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Journal articles on the topic 'Soil PLFA analysis'
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1
Roslev, Peter, and Niels Iversen. "Radioactive Fingerprinting of Microorganisms That Oxidize Atmospheric Methane in Different Soils." Applied and Environmental Microbiology 65, no. 9 (September 1, 1999): 4064–70. http://dx.doi.org/10.1128/aem.65.9.4064-4070.1999.
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ABSTRACT Microorganisms that oxidize atmospheric methane in soils were characterized by radioactive labelling with14CH4 followed by analysis of radiolabelled phospholipid ester-linked fatty acids (14C-PLFAs). The radioactive fingerprinting technique was used to compare active methanotrophs in soil samples from Greenland, Denmark, the United States, and Brazil. The 14C-PLFA fingerprints indicated that closely related methanotrophic bacteria were responsible for the oxidation of atmospheric methane in the soils. Significant amounts of labelled PLFAs produced by the unknown soil methanotrophs coeluted with a group of fatty acids that included i17:0, a17:0, and 17:1ω8c (up to 9.0% of the total 14C-PLFAs). These PLFAs are not known to be significant constituents of methanotrophic bacteria. The major PLFAs of the soil methanotrophs (73.5 to 89.0% of the total PLFAs) coeluted with 18:1 and 18:0 fatty acids (e.g., 18:1ω9, 18:1ω7, and 18:0). The 14C-PLFAs fingerprints of the soil methanotrophs that oxidized atmospheric methane did not change after long-term methane enrichment at 170 ppm CH4. The 14C-PLFA fingerprints of the soil methanotrophs were different from the PLFA profiles of type I and type II methanotrophic bacteria described previously. Some similarity at the PLFA level was observed between the unknown soil methanotrophs and the PLFA phenotype of the type II methanotrophs. Methanotrophs in Arctic, temperate, and tropical regions assimilated between 20 and 54% of the atmospheric methane that was metabolized. The lowest relative assimilation (percent) was observed for methanotrophs in agricultural soil, whereas the highest assimilation was observed for methanotrophs in rain forest soil. The results suggest that methanotrophs with relatively high carbon conversion efficiencies and very similar PLFA compositions dominate atmospheric methane metabolism in different soils. The characteristics of the methane metabolism and the 14C-PLFA fingerprints excluded any significant role of autotrophic ammonia oxidizers in the metabolism of atmospheric methane.
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Johnsen, Anders R., Anne Winding, Ulrich Karlson, and Peter Roslev. "Linking of Microorganisms to Phenanthrene Metabolism in Soil by Analysis of 13C-Labeled Cell Lipids." Applied and Environmental Microbiology 68, no. 12 (December 2002): 6106–13. http://dx.doi.org/10.1128/aem.68.12.6106-6113.2002.
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ABSTRACT Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [14C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [13C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed. Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil. In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU. 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium. The 13C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains. The 13C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils. Only in the roadside soil were 10me/12me18:0 PLFAs enriched in 13C, suggesting that actinomycetes metabolized phenanthrene in this soil. The 13C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains. In all of the soils investigated, no excess 13C was recovered in the 18:2ω6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of [13C]phenanthrene.
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Hanajík, Peter, Milan Zvarík, Hannu Fritze, Ivan Šimkovic, and Róbert Kanka. "Composition of microbial PLFAs and correlations with topsoil characteristics in the rare active travertine spring-fed fen." Ekológia (Bratislava) 35, no. 4 (December 1, 2016): 295–308. http://dx.doi.org/10.1515/eko-2016-0024.
