Search Results (23)

Background: Land use change fundamentally alters soil microbial communities and biochemical processes, yet the integrated effects on rhizosphere microbiome–metabolome networks remained poorly understood. Objective: This study investigated land uses as forest, grassland and intermediary edge shape the rhizosphere biochemical networks of naturally grown Barbarea vulgaris. Methods: Rhizosphere soils of Barbarea vulgaris were analysed for microbial community structure abundance, and metabolomic profile applying phospholipid fatty acid (PLFA) profiling and mass spectrometric untargeted metabolomics (GC–MS/MS and MALDI–TOF/TOF MS). These were coupled with co–inertia analysis to assess microbiome–metabolome interactions. Results: Microbial community analysis revealed significant effects of land use on bacterial community structure (G+/G−, p < 0.001). Untargeted metabolomics identified 248 metabolites, of which 161 were mapped to KEGG pathways. Amino acids and derivatives (21.1%) followed by organic acids (16.8%) were the most representative among identified metabolites. Pathway enrichment analysis revealed coordinated reprogramming of central carbon and nitrogen metabolism across land use gradients, particularly in the amino acid metabolism, TCA cycle, and glycolysis/gluconeogenesis pathways. Microbiome–metabolome coupling analysis revealed distinct correlation patterns between microbial phenotypes and metabolite classes, with forest environments showing the strongest biochemical network integration (RV = 0.91). Edge habitats presented intermediate signatures, supporting their role as transitional zones with unique biochemical properties. Conclusions: The environmental context fundamentally shapes rhizosphere biochemical network organization through coordinated shifts in bacterial community structure and metabolic pathway activity. These habitat-specific metabolic signatures suggest that land use change triggers adaptive biochemical responses that may influence plant performance and ecosystem functioning across environmental gradients. Full article

Despite the increasing recognition of the role of urban orchard ecosystems in sustainable urban development, the mechanistic understanding of how tree species soil biochemical heterogeneity drives microbial community assembly, the spatial patterns governing microbe-environment interactions, and their collective contributions to ecosystem multifunctionality remain poorly characterized. This study investigated how Prunus species and soil depth affect microbial biodiversity and metabolomic signatures in an urban orchard in Cluj-Napoca, Romania. Soil samples were collected from five fruit tree species (apricot, peach, plum, cherry, and sour cherry) across three depths (0–10, 10–20, and 20–30 cm), resulting in 225 samples. The microbial community structure was analyzed through phospholipid fatty acid (PLFA) profiling, whereas the soil metabolome was analyzed by mass spectrometry techniques, including gas chromatography–mass spectrometry (GC–MS/MS) and MALDI time-of-flight (TOF/TOF) MS, which identified 489 compounds across 18 chemical classes. The results revealed significant tree species-specific effects on soil microbial biodiversity, with bacterial biomarkers dominating and total microbial biomass varying among species. The soils related to apricot trees presented the highest microbial activity, particularly in the surface layers. Metabolomic analysis revealed 247 distinct KEGG-annotated metabolites, with sour cherry exhibiting unique organic acid profiles and cherry showing distinctive quinone accumulation. Depth stratification influenced both microbial communities and metabolite composition, reflecting oxygen gradients and substrate availability. These findings provide mechanistic insights into urban orchard soil biogeochemistry, suggesting that strategic species selection can harness tree species-soil microbe interactions to optimize urban soil ecosystem services and enhance urban biodiversity conservation. Full article

Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of 18 plots were considered in this study, with six plots for each fragment type. Intact interior forest (F), internal forest path fragment (IF), and external forest path fragment (EF) soils were sampled at 0–15, 15–30, and 30–45 cm depths and profiled through phospholipid-derived fatty acid (PLFA) chemotyping and amino sugar proxies for living microbiome and microbial-derived necromass assessment, respectively. Carbon fractionation was performed through the chemical oxidation method. Diversity indices (Shannon–Wiener, Pielou evenness, Margalef richness, and Simpson dominance) were calculated based on the determined fatty acids derived from the phospholipid fraction. The microbial biomass ranged from 85.1 to 214.6 nmol g⁻¹ dry soil, with the surface layers of F exhibiting the highest values (p < 0.01). Shannon diversity declined systematically from F > IF > EF. The microbial necromass varied from 11.3 to 23.2 g⋅kg⁻¹. Fragmentation intensified the stratification of carbon pools, with organic carbon decreasing by approximately 14% from F to EF. Our results show that EFs possess a declining microbiome continuum that weakens their carbon sequestration capacity in urban forests. Full article

