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In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Recent evidence suggests that changes in carbon-degrading extracellular enzyme activities (C-EEAs) can help explain soil organic carbon (SOC) dynamics under nitrogen (N) addition. However, the factors controlling C-EEAs remain unclear, impeding the inclusion of microbial mechanisms in global C cycle models. Using meta-analysis, we show that the responses of C-EEAs to N addition were best explained by mycorrhizal association across a wide range of environmental and experimental factors. In ectomycorrhizal (ECM) dominated ecosystems, N addition suppressed C-EEAs targeting the decomposition of structurally complex macromolecules by 13.1 %, and increased SOC stocks by 5.2 %. In contrast, N addition did not affect C-EEAs and SOC stocks in arbuscular mycorrhizal (AM) dominated ecosystems. Our results indicate that earlier studies may have overestimated SOC changes under N addition in AM-dominated ecosystems and underestimated SOC changes in ECM-dominated ecosystems. Incorporating this mycorrhizal-dependent impact of EEAs on SOC dynamics into Earth system models could improve predictions of SOC dynamics under environmental changes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles in biogeochemical cycles and ecosystem functions. Despite the extensive research on soil pH as a key predictor of microbial community and composition, a limitation of these studies lies in determining whether bacterial and/or fungal communities are directly or indirectly influenced by pH. We conducted a controlled laboratory experiment to investigate the effects of soil pH amendment (+/- 1-2 units) with six levels on soil microbial communities in two contrasting Chinese agricultural soils (pH 8.43 in Dezhou, located in the North China Plain, Shandong vs pH 6.17 in Wuxi, located in the Taihu Lake region, Jiangsu, east China). Results showed that the fungal diversity and composition were related to soil pH, but the effects were much lower than the effects of soil pH on bacterial community in two soils. The diversity and composition of bacterial communities were more closely associated with soil pH in Wuxi soils compared to Dezhou soils. The alpha diversity of bacterial communities peaked near in situ pH levels in both soils, displaying a quadratic fitting pattern. Redundancy analysis and variation partition analysis indicated that soil pH affected bacterial community and composition by directly imposing a physiological constraint on soil bacteria and indirectly altering soil characteristics (e.g., nutrient availability). The study also examined complete curves of taxa relative abundances at the phylum and family levels in response to soil pH, with most relationships conforming to a quadratic fitting pattern, indicating soil pH is a reliable predictor. Furthermore, soil pH amendment affected the transformation of nitrogen and the abundances of functional genes involved in the nitrogen cycle, and methane production and consumption. Overall, results from this study would enhance our comprehension of how soil microorganisms in contrasting farmlands will respond to soil pH changes, and would contribute to more effective soil management and conservation strategies., Importance: This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1-2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies., Competing Interests: The authors declare no conflict of interest.

Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments ( Tuber indicum : bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla ( Rokubacteria , Nitrospirae , Chloroflexi , and Planctomycetes ) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus , Bradyrhizobium , Aminobacter , and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.

Plant growth is often limited by highly activated aluminum (Al) and low available phosphorus (P) in acidic soil. Ectomycorrhizal (ECM) fungi can improve their host plants' Al tolerance by increasing P availability while decreasing Al activity in vitro or in hydroponic or sand culture systems. However, the effect of ECM fungi on inorganic P (IP) and labile Al in acidic soil in the field, particularly in conjunction with Al treatment, remains poorly understood. The present study aimed to determine the influence of ECM fungal association on the mobilization of IP and labile Al in rhizosphere soil of host plants grown in the field with external Al treatment and the underlying nutritional mechanism in plant Al tolerance. To do so, 4-week-old Pinus massoniana seedlings were inoculated with three ECM isolates ( Laccaria bicolor 270, L. bicolor S238A, and L. bicolor S238N) and grown in a Haplic Alisol field with or without Al treatment for 12 weeks. Results showed that L. bicolor association enhanced the available P depletion and facilitated the mobilization of IP and labile Al, in turn improving the capacity of host plant to use Al-bound P, Ca-bound P, and occluded P, particularly when P. massoniana seedlings were inoculated with L. bicolor S238A. Inoculation with L. bicolor isolates also enhanced the solubility of labile Al and facilitated the conversion of acid-soluble Al into exchangeable Al. Our findings suggested that ECM inoculation could enhance plant Al tolerance in the field by mobilizing IP to improve the P bioavailability but not by decreasing Al activity. IMPORTANCE Here, we reveal the underlying nutritional mechanism in plant Al tolerance conferred by ectomycorrhizal (ECM)-fungus inoculation in the field and report the screening of a promising ECM isolate to assist phytoremediation and afforestation using Pinus massoniana in acidic soil in southern China. This study advances our understanding of the contribution of ECM fungi to plant-ECM-fungus symbiosis and highlights the vital role of ECM-fungus inoculation in plant Al tolerance. In addition, the results described in the present study confirm the importance of carrying out studies in the field rather than only in vitro studies. Our findings strengthen our understanding of the role of ECM-fungus association in detecting, utilizing, and transporting unavailable nutrients in the soil to enhance host plant growth and adaptability in response to adverse habitats., (Copyright © 2020 American Society for Microbiology.)