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Abstract We studied soil PLFAs composition and specific soil properties among transect of small-scale fen in Stankovany, Slovakia. The aim of this study was to determine potential differences in the microbial community structure of the fen transect and reveal correlations among PLFAs and specific soil characteristics. PCA analyses of 43 PLFAs showed a separation of the samples along the axis largely influenced by i14:0, 16:1ω5, br17:0, 10Me16:0, cy17:0, cy17:1, br18:0 and 10Me17:0. We measured a high correlation of sample scores and distance from fen edge (Kendall’s test τ = 0.857, P < 0.01). Kendall’s test showed a negative correlation of PLFAs content (mol%) and distance from the fen border for Gram (+) bacteria, Actinomycetes, mid-chain branched saturated PLFAs and total PLFAs. The redundancy analysis of the PLFA data set for the eight samples using PLFAs as species and 21 environmental variables identified soil properties significantly associated with the PLFA variables, as tested by Monte Carlo permutation showing most significant environmental variables including dichlormethan extractables, water extractables, Klason lignin, acid-soluble lignin, holocellulose, total extractables, organic matter content, total PLFA amount, bacterial PLFA and total nitrogen negatively correlated to axis 1 and dry weight and carbonate carbon positively correlated to axis 1. The amounts of Klason lignin, acid-soluble lignin, holocellulose total extractables, total PLFA, bacterial PLFA and total nitrogen were significantly correlated positively to the distance from fen border while moisture and total carbonate carbon were correlated negatively.
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Swallow, Mathew J. B., and Sylvie A. Quideau. "Evidence of rapid non-targeted effects of cycloheximide on soil bacteria using 13C-PLFA analysis." Canadian Journal of Soil Science 100, no. 4 (December 1, 2020): 356–62. http://dx.doi.org/10.1139/cjss-2019-0152.
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Stable isotope probing of phospholipid fatty acids (PLFA-SIP) is useful when studying bacterial contributions to soil processes, and it is an effective way to separate fungal and bacterial activity by linking 13C enrichment to specific PLFAs. Distinguishing bacterial contributions to soil processes often employs selective inhibitors; however, studies demonstrating their efficacy when using PLFA-SIP are less common. Here, we determined the effect of the fungal inhibitor cycloheximide (4.8 mg g−1 dry soil) and the bacterial inhibitor bronopol (0.48 mg g−1 dry soil) on microbial communities white spruce [Picea glauca (Moench) Voss] forest floor by measuring the uptake of 13C-enriched glucose (2 mg g−1 dry soil) in microbial PLFAs. We targeted [13C]glucose uptake by the bacterial community conditioned to a stable soil environment of 23 °C for over 2 wk rather than new bacteria generated from active colony growth caused by glucose addition. Nearly all bacterial PLFAs exhibited pronounced inhibition of 13C enrichment in the presence of bronopol. Limited inhibition of 13C enrichment in the presence of cycloheximide was observed as bacterial PLFA affected by cycloheximide had roughly one third less 13C enrichment than samples emended with [13C]glucose alone. Inhibitory effects only reduced 13C enrichment and did not affect total PLFA concentrations, implying that the inhibitors in the concentrations applied were impeding bacterial activity without causing cell death. Based on this work, we conclude that bronopol is an effective inhibitor for bacteria. Additionally, non-targeted effects of cycloheximide on soil bacteria must be accounted for when it is used in soil incubations.
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Hanson, Jessica R., Jennifer L. Macalady, David Harris, and Kate M. Scow. "Linking Toluene Degradation with Specific Microbial Populations in Soil." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5403–8. http://dx.doi.org/10.1128/aem.65.12.5403-5408.1999.
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ABSTRACT Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.
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Li, Xin, Yan Jiao, and Ming De Yang. "Diversity of Soil Microbial Communities under Different Soil Salinity Levels Analyzing by PLFA." Advanced Materials Research 955-959 (June 2014): 314–20. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.314.
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Under different soil salinity levels, diversity of soil microbial communities from Hetao irrigated land of Inner Mongolia was studied by phospholipid fatty acid (PLFA) analysis. The study found that PLFAs biomass in saline soil was significantly lower than those of strongly salinized soil and slight salinized soil. Microbes was bacteria-based from these soil. The bacterial PLFA loading in saline soil is significantly less than those of strongly salinized soil and slight salinized soil . Cluster analysis showed that changes had obviously taken place on soil microbial composition and quantity under different soil salinity levels.About 76.89% of variation in PLFA patterns explained by PC1(the first principal components),and 17:1, 16:0, 18:1w9c, 18:1w9t, 18:2, 18:3w3c, 12:0 were strongly negatively correlated with PC1.However,soil salinity and pH were positively correlated with PC1.We conclude that soil salinity has a profound affect on the microbial community structure.
