Search Results (14)

With continuous increases in nitrogen (N) deposition in the future, its impacts on terrestrial ecosystems are attracting growing concern. Arbuscular mycorrhiza (AM) fungi play a crucial role in shaping both soil microbial and plant communities. AM fungi play a crucial role in shaping the soil microbial and plant communities, yet their patterns of influence under increased N deposition scenarios remain unclear, particularly in desert ecosystems. Therefore, we conducted a field experiment simulating increased N deposition and AM fungal suppression to assess the effects of increased N deposition and AM fungi on soil microbial communities, employing phospholipid fatty acid (PLFA) biomarker technology in the Gurbantunggut Desert of Xinjiang. We found that increased N deposition promoted soil microbial biomass, including AM fungi, fungi, Actinomycetes (Act), Gram-positive bacteria (G⁺), Gram-negative bacteria (G⁻), and Dark Septate Endophyte (DSE). AM fungal suppression significantly increased the content of soil Act and G⁺. There were clearly and significantly interactive effects of increased N deposition and AM fungi on soil microbial contents. Both increased N deposition and AM fungi caused significant changes in soil microbial community structure. Random forest analysis revealed that soil nitrate N (NO₃⁻-N), Soil Organic Carbon (SOC), and pH were main factors influencing soil microorganisms; soil AM fungi, G⁺, and Act significantly affected plant Shannon diversity; soil G⁻, Act, and fungi posed significant effects on plant community biomass. Finally, the structure equation model results indicated that soil fungi, especially AM fungi, were the main soil microorganisms altering the plant community diversity and biomass under increased N deposition. This study reveals the crucial role of AM fungi in regulating soil microbial responses to increased N deposition, providing experimental evidence for understanding how N deposition affects plant communities through soil microorganisms. 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

The integration of manure and straw substantially affects soil organic carbon (SOC) dynamics, transformation, and long-term stabilization in agricultural systems. Dissolved organic carbon (DOC), particulate organic carbon (POC), and mineral-associated organic carbon (MOC) are the three main components of the SOC pool, each influencing soil carbon dynamics and nutrient cycling. Current research gaps remain regarding how combined fertilization practices affect the inputs of plant-originated and microbe-derived carbon into SOC pools and stability mechanisms. Our investigation measured SOC fractions (DOC, POC, MOC), SOC mineralization rate (SCMR), microbial necromass carbon, lignin phenols, enzyme activities, and microbial phospholipid fatty acids (PLFAs) over a long-term (17 years) field experiment with four treatments: mineral fertilization alone (CF), manure-mineral combination (CM), straw-mineral application (CS), and integrated manure-straw-mineral treatment (CMS). The CMS treatment exhibited notably elevated levels of POC (7.42 g kg⁻¹), MOC (10.7 g kg⁻¹), and DOC (0.108 g kg⁻¹), as well as a lower SCMR value (1.85%), compared with other fertilization treatments. Additionally, the CMS treatment stimulated the buildup of both bacterial and fungal necromass while enhancing the concentrations of ligneous biomarkers (vanillin, syringyl, and cinnamic derivatives), which correlated strongly with the elevated contents of fungal and bacterial PLFAs and heightened activity of carbon-processing enzymes (α-glucosidase, polyphenol oxidase, cellobiohydrolase, peroxidase, N-acetyl-β-D-glucosidase). Furthermore, fungal and bacterial microbial necromass carbon, together with lignin phenols, significantly contributed to shaping the composition of SOC. Through random forest analysis, we identified that the contents of bacterial and fungal necromass carbon were the key factors influencing DOC and MOC. The concentrations of syringyl phenol and cinnamyl phenols, and the syringyl-to-cinnamyl phenols ratio were the primary determinants for POC, while the fungal-to-bacterial necromass carbon ratio, as well as the concentrations of vanillyl, syringyl, and cinnamyl phenols, played a critical role in SCMR. In conclusion, the manure combined with straw incorporation not only promoted microbial growth and enzyme activity but also enhanced plant- and microbial-derived carbon inputs. Consequently, this led to an increase in the contents and stability of SOC fractions (DOC, POC, and MOC). These results suggest that manure combined with straw is a viable strategy for soil fertility due to its improvement in SOC sequestration and stability. Full article