Grassland afforestation strongly influences the structure and function of soil microorganisms. Yet the mechanisms of how afforestation could simultaneously alter both the soil fungal and bacterial communities and its implications for ecosystem management are poorly understood, especially in nitrogen-limited ecosystems. Using high-throughput sequencing of 16S rRNA and ITS rRNA genes, the present study investigated the changes in soil properties and soil microorganisms after afforestation of natural grasslands with Chinese pine (Pinus tabuliformis) on the Loess Plateau in China. Results showed that soil bacterial diversity had no significant differences among the grassland (GL), forest-grassland transition zone (TZ), and forestland (FL), while soil fungal diversity in the GL was significantly higher than that in the FL and TZ (P < 0.05). The proportion of shared OTUs in the soil bacterial community was higher than that in the soil fungal community among the three land use types. The dominant bacterial phylum shifted from Proteobacteria to Actinobacteria, while the dominant fungal phylum shifted from Ascomycota to Basidiomycota after the GL conversion to the FL. The functional groups of ECM fungi increased significantly while biotrophic fungi decreased significantly after grassland afforestation. Both the soil bacterial and fungal communities in the TZ showed great similarity with those in the FL. In addition, among all examined soil properties, soil nitrogen (N) showed a more significant effect on the soil microbial communities. The reduction of soil N after grassland afforestation resulted in both the structure and function changes in soil microbial communities. Our results demonstrated simultaneously differential changes in the composition and diversity of both soil bacterial and fungal communities after afforestation from grasslands to planted forests., (Copyright © 2019 Elsevier B.V. All rights reserved.)

To evaluate the long-term effect of compost (CM) and inorganic fertilizer (NPK) application on microbial community structure and organic carbon (OC) accumulation at aggregate scale, soils from plots amended with CM, NPK and no fertilizer (control) for 20 years (1989-2009) were collected. Soil was separated into large macroaggregate (>2,000 μm), small macroaggregate (250-2,000 μm), microaggregate (53-250 μm), silt (2-53 μm) and clay fraction (<2 μm) by wet-sieving, and their OC concentration and phospholipid fatty acids (PLFA) were measured. The 20-year application of compost significantly (P<0.05) increased OC by 123-134% and accelerated the formation of macroaggregates, but decreased soil oxygen diffusion coefficient. NPK mainly increased OC in macroaggregates and displayed weaker influence on aggregation. Bacteria distributed in all aggregates, while fungi and actinobacteria were mainly in macroaggregates and microaggregates. The ratio of monounsaturated to branched (M/B) PLFAs, as an indicator for the ratio of aerobic to anaerobic microorganisms, increased inversely with aggregate size. Both NPK and especially CM significantly (P<0.05) decreased M/B ratios in all aggregates except the silt fraction compared with the control. The increased organic C in aggregates significantly (P<0.05) negatively correlated with M/B ratios under CM and NPK. Our study suggested that more efficient OC accumulations in aggregates under CM-treated than under NPK-treated soil was not only due to a more effective decrease of actinobacteria, but also a decrease of monounsaturated PLFAs and an increase of branched PLFAs. Aggregations under CM appear to alter micro-habitats to those more suitable for anaerobes, which in turn boosts OC accumulation.

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.