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Jiao, Hai Hua, Zhi Hui Bai, Ying Liu, Kai Wang, and Zhan Bin Huang. "Impact of Super Absorbent Polymer and Plants on Microbial Community and Petroleum Hydrocarbon Degradation in Contaminated Soil." Advanced Materials Research 807-809 (September 2013): 353–60. http://dx.doi.org/10.4028/www.scientific.net/amr.807-809.353.
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A greenhouse pot test, in which wheat, cabbage, spinach were cultivated separately in petroleum contaminated soil with and without super absorbent polymer (SAP), was conducted to evaluated the effect of plants and SAP on soil microbiological properties. phospholipid fatty acids (PLFAs) profiles were analyzed to reveal the microbial communities. As a measure of the functional activity of soil microbial community, the ratio of degraded to total petroleum hydrocarbon (TPH) in soil was estimated. The results indicated that SAP had an important effect on the soil microbial community and its degrading TPH activities. First, the principal component analysis (PCA) of the PLFA signatures revealed marked changes between soil with SAP and without SAP. In addition, the total amount and the profile of PLFA were significantly different between the untreated and SAP-amended soils. Using PLFA patterns as a biomarker, it was found that gram-positive bacteria (G+) were more sensitive to SAP than gram-negative bacteria (G-), and the biomass of G+ was higher in soil with SAP than in that without SAP. Second, the crop could stimulate the growth of soil microorganisms; however, the differences depended clearly on the crop species. The G+ and G- biomass was increased in cabbage, spinach soil containing SAP, but was decreased in wheat soils. The population of fungi was increased in cabbage and spinach soils containing SAP, but was decreased in wheat soil with SAP. The population of actinomycetes was decreased in all soils with SAP. Third, the ratio of degraded to TPH was slightly increased in soil with SAP treatment, but a significant change depended on the crop species. In total, 12 different PLFAs were identified, including saturated, monounsaturated, branched, and polyunsaturated species. There was a clear difference in the PLFAs composition between soils with and without SAP.
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Jiao, Hai Hua, Kai Wang, Jian Gang Pan, De Cai Jin, Zhan Bin Huang, and Zhi Hui Bai. "Impact of Humics and Plants on Microbial Community and Petroleum Hydrocarbon Degradation in Contaminated Soil." Advanced Materials Research 726-731 (August 2013): 131–40. http://dx.doi.org/10.4028/www.scientific.net/amr.726-731.131.
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A greenhouse pot experiment, in which 3 different crops (wheat, cabbage, spinach) were cultivated in soil with and without humics (HS), was conducted to evaluate the effect of HS on soil microbiological properties. Phospholipid fatty acid (PLFA) profiles were analyzed to reveal the microbial community structure. As a measure of the functional activity of soil microbial community, the ratio of degraded to total petroleum hydrocarbon in soil was estimated. The results indicated that HS had an important effect on the soil microbial community and its functional activities. First, the principal component analysis (PCA) of the PLFA signatures revealed marked changes between soil with HS and without HS. In addition, the total amount and the profile of PLFA were significantly different between the untreated and HS-amended soils. Using PLFA patterns as a biomarker, it was found that gram-positive bacteria (G+) were more sensitive to HS than gram-negative bacteria (G-), and the biomass of G+ was higher in soil with HS than in that without HS. Second, the crop could stimulate the growth of soil microorganisms; however, the differences depended clearly on the crop species. The G+ and G- biomass was increased in spinach soil containing HS, but was decreased in wheat and cabbage soils. The population of fungi was increased in wheat and spinach soils containing HS, but was decreased in cabbage soil. The population of actinomycetes was increased in cabbage soil, but was decreased in wheat and spinach soils containing HS. Third, the ratio of degraded to total petroleum hydrocarbon was also affected by the HS treatment. It was slightly increased in soil with HS treatment, but a significant change depended on the crop species. In general, fatty acids ranged from C13 to C19. In total, 25 different PLFAs were identified, including saturated (SAT), monounsaturated (MUFA), branched (BR), and polyunsaturated (PUFA) species. There was a clear difference in the PLFA composition between soils with and without HS.