Background/Objectives: This research aimed to investigate phospholipid fatty acid (PLFA) distribution in the brain, kidneys, and white adipose tissue (WAT) and lipid profiles in response to high-fat diets. Methods: Adult female C57BL/6 mice were fed high-fat diets containing 25% linseed, palm, or sunflower oil for 100 days. The fatty acid composition of dietary oils and tissue PL were analyzed using gas–liquid chromatography. Results: Linseed oil increased n-3 polyunsaturated fatty acids (PUFAs) with subsequent conversion into long-chain n-3 PUFAs in the brain and kidney PL, while only alpha-linolenic acid was elevated in WAT. Palm and sunflower oils resulted in unique PLFA distributions in the kidneys and WAT. Palm oil raised linoleic acid without conversion to pro-inflammatory n-6 PUFAs. Sunflower oil increased saturated palmitic acid, as opposed to the rise in monounsaturated oleic acid. Linseed oil also significantly improved lipid profiles, reducing LDL and increasing HDL levels while enhancing cardiovascular indices. Conclusions: This study demonstrates that dietary oils significantly impact organ-specific PLFA profiles, with linseed oil enriching brain and renal n-3 PUFAs, while palm and sunflower oils induce distinct modifications in the kidney and WAT. Moreover, linseed oil offers notable cardioprotective benefits due to the favorable lipid profile changes. These findings highlight the importance of dietary fat selection in achieving balanced lipid metabolism and suggest that diverse oil combinations may be essential for optimizing health outcomes. Full article

This study evaluated the changes in microbial activity in the course of time following the joint application of the herbicides S-metolachlor, foramsulfuron, and thiencarbazone-methyl to two soils (S1 and S2) under conventional tillage (CT) and non-tillage (NT) management in field conditions. The biochemical parameters of soil respiration (RES), dehydrogenase activity (DHA), microbial biomass (BIO), and the phospholipid fatty acid (PLFA) profile were determined at 1, 34, and 153 days during herbicide dissipation. In the absence of herbicides, all microbial activity was higher under NT than CT conditions, with higher or similar mean values for S1 compared to S2. A continuous decrease was detected for RES, while DHA and BIO recovered over time. In the presence of herbicides, a greater decrease in all microbial activity was detected, although the changes followed a similar trend to the one recorded without herbicides. In general, a greater decrease was observed in S1 than in S2, possibly due to the higher adsorption and/or lower bioavailability of herbicides in this soil with a higher organic carbon content. The decrease was also greater under CT conditions than under NT conditions because the herbicides can be intercepted by the mulch, with less reaching the soil. These changes involved evolution of the structure of the microbial community. Full article

Managed and natural vegetation restorations are two vital measures of land restoration; however, their effects on soil microbial communities at a large scale are not clearly understood. Hence, changes in the microbial community composition after 15 years of vegetation restoration along a climatic gradient in the subtropical karst region of Southwest China were assessed based on phospholipid fatty acids (PLFAs) profiles. Managed (plantation forest) and natural (naturally recovered to shrubbery) vegetation restoration types were compared, with cropland and mature forest serving as controls. Soil microbial community abundance was significantly higher under the two vegetation restoration types than in the cropland; however, it was lower than in the mature forest. The abundance, composition, and structure of soil microbial communities did not differ significantly between plantation forest and shrubbery. Soil organic carbon or total nitrogen was the primary factor positively affecting soil microbial abundance, whereas the mean annual temperature (MAT) was recognized as the primary factor contributing to the variation in the soil microbial community structure. Moreover, temperature had opposite effects on different indicators of microbial community structure. That is, it positively and negatively affected the ratios of gram-positive to gram-negative bacterial PLFAs (GP:GN) and fungal to bacterial PLFAs (F:B), respectively. Our results show that both vegetation restoration types have the ability to improve soil productivity in karst areas. Furthermore, shifts in soil microbial community structure (GP:GN and F:B ratios) induced by warming are likely to lead to a higher proportion of labile carbon, which is sensitive to soil tillage. Hence, more attention should be paid to ecological restoration in warmer karst areas to alleviate the severe loss of soil carbon in croplands. Full article