The aim of this study was to investigate influences of six-year past application rates of nitrogen and a catch crop, sweet corn (Zea maysL. ssp.SaccharataSturt), on soil microbial community and diversity in a greenhouse-based intensive vegetable soil in eastern China. Soil electrical conductivity, pH, mineral nitrogen, phospholipid fatty acids (PLFA) profiles and carbon sourceutilizationpatterns under five annually past nitrogen rates (0, 348, 522, 696 and 870 kg nitrogen ha−1) were evaluated after the establishment of sweet corn during 1–1.5-month fallow period over three-year tomato/cucumber/celery rotations. The past nitrogen application rates exerted significant effects on soil electrical conductivity, pH, nitrate-nitrogen, ammonium-nitrogen and carbon source utilization patterns, but not on PLFAs profiles. The sweet corn had a significant effect on soil chemical properties, total and actinobacterial PLFAs, but not on carbon source utilization patterns. Soil electrical conductivity, nitrate-nitrogen and the total PLFAs decreased whilst soil organic carbon, pH and the actinobacterial PLFAs increased after the establishment of sweet corn. Soil microbial functional diversity from carbon source utilization patterns and actinobacterial PLFAs were greatest after the establishment of sweet corn at a 60% of the conventional nitrogen rate (i.e. 522 kg nitrogen ha−1). Soil electrical conductivity and ammonium-nitrogen were two key factors to determine carbon source utilization patterns, whilst soil pH was the key factor to determine PLFAs profiles. A combination of the catch crop sweet corn during summer fallow and a 60% of the conventional nitrogen rate is a sustainable pathway of utilizing greenhouse-based intensive vegetable soils in eastern China. [ABSTRACT FROM AUTHOR]

Repeated compost or inorganic fertilization may increase soil organic C (SOC) but how SOC accumulation relates to changes in soil aggregation, microenvironment and microbial community structure is unclear. Arable soils (Aquic Inceptisol) following a 20-year (1989-2009) application of inorganic fertilizer nitrogen (N), phosphorus (P) and potassium (K) (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer PK (PK), compost (CM), half compost N plus half fertilizer N (HCM), and non-fertilization (Control) were collected to evaluate the relationship between SOC accumulation rate, soil aggregation, microenvironment and microbial community composition using phospholipid fatty acid (PLFA) analysis. Compared to the starting year, SOC content after 20 years under CM, HCM and NPK was significantly ( P < 0.05) increased by 172 %, 107 % and 56 %, respectively, and by less than 50 % under NP, NK and PK. The mass proportion of macroaggregates was increased by 101-250 % under CM, but was not significantly affected by inorganic fertilizations, except PK. Compost and NPK significantly ( P < 0.05) reduced the effective diffusion coefficient of oxygen primarily by increasing the proportion of pores <4 μm, and in contrast, increased the abundance of branched PLFAs and Gram-positive (G) bacteria, resulting in the reduction of the ratio of monounsaturated/branched PLFAs (M/B) compared with Control. The mass proportion of macroaggregates was significantly ( P < 0.01) and negatively correlated with the effective diffusion coefficient of oxygen; the latter was positively associated with M/B ratio. The SOC accumulation rate ( z) had a significant interaction with the mass proportion of macroaggregates ( x) and M/B ratio ( y) ( z = 0.514 + 4.345e-0.149e). Our results suggested that SOC accumulation promoted the macroaggregation and reduced the effective diffusion coefficient of oxygen, causing changes in microhabitats and a shift in microbial community composition to more facultative and/or obligate anaerobes; such microbial community shifts favored accumulation of SOC in turn. [ABSTRACT FROM AUTHOR]

This study addressed if long-term combined application of organic manure and inorganic fertilizers could improve the synchrony between nitrogen (N) supply and crop demand. N-labeled urea was applied to micro-plots within three different fertilized treatments (no fertilizer, No-F soil; inorganic NPK fertilizers, NPK soil; and manure plus inorganic NPK fertilizers, MNPK soil) of a long-term field trial (1990-2009) in a dryland wheat field in the south Loess Plateau, China. After one season of wheat harvest, N use efficiency was 20, 58, and 65 % in the No-F, NPK, and MNPK soil, respectively. During the early wheat growth stage, microbial immobilization of applied N was significantly ( P < 0.05) highest in the MNPK soil (15.3 %), higher in the NPK soil (12.6 %), and lowest in the No-F soil (7.4 %). Of the N immobilized by the soil microbial biomass, 69 % (NPK soil) to 83 % (MNPK soil) was released between the stem elongation and flowering of wheat. Compared with the NPK soil, the MNPK soil had significantly ( P < 0.05) higher grain yield. Our findings highlight that long-term application of organic manure with inorganic fertilizers cannot only improve the synchrony of N supply for crop demand but also increase N use efficiency and grain yield. [ABSTRACT FROM AUTHOR]