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Guan, Huiling, Jiangwen Fan, Haiyan Zhang, and Warwick Harris. "Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths." Agronomy 11, no. 1 (January 18, 2021): 173. http://dx.doi.org/10.3390/agronomy11010173.
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Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.
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Bach, Lisbet Holm, Åsa Frostegård, and Mikael Ohlson. "Variation in soil microbial communities across a boreal spruce forest landscape." Canadian Journal of Forest Research 38, no. 6 (June 2008): 1504–16. http://dx.doi.org/10.1139/x07-232.
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We investigated soil microbial community structure by phospholipid fatty acid (PLFA) analysis in a mature boreal spruce forest landscape in southern Norway, with low diversity of vascular plants. We investigated the spatial variation in PLFAs and the importance of environmental variables in 10 plots (each 13 samples) in a study area of 1 km × 1 km. The scales investigated were 15 cm to 10 m within study plots and 100 m to 1 km between study plots. Soil microbial biomass varied 10-fold and we found a large variation in microbial community structure, even at distances of 15 cm. Samples aggregated into plots when PLFAs were subjected to a principal components analysis. Plot identity explained 36.3% of the variation in the PLFAs and geostatistical analysis showed that the microbial community structure displayed spatial dependence at within-plot distances. Environmental variables differed significantly between all plots but explained only minor parts of the variation in the overall PLFA pattern. The vegetation variables were, however, the best at explaining the PLFA pattern, and up to 60% of within-plot variation in individual plots, respectively, could be explained by vegetation variables, pH, and soil depth.
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Mathew, Reji P., Yucheng Feng, Leonard Githinji, Ramble Ankumah, and Kipling S. Balkcom. "Impact of No-Tillage and Conventional Tillage Systems on Soil Microbial Communities." Applied and Environmental Soil Science 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/548620.
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Soil management practices influence soil physical and chemical characteristics and bring about changes in the soil microbial community structure and function. In this study, the effects of long-term conventional and no-tillage practices on microbial community structure, enzyme activities, and selected physicochemical properties were determined in a continuous corn system on a Decatur silt loam soil. The long-term no-tillage treatment resulted in higher soil carbon and nitrogen contents, viable microbial biomass, and phosphatase activities at the 0–5 cm depth than the conventional tillage treatment. Soil microbial community structure assessed using phospholipid fatty acid (PLFA) analysis and automated ribosomal intergenic spacer analysis (ARISA) varied by tillage practice and soil depth. The abundance of PLFAs indicative of fungi, bacteria, arbuscular mycorrhizal fungi, and actinobacteria was consistently higher in the no-till surface soil. Results of principal components analysis based on soil physicochemical and enzyme variables were in agreement with those based on PLFA and ARISA profiles. Soil organic carbon was positively correlated with most of the PLFA biomarkers. These results indicate that tillage practice and soil depth were two important factors affecting soil microbial community structure and activity, and conservation tillage practices improve both physicochemical and microbiological properties of soil.
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Shen, Jianxun. "Phospholipid biomarkers in Mars-analogous soils of the Atacama Desert." International Journal of Astrobiology 19, no. 6 (October 12, 2020): 505–14. http://dx.doi.org/10.1017/s1473550420000294.