We aimed to explore how the invasion of the alien plant Solanum elaeagnifolium affects soil microbial and nematode communities in Mediterranean pines (Pinus brutia) and maquis (Quercus coccifera). In each habitat, we studied soil communities from the undisturbed core of both formations and from their disturbed peripheral areas that were either invaded or not by S. elaeagnifolium. Most studied variables were affected by habitat type, while the effect of S. elaeagnifolium was different in each habitat. Compared to maquis, the soil in pines had higher silt content and lower sand content and higher water content and organic content, supporting a much larger microbial biomass (PLFA) and an abundance of microbivorous nematodes. The invasion of S. elaeagnifolium in pines had a negative effect on organic content and microbial biomass, which was reflected in most bacterivorous and fungivorous nematode genera. Herbivores were not affected. In contrast, in maquis, organic content and microbial biomass responded positively to invasion, raising the few genera of enrichment opportunists and the Enrichment Index. Most microbivores were not affected, while herbivores, mostly Paratylenchus, increased. The plants colonizing the peripheral areas in maquis probably offered a qualitative food source to microbes and root herbivores, which in pines was not sufficient to affect the much larger microbial biomass. Full article

Spent mushroom substrate (SMS) is the organic residue generated during mushroom cultivation, and it is being produced in ever-greater quantities around the world. Different applications for this residue have been proposed for its valorization, but its application as a soil amendment could be one of the most sustainable. SMS improves soil quality by increasing its organic matter (OM), thereby enhancing the sustainability of agricultural systems. The objective of this work was to evaluate the effect of the application of two doses of SMS on the chemical, biochemical, and microbiological characteristics of two degraded vineyard soils in La Rioja (Spain) with different textures, as a new regenerative agricultural practice. The variations in organic carbon (OC), micro- and macronutrients, soil microbial biomass (BIO), respiration (RES), dehydrogenase activity (DHA), and the profile of phospholipid fatty acids (PLFAs) extracted from the soils were evaluated over two years. An initial increase in soil OC content was recorded in both soils, although the content that remained over time differed for each site. In general, SMS enhanced DHA, RES, and BIO in the soils, but the effect varied, possibly being conditioned by the availability of OC for soil microorganisms. In general, changes in the soils’ microbial structure after SMS application were not very significant over the two-year experimental period. Full article

Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called ‘shiro’, which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types. Full article

An elevated CO₂ (eCO₂) fumigation experiment was carried out to study the influence of various CO₂ concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol⁻¹ CO₂ fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of ¹³C-PLFAs was much higher under eCO₂ treatment. Most of the ¹³C-CO₂ was incorporated into the ¹³C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G⁻) and i17:0 (Gram-positive bacteria, G⁺) via rhizodeposition from tomato under ambient CO₂ (aCO₂) and eCO₂ treatments, suggesting similar responses of active microorganisms to different CO₂ treatments. However, the fungi (characterized by the ¹³C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO₂. Actinomycetes, marked by the ¹³C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO₂ treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO₂ significantly affected microbial biomass and microbial community structures involved in the incorporation of ¹³C-CO₂ via tomato root secretions, as supported by Adonis analysis and the Mantel test. Full article

Pomegranate (Punica granatum L.) is one of the most important fruit trees in semi-arid land. Previous studies were primarily focused on soil microbial community composition under different pomegranate plantation managements. However, soil microbial community composition under long-term pomegranate plantation has rarely been studied. We investigated pomegranate plantation along with an age sequence (i.e., 1, 3, 5, and 10 years after pomegranate plantation; abbreviated by P1, P3, P5, P10, respectively) in the Middle Yellow River floodplain. Our objectives were to address (1) variations of soil physicochemical properties and (2) changes in soil microbial community composition and the influential factors. The results demonstrated that the soil water content of pomegranate plantation decreased with the increase of pomegranate plantation stand age. Specifically, dissolved organic carbon, ammonium, and available phosphorus increased significantly with stand age both at 0–10- and 10–20-cm soil depths. The P10 had the highest microbial phospholipid fatty acid (PLFA) profiles, including fungi, bacteria, Gram-positive bacteria, Gram-negative bacteria, and arbuscular mycorrhizal fungi. The ratio of fungal PLFAs to bacterial PLFAs increased and the ratio of Gram-positive to Gram-negative bacterial PLFAs decreased along the pomegranate plantation stand age. Dissolved organic carbon was the most important influential factor among the studied variables, which explained 42.2% variation of soil microbial community. In summary, the long-term plantation of pomegranate elevated soil microbial biomass and altered microbial community composition. Full article

