests with unvarying canopy vegetation. We used an elevation gradient with similar annual precipitation but a clear temperature gradient, and phospholipid fatty acids (PLFAs) were measured to determine the seasonal variations in the composition of soil microbial communities in response to rising temperatures. Our results showed that the abundance of Gram-negative bacteria and total PLFAs were the lowest at low elevations in winter, and the ratio of Gram-positive to Gram-negative bacteria decreased with increasing elevation. However, the biomass of other microbial groups was the highest at medium elevations in summer, with the exception of actinomycetes species and fungi. Regardless of seasonal changes, soil fungal biomass tended to increase with increasing elevation. Moreover, in summer, microbial carbon use efficiency (CUE) increased with increasing elevation, whereas an opposite trend was observed in winter. Redundancy analysis and structural equation modeling showed that the dissolved organic carbon in soil was the main factor affecting the microbial communities along the elevation gradient in winter, whereas in summer, the microbial community structure was driven by shifting nitrogen availability, with both being associated with changing microbial CUE. As such, this study demonstrates distinct seasonal changes in the soil microbial community composition across an elevation gradient that are driven by carbon and nitrogen resource availability and shifts in microbial CUE. Furthermore, our results suggest that the interaction of underground plant roots and microbes drives changes in resource availability, thereby resulting in seasonal variation in soil microbial community composition across an elevation gradient.

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

Stand age is one of the most important indicators of plantation development status after afforestation. Soil microbial community plays an essential role in ecosystem functioning. Yet, the responses of soil microbial community composition and diversity to stand development are inadequately understood. Here, we examined changes in community composition and diversity of soil bacteria and fungi in poplar plantations across stand ages and their relationships with soil chemical and biochemical properties in Northeast China. We measured soil chemical properties (organic carbon, total nitrogen, total phosphorus and their stoichiometries), soil biochemical properties (microbial biomass, soil enzyme activity and their stoichiometries), and composition and diversity of soil bacterial and fungal communities in a chronosequence (1, 4, 7 and 9 years) of poplar plantations. Furthermore, we analyzed microbial co-occurrence network and the relationships of soil bacterial and fungal community diversity and composition with soil chemical and biochemical properties. The Chao1 index of soil bacteria was lowest in the 9-year-old plantation, and Chao1 index of soil fungi was lowest in the 7-year-old plantation. Soil bacterial and fungal diversity showed a significant relationship with soil microbial biomass. The most dominant bacterial species were from Proteobacteria, Acidobacteriota, Actinobacteriota, Firmicutes and Chloroflexi, and fungal species were from Ascomycota, Basidiomycota and Mortierellomycota. The number of links and average degree of bacterial communities decreased as stand age of poplar plantations increased, while those of fungal communities increased. Soil bacterial and fungal network parameters showed significant relationship with soil microbial biomass ang microbial stoichiometry. Our results showed that the impact of stand age on soil microbial community diversity and composition is specific and stage-dependent, rather than following a simple linear trend with increasing age, and this may be due to the influence of stand age on stoichiometry of soil microbial biomass.

Investigating the response of soil microbial communities to nitrogen (N) deposition is critical to understanding biogeochemical processes and the sustainable development of forests. However, whether and to what extent different forms of N deposition affect soil microbial communities in temperate forests is not fully clear. In this work, a field experiment with three years of simulated nitrogen deposition was conducted in temperate forests. The glycine and urea were chosen as organic nitrogen (ON) source, while NH4NO3 was chosen as inorganic nitrogen (IN) source. Different ratios of ON to IN (CK = 0:0, Mix-1 = 10:0, Mix-2 = 7:3, Mix-3 = 5:5, Mix-4 = 3:7, Mix-5 = 0:10) were mixed and then used with equal total amounts of 10 kg·N·ha−1·a−1. We determined soil microbial diversity and community composition for bacteria and fungi (16S rRNA and ITS), and soil parameters. Different forms of N addition significantly changed the soil bacterial and fungal communities. Mixed N sources had a positive effect on soil bacterial diversity and a negative effect on fungal diversity. Bacterial and fungal community structures were significantly separated under different forms of N addition. Soil pH was the main factor affecting the change in fungal community structure, while bacterial community structure was mainly controlled by STN. We also found that Proteobacteria, Acidobacteriota, Basidiomycota and Ascomycota were the most abundant phyla, regardless of the form of N addition. RDA showed that C/P and NH4+ were the main factors driving the change in bacterial community composition, and C/P, pH and C/N were the main factors driving the change in fungal community composition. Our results indicate that different components of N deposition need to be considered when studying the effects of N deposition on soil microorganisms in terrestrial ecosystems.

Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, we employed a "time and space parallel" method. Four restoration stages, namely corn field (Corn), short-term restoration wetland (2 years, ST), long-term restoration wetland (8 years, LT) and natural wetland (>25 years, NW), were selected to represent the restoration time and geographical location in Naolihe Nature Wetland. We investigated the composition and diversity of soil microbial communities in different restoration wetland (from corn fields to natural wetlands) by using 16S rRNA and ITS rRNA gene sequencing. We also performed chemical experiments to measure soil enzyme activity and physicochemical properties at each sampling site. The results showed that soil physicochemical properties and enzyme activities significantly differed with the extension of wetland restoration years (p < 0.05). Proteobacteria, Acidobacteria, and Actinobacteria are the most dominant phyla in bacterial. The alpha diversity of soil bacteria was the highest in the corn field (Corn), and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. There are two most dominant phyla (Ascomycota and Mucoromycota) in fungal. However, the alpha diversity of soil fungi was the lowest in the Corn and LT stage, and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. The research findings indicated that the changes in soil physicochemical properties with the extension of wetland restoration years play a significant role in shaping the structure and diversity changes of soil microbial communities. Through the analyses of bacterial and fungal functions using the FUNGuild and FAPROTAX databases, the results showed that the abundance of aerobic bacteria in the soil increased more than that of anaerobic bacteria as the wetland restoration years prolonged, while the abundance of saprotrophic, symbiotic, and pathogenic fungi in the soil significantly decreased with the prolonged wetland restoration years. This study will help us better understand the process of restoration after farmland abandonment, providing valuable reference information for the implementation of a series of wetland ecological restoration projects in the future.

Soil microbial community plays important roles in altering ecological processes and biogeochemical cycles in ecosystems. However, little is known about how afforestation influences the diversity, composition, and ecological network of soil microbial community in karst regions. In this study, soil samples were collected from one farmland (FL) and three afforestation lands including one bamboo forest (BA), one landscape tree planting forest (LAT), and one orange orchard (ORO) in a karst region of Southwest China. The bacterial and fungal communities were characterized using the high‐throughput sequencing approach, and soil properties including soil organic carbon, pH, soil water content, and soil total and available nutrient contents were measured under different land use treatments. Results showed that conversion from FL to BA and LAT significantly reduced the Shannon diversity of bacterial community. At the phylum level (top 10), genus level (top 30), and operational taxonomic units (OTUs) level, afforestation from FL resulted in significant changes in nine phyla, 24 genera, and 31.32% OTUs of bacterial community, and in three phyla, 13 genera, and 11.62% OTUs of fungal community. The number of nodes, number of negative edges, connectivity, average degree, and relative modularity of the microbial network under afforestation lands decreased by 9.33%–18.66%, 47.98%–72.75%, 0.45%–5.93%, 14.73%–22.29%, and 6.46%–23.50%, respectively, compared with FL. The soil organic carbon, total potassium and total phosphorus were identified as the key soil properties affecting the microbial community. Compared with LAT and ORO, the changes in bacterial and fungal communities under BA were more obvious because of the higher contents in soil organic carbon (13.48%) and total potassium (27.18%). In conclusion, afforestation significantly changed compositions and ecological network complexity of soil microbial community in karst regions, and conversion from FL to BA had stronger influences on the changes of soil microbial community than other afforestation lands in Southwest China. These findings provide the context necessary to evaluate the responses of soil microbial community to land use changes in karst regions.

Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the “space instead of time” approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.

Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO2 production

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

Soil microbial communities play an important role in maintaining the ecosystem during forest secondary succession. However, the underlying mechanisms that drive change in soil microbial community structures during secondary succession remain poorly defined in species-rich subtropical coniferous forests. In this study, Illumina high-throughput sequencing was used to analyze the variations in soil microbial community structures during forest secondary succession in subtropical coniferous forests in China. The role of soil properties and plant diversity in affecting soil bacterial and fungal communities was determined using random forest and structural equation models. Highly variable soil microbial diversity was observed in different stages of secondary succession. Bacterial community diversity rose from early to middle and late successional stages, whereas fungal community diversity increased from early to middle successional stages and then declined in the late stage. The relative abundance of Acidobacteria, Gemmatimonadetes, Eremiobacterota(WPS-2), Rokubacteria, and Mortierellomycota increased during succession, whereas the relative abundance of Ascomycota and Mucoromycota decreased. The community composition and diversity of the soil microbial community were remarkably influenced by plant diversity and soil properties. Notably, tree species richness (TSR) displayed a significant and direct correlation to the composition and diversity of both bacterial and fungal communities. The carbon-to-nitrogen (C:N) ratio had a direct impact on the bacterial community composition and diversity, and pH had a marked impact on the fungal community composition and diversity. Furthermore, succession stage and plant diversity indirectly impacted the composition and diversity of soil bacterial and fungal communities via soil properties. Overall, it can be concluded that soil intrinsic properties and plant diversity might jointly drive the changes in soil microbial community composition and diversity during secondary succession of subtropical coniferous forests.

Cushion plants are specialized keystone species of alpine environments that can have a positive effect on ecosystem structure and function. However, we know relatively little about how cushion plants regulate the diversity and composition of soil microbial communities, major drivers of soil processes and ecosystem functioning. Identifying what factors drive the diversity and composition of soil microbial communities in high-elevation ecosystems is also fundamental to predict how global changes will affect their conservation and the services and functions they provide. Thus, we sampled four sites along the southern Andes following the vegetation belt of Azorella cushion species. The field sites spread along a latitudinal gradient and had contrasting levels of aridity, UV-B radiation, mean temperature and soil properties. Overall, Azorella, as well as aridity and UV-B radiation, were the major drivers of the distribution, composition and diversity of soil microbial communities in the studied ecosystems of the Chilean Andes. UV-B radiation affected particularly soil fungi, while soil properties such as pH, total C and N content, essential predictors of microbial diversity globally, had a much lower effect on the composition of soil microbial communities. Understanding the factors driving the structure and composition of microbial communities, particularly the role of cushion plants and the feedbacks between plant, climate and soil is of uttermost importance for the preservation of the functionality of high-elevation ecosystems threatened by climate change.