Rock dust (RD) is a by-product of the precious metal mining industry. Some mining operations produce close to 2,000,000 Mg of RD/year, posing disposal issues. This study evaluated the physicochemical and microbial properties of RD from gold mining and its potential use in RD-based growing media. Ten media formulations were tested: Promix (Control), 100% (RD), 100% topsoil (TS), 50% RD + 50% topsoil (RDT), 25% RD + 75% topsoil (RT), 50% RD + 50% Promix (RP), 50% RD + 25% biochar + 25% Promix (RBP), 50% RD + 25% compost + 25% Promix (RCP), 50% RD + 50% biochar (RB), and Huplaso (negative control). RD particle size ranged from 0.1 to 2 mm with a bulk density of 1.5 g cm⁻³, while RD-based media ranged from 0.8 to 1.1 g cm⁻³ showing increased porosity. Nutrient content was analyzed using Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES), and the active microbial community assessed using PLFA biomarkers via GC-MS/FID, n = 4 and p = 0.05. Microbial analysis identified five classes (protozoa, eukaryotes, Gram-positive (G+), Gram-negative (G−), and fungi (F)), with a significant increase in G−, G+, and F in RD-based amendment RBP (28%) compared to control P (9%). G+, G−, and F showed a strong negative correlation (r = −0.98) with pH, while calcium correlated positively (r = 0.85) with eukaryotes and a strong positive correlation (r = 0.95) of cation exchange capacity with G+. This study suggests blending RD with organic amendments improves physicochemical quality and microbial activity, supporting its use in crop production over disposal. Full article

The phospholipid fatty acid method was used to determine the shifts in microbial biomass due to irrigation with reverse-osmosis (RO) concentrate (or highly saline reject water) and brackish groundwater (BGW). In this greenhouse study, RO concentrate and BGW were applied to irrigate pecan trees for 8 months for two consecutive seasons. The objectives of the study were to (i) evaluate how irrigation with RO concentrate and BGW impacts soil microbial composition in pecan rhizospheres using microbial phospholipid fatty acid (PLFA) biomarkers as indicators, and (ii) evaluate its implications on soil health. Three treatments of RO concentrate (EC = 8.0 dS/m), BGW (EC = 4.0 dS/m), and the city of Las Cruces’s water (EC = 0.8 dS/m) as a control were used to irrigate pecan trees. EC, pH, and organic matter (OM%) content of the soil samples were measured, and PLFA biomarkers for the microbial community were determined. Na-, Cl-, and K-ion concentrations were 26.16, 32.54, and 5.93 meq/L in 2017 and 25.44, 24.26, and 5.49 meq/L in 2018, respectively, in RO irrigation pots. For two seasons, gram-positive bacteria were dominant, while gram-negative bacteria were not detected in the second season. PLFA biomarkers of fungi were found among all three treatments in the first season; however, they appeared only with BGW in the second season. Actinomycetes were recorded in the first season while they were not seen in the second season. Increases in soil salinity and microbial shifts could have important implications for soil health. Irrigating with RO and BGW shifted the soil microbial composition; therefore, long-term irrigation with BGW and RO concentrate would be deleterious for pecan production and soil health. Full article

The wetlands in China’s Sanjiang Plain have experienced intensive anthropogenic disturbance recently, and this has obviously changed their environmental characteristics. Soil microorganisms play an important role in wetland ecosystems. However, the effects of different wetland types on soil microbial diversity and community composition remain largely unclear. Therefore, we assessed the effects of three typical wetland types—permanently flooded wetlands, seasonally flooded wetlands and non-flooded wetlands—on soil microbial communities in the Sanjiang Plain, using phospholipid fatty acid analysis (PLFA) technology. A total of 56 different PLFA compounds were identified, of which 10 are typically produced by uncharacterized bacteria, 15 by Gram-positive bacteria, and 11 by Gram-negative bacteria. In addition, 2 fungal groups were identified, based on four PLFAs, and four PLFAs typical for protozoa were detected. High levels were detected for 16:0 (attributed to bacteria) and i17:1ω9c (produced by Gram-positive bacteria). The latter (i17:1ω9c) was exceptionally high in non-flooded soil (8407.15 ± 2675.84 ng/g). High levels of 18:1ω7c (1939.15 ± 666.13 ng/g) and 18:1ω9c (1713.26 ± 360.65 ng/g) were detected in permanently flooded wetlands and about the same in seasonally flooded wetlands, but lower ranks were present in the drier non-flooded wetlands. The Shannon-Wiener diversity index decreased with permanently flooded wetlands (3.05) > seasonally flooded wetlands (3.02) > non-flooded wetlands (2.12). Redundancy analysis showed that the two axes could explain a total of 94.48% of soil microbial communities. Soil water content, total and available phosphorus, and total and available nitrogen correlated significantly with soil microbial communities of three wetland types. Cluster analysis of correlations between individual PLFA biomarkers and soil physiochemical properties demonstrated the complexity of the community responses to the three different habitats. This study demonstrates that microbial diversity and composition changed sensitivity among the three wetland types, and soil moisture content was the key environmental factor to affect the soil microbial communities. Full article

