Soil Microbial Community Dynamics Research Articles

Transient hypoxia drives soil microbial community dynamics and biogeochemistry during human decomposition.

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products.

Effect of nitrogen and phosphorus fertilization on the temporal dynamics of soil microbial community and multifunctionality in young and mature subtropical forests

Effect of nitrogen and phosphorus fertilization on the temporal dynamics of soil microbial community and multifunctionality in young and mature subtropical forests

Enhanced salt tolerance in Glycyrrhiza uralensis Fisch. via Bacillus subtilis inoculation alters microbial community.

The widespread prevalence of saline environments poses a significant global environmental challenge. Salt stress, induced by saline soils, disrupts soil microecology and affects the plant-microbe-soil cycling process. Utilizing microbial fungicides stands as a primary strategy to mitigate salt stress-induced damage to plants and soils. This study investigated the influence of Bacillus subtilis (Bs) inoculation on the microbial community, assembly processes, and functional changes in bacteria and fungi in Glycyrrhiza uralensis Fisch. (licorice) seedlings under varying salt stress levels, primarily employing microbiomics techniques. Soil enzyme activities displayed a declining trend with increasing salt stress, which was mitigated by Bs inoculation. Microbiome analysis revealed a significant increase in bacterial and fungal operational taxonomic units, particularly in Ascomycetes and Nitrogen-fixing Bacteria, thereby enhancing soil denitrification. The abundance of Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes in bacteria, as well as Ascomycota in fungi, increased with higher salt stress levels, a process facilitated by Bs inoculation. However, functional predictions indicated a reduction in the relative abundance of Dung Saprotrophs with Bs inoculation. Salt stress disrupted soil assembly processes, showcasing a continuous decline in diffusion limitation with increased salt concentration, where Bs inoculation reached a peak under moderate stress. In summary, this research elucidates the communication mechanism of Bs in enhancing salt tolerance in licorice from a microbiome perspective, contributing to a comprehensive understanding of abiotic and biotic factors.IMPORTANCELicorice is a herb that grows in deserts or saline soils. Enhancing the salt tolerance of licorice is necessary to maintain the quality of cultivated licorice and to ensure the supply of medicinal herbs. In the past, we have demonstrated the effectiveness of inoculation with Bacillus subtilis (Bs) to enhance the salt tolerance of licorice and revealed the key metabolic pathways for the development of salt tolerance through multi-omics. In this study, we used the microbiomics approach to reveal the plant-microbe-soil interactions at the level of inoculation of Bs affecting the dynamics of soil microbial communities from bacterial and fungal perspectives, thus bridging the interactions between biotic and abiotic factors.

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3−-N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

Unveiling soil microbial community dynamics in desertification: A case study from the tianshan mountains, xinjiang

Microorganisms constitute the primary ecological group in desertified soil, driving soil biogeochemical cycles. Understanding their structure and diversity is crucial for the ecological restoration of desertification areas. This study focuses on the typical desert slopes in the eastern section of the northern foothills of the Tianshan Mountain in Xinjiang, China. It investigates changes in the main prokaryotic microbial community structure, including bacteria and archaea, and their relationship with environmental factors. Results show generally low soil water content, increasing with depth, and a weak alkaline nature with no significant vertical variations. While microbial communities do not distinctly respond to soil water content, there are noticeable variations in microbial diversity with clear stratification, negatively correlated with total organic carbon. Molecular ecological network analyses of five bare soil profiles in Xinjiang’s Hami Tianshan Desert reveal positive interactions among soil microorganisms in vertical layers. Surprisingly, the topsoil, despite having complex networks, shows low diversity and weak interconnectivity. Intriguingly, subsurface soils exhibit distinct molecular ecological networks similar to those found in ecological transition zones (These zones are characterized by rapid environmental shifts from one type to another), further highlighting significant ecological disparities between surface and subsurface soils. By analyzing the structure of soil microbial communities and their relationship with environmental factors on typical desert slopes in the Tianshan Mountains of Xinjiang, significant microbial ecological differences are found between surface and subsurface soils. Notably, in subsurface soils, microbial networks similar to those in ecological transition zones are discovered. These areas have complex microbial community structures and diverse ecological functions, providing new insights into the mechanisms of ecological restoration in desertified soils. Consequently, this study suggests that the vertical distribution patterns of microbial communities in bare desert soil areas differ from those in vegetated areas such as forests and grasslands. The interactions among species, the unique distribution of soil organic matter, and various physical factors are likely pivotal in the distribution patterns of microbial communities in bare desert soils. This research provides foundational theories and empirical support for the ecological restoration of bare desert soils.

Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.

Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.

Soil microbial community dynamics in response to Tamarix ramosissima afforestation in desert lands: Metagenomic insights

AbstractUnderstanding the influence of afforestation on soil microorganisms, the major drivers of soil processes, is essential for maintaining soil health and sustainability. However, in a desert‐oasis ecotone, variations in the microbial community along shrub afforestation years remain unclear. We conducted a metagenomic analysis to study the temporal changes in microbial community structure in 0–100 cm soil following 3‐, 7‐, and 10‐year afforestation of Tamarix ramosissima Ledeb. on the southern edge of the Taklimakan Desert. Compared to the unreclaimed desert land, in 3‐year or 7‐year stands, soil organic carbon (SOC), nitrate nitrogen, available phosphorus and potassium (AK) contents significantly increased on average by 60%, 852%, 72%, and 299%, respectively. Soil archaeal and bacterial community composition were significantly affected by afforestation; their α‐diversity increased on average by 5.9% and 11.1%, respectively, after afforestation, showing a unimodal pattern along afforestation years. In contrast, fungal α‐diversity and community composition did not show significant variation over the afforestation period. The influence of AK outweighed that of SOC and other nutrients on soil microbial community composition. These findings suggest that T. ramosissima afforestation in the desert‐oasis ecotone has significant impacts on the community composition and α‐diversity of archaea and bacteria, but not fungi, by modifying soil physicochemical properties. This research provides valuable implications for soil management and microbial processes related to the afforestation of salt‐secreting shrubs.

Warming effects on grassland soil microbial communities are amplified in cool months.

Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.

Continuous cropping system altered soil microbial communities and nutrient cycles.

Understanding the response of microbial communities and their potential functions is essential for sustainability of agroecosystems under long-term continuous cropping. However, limited research has focused on investigating the interaction between soil physicochemical factors and microbial community dynamics in agroecosystems under long-term continuous cropping. This study probed into the physicochemical properties, metabolites, and microbial diversity of tobacco rhizosphere soils cropped continuously for 0, 5, and 20 years. The relative abundance of bacterial genera associated with nutrient cycling (e.g., Sphingomonas) increased while potential plant pathogenic fungi and beneficial microorganisms showed synergistic increases with the duration of continuous cropping. Variations in soil pH, alkeline nitrogen (AN) content, and soil organic carbon (SOC) content drove the shifts in soil microbial composition. Metabolites such as palmitic acid, 3-hydroxypropionic acid, stearic acid, and hippuric acid may play a key role in soil acidification. Those results enhance our ability to predict shifts in soil microbial community structure associated with anthropogenic continuous cropping, which can have long-term implications for crop production.

Unraveling the Complex Dynamics of Soil Microbiome Diversity and Its Implications for Ecosystem Functioning: A Comprehensive Review

Soil microbiome diversity plays a pivotal role in shaping terrestrial ecosystems and the myriad functions. This comprehensive review delves into the intricate dynamics of soil microbial communities, exploring their composition, interactions, and responses to environmental factors. By synthesizing findings from cutting-edge research, we aim to elucidate the complex interplay between soil microbiome diversity and ecosystem functioning. We discuss the application of advanced techniques, such as high-throughput sequencing and metagenomic analysis, which have revolutionized our understanding of soil microbial diversity. The review highlights the influence of biotic and abiotic factors, including plant diversity, soil properties, climate, and land-use practices, on the structure and diversity of soil microbial communities. We examine the mechanisms through which soil microbes drive critical ecosystem processes, such as nutrient cycling, carbon sequestration, and plant productivity. The review also explores the resilience and adaptability of soil microbial communities in the face of global change pressures, such as climate change, land-use intensification, and biodiversity loss. We discuss the potential implications of altered soil microbiome diversity for ecosystem functioning and the provision of essential ecosystem services. Furthermore, we identify knowledge gaps and propose future research directions to advance our understanding of soil microbiome diversity and its role in maintaining healthy and productive ecosystems. This review provides a comprehensive framework for understanding the complex dynamics of soil microbiome diversity and underscores its critical importance in shaping the functioning and sustainability of terrestrial ecosystems in a changing world.