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AbstractIn Mars-analogous hyperarid soils of the Atacama Desert, phospholipid fatty acids (PLFAs) as the main component of biomembrane play a role in reliably determining viable microbes. PLFA analyses illustrated a rise of the microbial abundance (from 5.0 × 106 to 4.2 × 107 cells g−1) and biodiversity (from 7 to 15 different individual PLFAs) from the north hyperarid core of the Atacama Desert to the southern arid region. Abundant cyclopropyl PLFAs (47.2 ± 4.6%) suggested the resistance to oligotrophic and hypersaline environments by Atacama microbial communities. The southernmost arid site had the highest proportion (8.7%) of eukaryotic and fungal lipid biomarkers. Different precipitations (ranging from 0.7 to 2 mm year−1) in the hyperarid core exerted different effects on microbial biomass, PLFA diversity, bacteria and microeukaryotes. By principal component analysis (cumulative 74.6% of variance), the dominance of PLFA hydroxylation was associated with the microbial viability; bacteria rich in C16:0, C18:0 and C16:1ω9 favoured higher soil conductivity and nitrate; and other PLFAs contributed more to the organic content. Additionally by comparing the ratios of PLFAs to well-preserved organics (e.g., mineral-bound organic carbon and microbial phosphorus), I found that the degradation of PLFAs decreased to a minimum when the mean annual precipitation is lower than 2 mm. These findings may further specify identifiable biomarkers on Mars, if potentially extant Martian microbes possess comparable phospholipid membrane structure.
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Luo, Chaoyi, Bingxue Zhang, Jiang Liu, Xiaoxia Wang, Fengpeng Han, and Jihai Zhou. "Effects of Different Ages of Robinia pseudoacacia Plantations on Soil Physiochemical Properties and Microbial Communities." Sustainability 12, no. 21 (November 4, 2020): 9161. http://dx.doi.org/10.3390/su12219161.
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Robinia pseudoacacia is widely planted on the Loess Plateau as a strong drought-tolerant and salt-tolerant species for vegetation restoration. However, this mode of pure plantation has triggered great concern over the soil ecosystem. The aim of this study was to explore the effects of the plantation on soil physiochemical properties, soil microorganisms, and the relationship between them in Robinia pseudoacacia plantations of different ages. Four different ages of Robinia pseudoacacia stands, including 10-year-old, 15-year-old, 25-year-old, and 40-year-old (abbreviated as Y10, Y15, Y25, and Y40, respectively) were selected, and 20 soil physicochemical and biological indicators were determined. The variation in soil microbial biomass was influenced by sampling depth, and consistent with the variations in TN (soil total nitrogen) and SOC (soil organic carbon) during 25 years’ artificial forestation. Soil moisture increased significantly at Y15 and then decreased at Y40 but other soil properties remained relatively stable. The contents of phosphor lipid fatty acid (PLFA) of different microbial groups followed the order of B (Bacteria) > G− (Gram-negative) > G+ (Gram-positive) > A (Actinomycetes) > F (Fungi). The ratios of F/B (Fungi to Bacteria) and Sat/Mono (Saturated PLFAs to Monosaturated PLFAs) of different ages of plantations showed a similar trend, i.e., declined first, then rose, and declined again. The ratios of Cy/Pre (Cyclopropyl PLFAs to Precursor PLFAs) and G+/G− (Gram-positive to Gram-negative) of the soil of all ages of plantations showed a trend of slow growth and a trend of rapid growth, respectively. Redundancy analysis showed that the contents of individual PLFAs and total PLFA were positively correlated with SOC and TN, but variations of soil PLFA ratios mostly depended on other soil properties. After artificial forestation, the ratios of F/B and Sat/Mono were lower than before forestation, while the ratio of Cy/Pre varied with different soil layers. The ratio of G+/G− increased with the increase in afforestation time, peaking at the 25th year. The contents of individual PLFAs and total PLFA may be sensitive indicators of SOC and TN within 25 years’ plantation. Lower ratio of F/B and higher G+/G− suggest that the sustainability of the ecosystem is weaker and the fertility of the soil is lower after plantation of Robinia pseudoacacia.
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Chang, Tian, Shiau, Chen, and Chiu. "Influence of Thorny Bamboo Plantations on Soil Microbial Biomass and Community Structure in Subtropical Badland Soils." Forests 10, no. 10 (October 1, 2019): 854. http://dx.doi.org/10.3390/f10100854.