Dumped waste is not only a problem from an aesthetic point of view, but also has an environmental polluting effect, or can even pose a direct danger if the waste is dumped in illegal landfills in an uncontrolled manner with unknown composition. In the case of soil pollution, the assessment of the changing microbial state can be used as an indicator of initial changes, since waste as a pollutant impacts the diversity of the landfill’s microbial community. The degree of change depends on the qualitative and quantitative composition of the pollutants, which can be measured through the microbial phospholipid fatty acid (PLFA) pattern. The aim was a comprehensive assessment of the soil microbiological and toxicological hazards of various illegal landfill. Cluster-analysis of the average principal component revealed significant differences between the experimental sites. In comparison with the control site, the percentage of fatty acid biomarkers of Gram-positive bacteria was significantly higher in the contaminated areas, as well as the ratio of trans/cis isomerization in the case of 16:1ω7 and 18:1ω7 fatty acids. The inverse tendency was observed in the relative quantities of fatty acid biomarkers of Gram-negative bacteria compared to Actinomycetes, and in the fungal-bacterial ratio. Full article

Soil microorganisms and dissolved organic matter (DOM) play vital roles in nutrient cycling and maintaining plant diversity. The aim of this study was to clarify the relationship between DOM component characteristics and microbial community structure in the soil of Larix principis-rupprechtii Mayr. plantations. We quantified the responses of the soil microbial and DOM characteristics to stand age in a plantation forest ecosystem using phospholipid fatty acid (PLFA) analyses, ultraviolet-visible spectroscopy, and fluorescence spectroscopy. Three humic-like components and a fulvic-like component were identified from the soil samples, and humic-like substances were the dominant component of the soil DOM of the stands of different ages. The fluorescence index showed that the sources of soil DOM in the stands of different ages throughout the growth stages may be mostly plant residues, with very little contribution from microbial sources. Furthermore, the results demonstrated that stand age and growth season had a significant effect on the contents of the soil PLFA biomarkers of L. principis-rupprechtii Mayr. Additionally, significantly higher contents of different species of soil PLFA biomarkers were observed in the young forest (17a) than in the sapling forest (7a) and half-mature forest (27a), suggesting that stand age differences in the quality and quantity of larch litter and soil physicochemical characteristics affect the microbial community structure. Redundancy analysis (RDA) showed that changes in the soil DOM quality and components that were driven by growth season and stand age were the major drivers of variations in the soil microbial community structure in the study region. Overall, the seasonal variations in DOM quality and components may contribute to the variability of soil microorganisms, and the soil microbial responses to tree age will depend upon the provisioning of these resources. Full article

We investigated the effects of three botanicals with nematicidal properties (anise-Pimpinella anisum, parsley-Petroselinum crispum, and rocket-Eruca sativa) on the soil nematode community, in terms of trophic structure and nematode genera composition. We compared effects with those of fluopyram (synthetic nematicide) and Nemagold (bionematicide). We assessed the role of time, by sampling 15 and 45 days after treatments and analyzing nematode genera and microbial phospholipid fatty acid biomarkers (PLFA). Soil incorporation of botanicals reduced plant parasitic nematodes, increased bacterivores, especially the enrichment opportunists and among them Rhabditis, having no effect on fungivores and non-parasitic plant feeders. Neither the number nor the composition and dominance hierarchy of nematode genera were affected. Nemagold did not induce any significant change, while fluopyram decreased both free-living and parasitic nematodes, but with no uniform effect against all genera. The least affected genus was the fungivorous Aphelenchus. While most microbial PLFAs increased with time, the abundances of nematode genera did not change, except the Meloidogyne incognita second stage juveniles, which emerged in soil only 45 days after treatments. The low enrichment index and high channel index values of the fluopyram soil samples indicated a stressful environment. The opposite was observed in the botanical treatments, especially parsley and rocket. 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

Sugarcane (Saccharum spp. hybrid) successive planting (also called monoculture) causes serious yield losses and its management is not well studied in Histosols. Based on very few studies in other sugarcane regions, root colonization by harmful soil fungi is considered as a major cause of this yield decline, but there is lack of knowledge on its management in Histosols. A two-year greenhouse study was conducted with soil-drench application of mancozeb, mefenoxam, and azoxystrobin fungicides to determine their effects on early root and shoot growth, soil microbial communities, and nutrient uptake by plants. The study indicated that mancozeb soil application improved sugarcane-shoot and -root dry matter by 3–4 times and shoot-root length, fine-root length, and root surface area by 2–3 times compared to untreated soil. Phospholipid fatty acid (PLFA) analyses of sugarcane rhizosphere soil showed significant reduction in fungal-biomarker abundance with mancozeb and azoxystrobin in comparison to the untreated check or mefenoxam treatments. Bacterial functional-group abundance was reduced by mancozeb and mefenoxam. All fungicides significantly reduced mycorrhizal colonization but not mycorrhizal spore counts. There was a functional relationship between fine-root systems and higher tissue concentration of nitrogen and silicon. The study indicated that application of fungicides to the soil may improve early root and shoot growth and plant-cane establishment that can potentially reduce the yield decline in successively planted sugarcane in histosols. Additional field research is needed in the future to determine the fungicide soil application method, sugarcane growth response in whole crop cycles, and any environmental effects. Full article