Due to the ever-increasing worldwide plantation of sweet leaf Stevia rebaudiana (Bertoni), how to efficiently and effectively utilize the huge amounts of leaf residues that contain abundant nutrients after sweetener extraction becomes an eminent issue. One option is to return these residues into soil, as organic manure in the fresh or composted form, in order to both sustain soil fertility and avoid potential environmental pollution. In a field experiment, we studied if the Stevia leaf residue returning affected both plant and soil microbial growths as well as the possible change of soil microbial community composition. In doing so, four treatments were employed: (1) no chemical fertilization and no Stevia residue returning (no-fertilization control); (2) chemical N, P, and K fertilization (NPK); (3) fresh Stevia residue plus NPK (FS + NPK); and (4) composted Stevia residue plus NPK (CS + NPK). Responses of plant and soil microbial communities to Stevia residue input after 1-year fertilizations were investigated by multiple approaches, including soil enzyme assay, real-time quantitative polymerase chain reaction, and PCR-denaturing gradient gel electrophoresis. Our results showed that compared to the sole NPK and no-fertilization control, returning Stevia residues to soil stimulated the enzyme activities of dehydrogenase, invertase, and urease, except neutral phosphomonoesterase; thereby, both the Stevia leaf biomass and sweet glycoside of rebaudioside A were increased. The soil microbial community abundance was increased by the returning of Stevia residues, and their composition was shifted, evidenced by an increase of relative abundance of some genotypic groups, such as Bacillales. Further molecular analysis of Bacillus confirmed that this guild composition was positively influenced by Stevia residue returning, especially for Bacillaceae. Our results demonstrated an effective use of Stevia residues as organic manure for promoting Stevia yield and quality through stimulating soil microbial growth and enzyme activities. [ABSTRACT FROM AUTHOR]

Abstract: This study compared the responses of soil chemical and microbial indicators to the conservational tillage (CT) versus traditional tillage (TT) in a Haplic Cambisol in the North China Plain (NCP). These indicators included soil organic C (SOC), soil total N (STN), soil available P (SAP), cation exchange capacity (CEC), exchangeable Ca2+ and Mg2+, microbial biomass C (MBC), microbial biomass N (MBN), alkaline phosphomonoesterase (AP), β-glucosidase, N-acetyl-β-glucosaminidase (NAG), nitrate reductase (NR), protease, urease and the geometric mean of the assayed enzymes (GMea). Our results showed that almost all investigated parameters, except the contents of CEC, Ca2+, Mg2+ and the ratios of GMea/MBN and C/N, were significantly higher under the CT (no-till, NT and reduced-till, RT) than those under the TT, whilst the crop yield was not significantly affected by tillage treatments. Principle component analysis (PCA) showed that the first and second component explained 67.2% and 16.6% of the total variation, respectively. The first component was significantly correlated with GMea, MBC, MBN and β-glucosidase, and effectively discriminated soils under the NT or RT from those under the TT. Our results indicated that the 6-year CT improved the quality of the Haplic Cambisol by enhancing its chemical and microbial properties, whilst GMea, MBC, MBN and β-glucosidase were among the most effective indicators for monitoring these improvements. [Copyright &y& Elsevier]

Canopy gaps are a key component of the disturbance regime and old-growth character in subalpine coniferous forests. Despite the importance of canopy gaps in the dynamics and management of subalpine forests, limited information is available on the temporal dynamics of microbial pools and their roles in the responses of soil organic matter and nutrient flux to canopy gaps. This study tests the hypothesis that gap creation facilitates soil organic carbon (C) retention by soil microbial biomass in the organic horizon. Based on the degree of decomposition, the organic horizon can be divided into fresh litter layer (LL), fragmented litter layer (FL) and humified litter layer (HL) components; these layers represent different stages of litter decomposition. We examined the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) from the gap center to closed canopy in a subalpine Minjiang fir ( Abies faxoniana ) forest during different seasons. Gap creation promoted soil organic C retention by soil microbial biomass in the organic horizon. Storage of total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) accumulated in the HL. Moreover, gap creation accelerated C, nitrogen (N) and phosphorus (P) releases from the LL but inhibited C, N and P outputs from the HL. Microbial biomass in the LL responded rapidly and sensitively to canopy gaps. The most important factors affecting microbial biomass in the organic horizon were soil temperature and snow cover, which are governed by the canopy gap. Microbial pools and their stoichiometry were significantly and positively correlated with TOC. A thorough comprehension of the spatio-temporal traits of microbial biomass pools in the organic horizon under gap creation could aid the regeneration of protected subalpine fir forest on the eastern Tibetan Plateau. [ABSTRACT FROM AUTHOR]