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Vegetation in southeastern Taiwan plays an important role in rehabilitating badland soils (high silt and clay content) and maintaining the soil microbial community. The establishment of thorny bamboo (Bambusa stenostachya Hackel) may have had a profound impact on the abundance and community structure of soil microorganisms. However, little is known regarding the influence of bamboo on soil biota in the badland ecosystem. The present study was conducted at three badland sites in southwestern Taiwan and focused on the measurement of phospholipid fatty acids (PLFA) together with soil microbial biomass C (Cmic) and N (Nmic) contents, enzyme activities, and denaturing gradient gel electrophoresis (DGGE) assessments. The abundances of whole soil microbes as well as bacterial and fungal groups—as evident by PLFA, Cmic and Nmic contents—were much higher in the bamboo plantation soils than the bare land soils. The increased soil organic matter in bamboo plantations relative to the control largely explained the enhancement, the abundance and diversity in the soil microbial community. Principal component analysis of individual PLFA peaks separated the bamboo plantation soil from the non-plantation bare land soil. DGGE analysis also revealed a difference in both bacterial and fungal community structures between soil types. Redundancy analysis of PLFA peak abundance and soil properties indicated that microbial community structure was positively correlated with soil organic C and total N and negatively correlated with pH. This differentiation could be attributed to bamboo in suitable habitats providing an essential nutrient source for soil microbes. The pH reduction in these alkaline soils also contributed to the increase in the size of the microbial community in bamboo-regenerated soils. Together, the results of this study indicate that bamboo plantations are beneficial for soil microbial activities and soil quality in badland areas.
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Rethemeyer, Janet, Christiane Kramer, Gerd Gleixner, Guido L. B. Wiesenberg, Lorenz Schwark, Nils Andersen, Marie-J. Nadeau, and Pieter M. Grootes. "Complexity of Soil Organic Matter: AMS 14C Analysis of Soil Lipid Fractions and Individual Compounds." Radiocarbon 46, no. 1 (2004): 465–73. http://dx.doi.org/10.1017/s0033822200039771.
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Radiocarbon measurements of different lipid fractions and individual compounds, isolated from soil samples collected on 2 different agricultural long-term study sites, located in the rural area of Rotthalmünster (Germany) and in the city of Halle/Saale (Germany), were analyzed to obtain information about sources and the stability of soil organic matter (SOM). Different lipid compound classes were isolated by automated solvent extraction and subsequent medium-pressure liquid chromatography. Generally, 14C contents of lipid compound classes from topsoil samples of maize plots at Rotthalmünster are close to the modern atmospheric 14C content. Lower 14C values of aliphatic and aromatic hydrocarbons isolated from neutral lipids suggest a contribution of old carbon to these fractions. In contrast, 14C values of bulk soil (52 pMC) as well as isolated lipid classes from Halle are highly depleted. This can be attributed to a significant contribution of fossil carbon at this site. Extremely low 14C contents of aromatic (7 pMC) and aliphatic hydrocarbons (19 pMC) reflect the admixture of fossil hydrocarbons at the Halle site. Individual phospholipid fatty acids (PLFA), which are used as a proxy for viable microbial biomass, were isolated by preparative capillary gas chromatography (PCGC) from topsoils at Rotthalmünster and Halle. PLFA 14C values are close to atmospheric 14C values and, thus, indicate a clear microbial preference for relatively young SOM. At Rotthalmünster, the 14C concentration of short-chain unsaturated PLFAs is not significantly different from that of the atmosphere, while the saturated PLFAs show a contribution of sub-recent SOM extending over the last decades. At Halle, up to 14% fossil carbon is incorporated in PLFAs n-C17:0 and cy-C18:0, which suggests the use of fossil carbon by soil microorganisms. Moreover, it can be concluded that the 14C age of soil carbon is not indicative of its stability.
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Santás-Miguel, Vanesa, Montserrat Díaz-Raviña, Angela Martín, Elena García-Campos, Ana Barreiro, Avelino Núñez-Delgado, Esperanza Álvarez-Rodríguez, Manuel Arias-Estévez, and David Fernández-Calviño. "Soil Enzymatic Activities and Microbial Community Structure in Soils Polluted with Tetracycline Antibiotics." Agronomy 11, no. 5 (May 5, 2021): 906. http://dx.doi.org/10.3390/agronomy11050906.