Biogeographic separation has been an important cause of faunal and floral distribution; however, little is known about the differences in soil microbial communities across islands. In this study, we determined the structure of soil microbial communities by analyzing phospholipid fatty acid (PLFA) profiles and comparing enzymatic activities as well as soil physio-chemical properties across five subtropical granite-derived and two tropical volcanic (andesite-derived) islands in Taiwan. Among these islands, soil organic matter, pH, urease, and PLFA biomass were higher in the tropical andesite-derived than subtropical granite-derived islands. Principal component analysis of PLFAs separated these islands into three groups. The activities of soil enzymes such as phosphatase, β-glucosidase, and β-glucosaminidase were positively correlated with soil organic matter and total nitrogen. Redundancy analysis of microbial communities and environmental factors showed that soil parent materials and the climatic difference are critical factors affecting soil organic matter and pH, and consequently the microbial community structure. Full article

Although elevated CO₂ (eCO₂) in the atmosphere is one of the main factors influencing climate and ecosystem stability, less research on eCO₂ in greenhouse soil systems has been conducted, despite their prevalence. In this article, phospholipid fatty acid (PLFA) profiling, 16S rRNA and Internally Transcribed Spacer (ITS) gene sequencing and high-throughput quantity polymerase chain reactions (HT-qPCRs) for 72 biogeochemical cycling-related genes were used to reveal the comprehensive responses of microbes to 23 days eCO₂ fumigation in the soil of a tomato greenhouse. Our results indicated that eCO₂ significantly increased microbial biomass (p < 0.05). The fungal community was more susceptible to eCO₂ than the bacterial community; the fungal alpha diversity indices decreased significantly under eCO₂ (p < 0.05) and the abundance of Ascomycota and its lower level taxa also increased significantly (p < 0.01). The absolute abundance of numerous C, N, P, S and methane cycling related genes increased significantly (p < 0.05) under eCO₂. Furthermore, the microbial community structure and function were correlated with certain measured plant characteristics. Hence, the microbial ecosystem of the tomato greenhouse soil system was stimulated under eCO₂. These results contribute to a greater understanding of how eCO₂ in the atmosphere affects terrestrial ecosystem stability. Full article

The soil microbial activity, biomass and structure were evaluated in an unamended (S) and organically amended soil treated with two commercial formulations of the herbicides chlorotoluron (Erturon^®) and flufenacet plus diflufenican (Herold^®) under field conditions. Soils were amended with spent mushroom substrate (SMS) or green compost (GC). Soil microbial dehydrogenase activity (DHA), biomass and structure determined by the phospholipid fatty acid (PLFA) profiles were recorded at 0, 45, 145, 229 and 339 days after herbicide treatment. The soil DHA values steadily decreased over time in the unamended soil treated with the herbicides, while microbial activity was constant in the amended soils. The amended soils recorded higher values of concentrations of PLFAs. Total soil microbial biomass decreased over time regardless of the organic amendment or the herbicide. Herbicide application sharply decreased the microbial population, with a significant modification of the microbial structure in the unamended soil. In contrast, no significant differences in microbial biomass and structure were detected in S + SMS and S + GC, untreated or treated with herbicides. The application of SMS and GC led to a significant shift in the soil microbial community regardless of the herbicides. The use of SMS and GC as organic amendments had a certain buffer effect on soil DHA and microbial biomass and structure after herbicide application due to the higher adsorption capacity of herbicides by the amended soils. Full article

Background and Aims: The association of fatty acids with coronary heart disease (CHD) has been examined, mainly through dietary measurements, and has generated inconsistent results due to measurement error. Large observational studies and randomized controlled trials have shown that plasma phospholipid fatty acids (PL-FA), especially those less likely to be endogenously synthesized, are good biomarkers of dietary fatty acids. Thus, PL-FA profiles may better predict CHD risk with less measurement error. Methods: We performed a matched case-control study of 2428 postmenopausal women nested in the Women’s Health Initiative Observational Study. Plasma PL-FA were measured using gas chromatography and expressed as molar percentage (moL %). Multivariable conditional logistic regression was used to calculate odds ratios (95% CIs) for CHD associated with 1 moL % change in PL-FA. Results: Higher plasma PL long-chain saturated fatty acids (SFA) were associated with increased CHD risk, while higher n-3 polyunsaturated fatty acids (PUFA) were associated with decreased risk. No significant associations were observed for very-long-chain SFA, monounsaturated fatty acids (MUFA), PUFA n-6 or trans fatty acids (TFA). Substituting 1 moL % PUFA n-6 or TFA with an equivalent proportion of PUFA n-3 were associated with lower CHD risk. Conclusions: Higher plasma PL long-chain SFA and lower PUFA n-3 were associated with increased CHD risk. A change in diet by limiting foods that are associated with plasma PL long-chain SFA and TFA while enhancing foods high in PUFA n-3 may be beneficial in CHD among postmenopausal women. Full article