Soil, Plant, and Microorganism Interactions Drive Secondary Succession in Alpine Grassland Restoration.

Plant secondary succession has been explored extensively in restoring degraded grasslands in semiarid or dry environments. However, the dynamics of soil microbial communities and their interactions with plant succession following restoration efforts remain understudied, particularly in alpine ecosystems. This study investigates the interplay between soil properties, plant communities, and microbial populations across a chronosequence of grassland restoration on the Qinghai-Tibet Plateau in China. We examined five succession stages representing artificial grasslands of varying recovery durations from 0 to 19. We characterized soil microbial compositions using high-throughput sequencing, enzymatic activity assessments, and biomass analyses. Our findings reveal distinct plant and microbial secondary succession patterns, marked by increased soil organic carbon, total phosphorus, and NH4+-N contents. Soil microbial biomass, enzymatic activities, and microbial community diversity increased as recovery time progressed, attributed to increased plant aboveground biomass, cover, and diversity. The observed patterns in biomass and diversity dynamics of plant, bacterial, and fungal communities suggest parallel plant and fungal succession occurrences. Indicators of bacterial and fungal communities, including biomass, enzymatic activities, and community composition, exhibited sensitivity to variations in plant biomass and diversity. Fungal succession, in particular, exhibited susceptibility to changes in the soil C: N ratio. Our results underscore the significant roles of plant biomass, cover, and diversity in shaping microbial community composition attributed to vegetation-induced alterations in soil nutrients and soil microclimates. This study contributes valuable insights into the intricate relationships driving secondary succession in alpine grassland restoration.

Dynamics of soil properties and microbial communities by crop rotation length: unveiling the key factors for enhanced sugar yield

Dynamics of soil properties and microbial communities by crop rotation length: unveiling the key factors for enhanced sugar yield

Soil carbon mineralization and microbial community dynamics in response to pyrogenic organic matter addition

Wildfires can either negatively impact soil carbon (C) stocks through combustion or increase soil carbon stocks through the production of pyrogenic organic matter (PyOM), which is highly persistent and can affect non-pyrogenic soil organic carbon (SOC) mineralization rates. In this study, we used fine-resolution 13CO2 flux tracing to investigate PyOM-C mineralization, soil priming effects, and their impacts on soil microbial communities in a Californian mixed conifer forest Xerumbrept soil burned in the 2014 King Fire. We added PyOM produced from pine biomass at 350 °C and 550 °C to the soil and separately traced the mineralization of 13C-labeled water-extractable and non-water-extractable PyOM-C fractions in a short-term 30-day incubation.Our results indicate that at the end of the incubation period, the water-extractable fraction was 10-50x more mineralizable in both 350 °C and 550 °C PyOM treatments than the SOC or non-water-extractable PyOM fraction. The addition of 350 °C PyOM led to a short-term positive priming effect, likely due to co-metabolism of easily mineralizable PyOM-C and the SOC, whereas 550 °C PyOM addition induced negative priming, potentially due to physical protection of SOC. We observed significant shifts in bacterial community composition in response to both 350 °C and 550 °C PyOM, and identified positive PyOM responders that increased in relative abundance belonging to the genera Noviherbaspirillum, Pseudonocardia, and Gemmatimonas. In contrast, fungal communities were less responsive to PyOM additions. Our findings expand our understanding of the post-fire cycling of PyOM and SOC, providing insights into the microbial mineralization of different PyOM-C fractions and their influence on soil C dynamics in fire-affected ecosystems.

Modern research on the dynamics of soil microbial communities in soils of Azerbaijan

In soils with minimal anthropogenic load the following were found B.cereus, B.muralis, B. Cibi, B. Simplex, Br.laterosporus, and in soils with high anthropogenic load the following were found B. cibi, B.cereus, P.lautus, B. pseudomycoides, B. niacini, B. mojavensis, B. agaradhaerens, B.arsenicus, B.firmus, B.licheniformis, B.atrophaeus, P. polymyxa, B.acidicola, B.drentensis, Br.laterosporus, B.subtilis. In anthropogenically transformed soils, the number of common bacilli species was reduced, while at each point species were found that were not found at other points. The proportion of microorganisms that utilize natural substrates is sharply reduced - in urban soils the number of aerobic spore-forming bacteria of the order Bacillales decreases several times.

Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China.

Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p > 0.05) and the amylase gene abundance decreased firstly in middle-succession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling.

Increased precipitation alters the effects of nitrogen deposition on soil bacterial and fungal communities in a temperate forest

Anthropogenic nitrogen (N) deposition and increased precipitation are known to alter soil microbial communities. However, the combined effects of elevated N deposition and increased precipitation on soil microbial community dynamics and co-occurrence networks in temperate forests remain elusive. In this study, we conducted a field manipulation experiment by applying N solution and water to the forest canopy to simulate natural N deposition and increased precipitation in a temperate forest. We collected samples in the litter layer, organic soil layer, and mineral soil layer in 2018–2019 after 6–7 years of N and water treatments, and explored how elevated N deposition and increased precipitation regulate soil microbial diversity, community composition, and co-occurrence networks in different soil layers and at different sampling times. We found that the effects of N deposition and increased precipitation on soil microbial communities varied with soil layers and sampling times. Compared to the ambient environment, single canopy N addition (CN) or single canopy water addition (CW) did not affect bacterial Shannon diversity in the mineral soil layer in 2018, but the combined canopy N and water additions (CNW) decreased it in this layer at this time. CN increased fungal OTU richness in the organic and mineral soil layers in 2018; however, CW and CNW did not have an effect on it in the same layer at the same time. CW and CNW, but not CN, significantly affected bacterial and fungal community compositions in the litter layer in 2018 and in the organic soil layer in 2019. In contrast, CN, but not CW or CNW, significantly affected fungal community composition in the litter layer in 2019. CNW exhibited higher complexities of bacterial and fungal co-occurrence networks than CN and the ambient environment, indicating increased precipitation can strengthen the effect of N deposition on the complexity of bacterial and fungal co-occurrence networks. Our findings suggest that increased precipitation alters the effects of atmospheric N deposition on soil bacterial and fungal communities in this temperate forest, depending on soil layer and sampling time. Moreover, both bacterial and fungal community compositions are sensitive to increased precipitation, but the bacterial community composition is more sensitive to N deposition than the fungal community composition in the organic and mineral soil layers in this forest.

Initial microbiome and tree root status structured the soil microbial community discrepancy of the subtropical pine-oak forest in a large urban forest park.

Plant-microbe-soil interactions control over the forest biogeochemical cycling. Adaptive plant-soil interactions can shape specific microbial taxa in determining the ecosystem functioning. Different trees produce heterogeneous soil properties and can alter the composition of soil microbial community, which is relevant to the forest internal succession containing contrasting stand types such as the pine-oak forests. Considering representative microbial community characteristics are recorded in the original soil where they had adapted and resided, we constructed a soil transplant incubation experiment in a series of in situ root-ingrowth cores in a subtropical pine-oak forest, to simulate the vegetational pine-oak replacement under environmental succession. The responsive bacterial and fungal community discrepancies were studied to determine whether and how they would be changed. The pine and oak forest stands had greater heterogeneity in fungi composition than bacteria. Original soil and specific tree root status were the main factors that determined microbial community structure. Internal association network characters and intergroup variations of fungi among soil samples were more affected by original soil, while bacteria were more affected by receiving forest. Specifically, dominant tree roots had strong influence in accelerating the fungi community succession to adapt with the surrounding forest. We concluded that soil microbial responses to forest stand alternation differed between microbiome groups, with fungi from their original forest possessing higher resistance to encounter a new vegetation stand, while the bacteria community have faster resilience. The data would advance our insight into local soil microbial community dynamics during ecosystem succession and be helpful to enlighten forest management.