Forest management often results in changes in soil microbial communities. To understand how forest management can change microbial communities, we studied soil microbial abundance and community structure in a natural Chamaecyparis (NCP) forest, a disturbed Chamaecyparis (DCP) forest, a secondary (regenerated) Chamaecyparis (SCP) forest and a secondary (reforested) Cryptomeria (SCD) forest. We analyzed soil microbial abundance by measuring phospholipid fatty acids (PLFAs) and microbial community structure by denaturing gradient gel electrophoresis (DGGE) in the studied forest soils. The content of the soil PLFA fungal biomarker decreased from NCP to SCP, DCP and SCD forest soils, associated with the degree of disturbance of forest management. The ratio of soil Gram positive–to-negative bacteria and the stress index (16:1ω7t to 16:1ω7c) increased from NCP to SCP and DCP soils; thus, disturbed forests except for SCD showed increased soil microbial stress. Principal component analysis of soil microbial groups by PLFAs separated the four forest soils into three clusters: NCP, DCP and SCP, and SCD soil. The DGGE analysis showed no difference in the microbial community structure for NCP, DCP and SCP soils, but the community structure differed between SCD and the three other forest soils. In cloud montane forests, disturbance due to forest management had only a slight influence on the soil microbial community, whereas reforestation with different species largely changed the soil microbial community structure. Full article

Soil-based wastewater treatment systems, or leachfields, rely on microbial processes for improving the quality of wastewater before it reaches the groundwater. These processes are affected by physicochemical system properties, such as O2 availability, and disturbances, such as the presence of antimicrobial compounds in wastewater. We examined the microbial community structure of leachfield mesocosms containing native soil and receiving domestic wastewater under intermittently-aerated (AIR) and unaerated (LEACH) conditions before and after dosing with tetracycline (TET). Community structure was assessed using phospholipid fatty acid analysis (PLFA), analysis of dominant phylotypes using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE), and cloning and sequencing of 16S rRNA genes. Prior to dosing, the same PLFA biomarkers were found in soil from AIR and LEACH treatments, although AIR soil had a larger active microbial population and higher concentrations for nine of 32 PLFA markers found. AIR soil also had a larger number of dominant phylotypes, most of them unique to this treatment. Dosing of mesocosms with TET had a more marked effect on AIR than LEACH soil, reducing the size of the microbial population and the number and concentration of PLFA markers. Dominant phylotypes decreased by ~15% in response to TET in both treatments, although the AIR treatment retained a higher number of phylotypes than the LEACH treatment. Fewer than 10% of clones were common to both OPEN ACCESS Water 2013, 5 506 AIR and LEACH soil, and fewer than 25% of the clones from either treatment were homologous with isolates of known genus and species. These included human pathogens, as well as bacteria involved in biogeochemical transformations of C, N, S and metals, and biodegradation of various organic contaminants. Our results show that intermittent aeration has a marked effect on the size and structure of the microbial community that develops in a native leachfield soil. In addition, there is a differential response of the microbial communities of AIR and LEACH soil to tetracycline addition which may be linked to changes in function. Full article

Supercritical fluid extraction (SFE) was used in the analysis of bacterial respiratory quinone (RQ), bacterial phospholipid fatty acid (PLFA), and archaeal phospholipid ether lipid (PLEL) from anaerobically digested sludge. Bacterial RQ were determined using ultra performance liquid chromatography (UPLC). Determination of bacterial PLFA and archaeal PLEL was simultaneously performed using gas chromatography-mass spectrometry (GC-MS). The effects of pressure, temperature, and modifier concentration on the total amounts of RQ, PLFA, and PLEL were investigated by 23 experiments with five settings chosen for each variable. The optimal extraction conditions that were obtained through a multiple-response optimization included a pressure of 23.6 MPa, temperature of 77.6 °C, and 10.6% (v/v) of methanol as the modifier. Thirty nine components of microbial lipid biomarkers were identified in the anaerobically digested sludge. Overall, the SFE method proved to be more effective, rapid, and quantitative for simultaneously extracting bacterial and archaeal lipid biomarkers, compared to conventional organic solvent extraction. This work shows the potential application of SFE as a routine method for the comprehensive analysis of microbial community structures in environmental assessments using the lipid biomarkers profile. Full article