Legacy effects of earthworms on soil microbial abundance, diversity, and community dynamics

The earthworm species Lumbricus terrestris L. feeds on plant litter mixed with surrounding soil. Here, we analyzed with a mesocosm approach and soil incubations how that activity and subsequent ageing of casts (feces) affects the abundance and diversity of the soil microbiome. Earthworms were fed either with straw of sainfoin (SA, Onobrychis viciifolia; C/N ratio 22) or winter wheat (WW, Triticum aestivum, C/N ratio 101). The gut transit increased the abundances of bacteria and fungi, but reduced archaea. As indicated at the DNA and RNA level, main beneficiaries of the facilitated access to nutrients were members of Bacteroidota, especially Flavobacteriales with an estimated generation time of only 2 h. While Alphaproteobacteria were reduced, Gammaproteobacteria also increased in abundance and activity. SA was more nutritious for L. terrestris, and supported a higher bacterial abundance, probably because more N was available for growth and denitrification. During cast ageing, prokaryotic community compositions became increasingly similar to bulk soil communities. However, they remained distinguishable even after 168 d, suggesting that effects can last beyond a vegetation period. Dry-wet conditions preserved these differences better than continuous moisture. During ageing, more complex prokaryotic networks were detected with WW and dry-wet conditions. Thus, N and water limitations appeared to enhance cooperation rather than competition between the prokaryotes. Overall, this study demonstrates that earthworm soil interactions strongly affect the diversity and temporal dynamics of the soil microbiome. Legacy effects of earthworm activities should thus be kept in mind when investigating the environmental variation of soil microbiomes.

Machine learning models reveal how biochar amendment affects soil microbial communities

The biochar amendment plays a vital role in maintaining soil health largely due to its effects on soil microbial communities. However, individual cases and the variability in biochar properties are not sufficient to draw universal conclusions. The present study aimed to reveal how the biochar application affects soil microbial communities. Metadata of 525 ITS and 1288 16S rRNA sequencing samples from previous studies were reanalyzed and machine learning models were applied to explore the dynamics of soil microbial communities under biochar amendment. The results showed that biochar considerably changed the soil bacterial and fungal community composition and enhanced the relative abundances of Acidobacteriota, Firmicutes, Basidiomycota, and Mortierellomycota. Biochar enhanced the robustness of the soil microbial community but decreased the interactions between fungi and bacteria. The random forest model combined with tenfold cross-validation were used to predict biomarkers of biochar response, indicating that potentially beneficial microbes, such as Gemmatimonadetes, Microtrichales, Candidatus_Kaiserbacteria, and Pyrinomonadales, were enriched in the soil with biochar amendment, which promoted plant growth and soil nutrient cycling. In addition, the biochar amendment enhanced the ability of bacteria to biosynthesize and led to an increase in fungal nutrient patterns, resulting in an increase in the abundance and diversity of saprophytic fungi that enhance soil nutrient cycling. The machine learning model more accurately revealed how biochar affected soil microbial community than previous independent studies. Our study provides a basis for guiding the reasonable use of biochar in agricultural soil and minimizing its negative effects on soil microecosystem.Graphical

Effect of soil microbial community structure on the chemical compositions of different soil organic matter fractions in land uses of the Pearl River Estuary

Understanding the interactions between the dynamics of soil organic matter (SOM) and soil microbial communities is important for predicting the stability and fate of estuarine SOM following anthropogenic disturbance. However, current knowledge on the influence of microbial communities on the chemical compositions of different SOM fractions in estuarine land uses still remains incomplete. In this study, we used high-throughput sequencing, Fourier transform infrared spectroscopy, UV–Vis absorption, and fluorescence spectroscopy to investigate soil microbial communities and characterize the chemical compositions of bulk SOM and water-extractable organic matter (WEOM) across different land uses (artificial forests (AF), farmland (FL), natural wetland (NW), construction land (CL), and abandoned land (AL)) in the Pearl River Estuary. The results showed that the bulk SOM in FL and AL exhibited comparable or higher levels of aromatic functional groups (aromatic CH and aromatic CC) compared to other land uses. The HIX and SUV254 indexes further confirmed that AF and FL had more aromatic and hydrophobic WEOM. Apart from FL, where anthropogenic humus constituted the largest proportion, the WEOM fraction predominantly consist of three components in the following order across all land uses, ordered as anthropogenic humus < microbial humus < protein humus. The chemical compositions of the different SOM fractions showed a stronger correlation with the dominant bacterial phylum composition, especially for the WEOM fraction, compared to the fungal composition. Meanwhile, our findings demonstrate that bacterial diversity showed a stronger relationship with the chemical composition of WEOM compared to abundance. Overall, this study sheds light on the impact of land use on the quantity and quality of SOM fractions, underscoring the varying influence of microorganisms on the chemical compositions of different SOM fractions within estuarine environments.