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A laboratory experiment was performed to examine the medium-term influence of three tetracycline antibiotics (chlortetracycline, CTC; tetracycline, TC and oxytetracycline, OTC) at different concentrations in four agricultural soils with similar pH and different soil organic content. After a 42-days incubation period, three different soil enzymes (β-glucosidase, urease, and phosphomonoesterase) were estimated, as well as the phospholipid fatty acids (PLFAs). A residual effect was observed on all microbial parameters measured in the four soils affecting to the soil enzymes activity and soil microbial communities structure (PLFA pattern). A different microbial sensitivity to antibiotics was detected depending on both, soil type and the microbial property considered. Specifically, in general, no antibiotic effect or even a slight positive effect was observed for phosphomonoesterase and β-glucosidase enzyme activities, respectively, while a negative effect was detected for urease activity values, particularly at higher doses of the antibiotics in a soil with a low organic matter content. The principal component analysis performed with the PLFAs data obtained for all soil samples showed different microbial communities depending mainly on soil type, followed by the antibiotic added to the soil (CTC, TC or OTC) and, in a lesser extent, by its concentration. In general, the PLFA patterns showed similar microbial communities structure due to OTC and TC addition in comparison to the microbial communities structure of soil treated with CTC. These results could be environmentally relevant, especially as regards potential effects of antibiotics on the soil microbiome and hence on health risk assessment of these antibiotics in soils.
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Chang, Ed-Haun, Isheng Jason Tsai, Shih-Hao Jien, Guanglong Tian, and Chih-Yu Chiu. "Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan." Forests 12, no. 1 (December 22, 2020): 4. http://dx.doi.org/10.3390/f12010004.
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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.
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Xue, Dong, Xiang Dong Huang, and Lian Xue. "Soil Microbial Community Structure in Tree Peony (Paeonia suffruticosa) Garden Based on PLFA Analysis." Applied Mechanics and Materials 675-677 (October 2014): 82–85. http://dx.doi.org/10.4028/www.scientific.net/amm.675-677.82.
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Understanding the chronological change in soil microbial community structure of tree peony garden ecosystem is important from ecological, environmental, and management perspectives. Soil samples were collected from three tree peony garden systems (5-, 12-, and 25-year-old tree peony gardens), and adjacent wasteland at Luoyang, Henan Province of China. Soil microbial community structure was analyzed by phospholipid fatty acid (PLFA) method. The bacterial and actinomycete PLFAs increased from the wasteland to 5-year-old tree peony garden and then decreased from the 5- to 25-year-old tree peony garden, and the fungal PLFA first increased and then decreased with the increasing planting years, with the greatest amount found in the 12-year-old tree peony garden. The conversion from the wasteland to tree peony garden resulted in a significant increase in Shannon index, Richness, and Evenness. However, with the succeeding development of tree peony garden ecosystems, Shannon index, Richness, and Evenness decreased from the 5- to 25-year-old tree peony garden.
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Lozano, Elena, Fuensanta García-Orenes, Gema Bárcenas-Moreno, Patricia Jiménez-Pinilla, Jorge Mataix-Solera, Victoria Arcenegui, Alicia Morugán-Coronado, and Jorge Mataix-Beneyto. "Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest." Journal of Hydrology and Hydromechanics 62, no. 2 (June 1, 2014): 101–7. http://dx.doi.org/10.2478/johh-2014-0017.
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Abstract Soil water repellency (SWR) can influence many hydrological soil properties, including water infiltration, uneven moisture distribution or water retention. In the current study we investigated how variable SWR persistence in the field is related to the soil microbial community under different plant species (P. halepensis, Q. rotundifolia, C. albidus and R. officinalis) in a Mediterranean forest. The soil microbial community was determined through phospholipid fatty acids (PLFA). The relationships between microbiological community structure and the soil properties pH, Glomalin Related Soil Protein (GRSP) and soil organic matter (SOM) content were also studied. Different statistical analyses were used: Principal Component Analysis (PCA), ANOVA, Redundancy Analysis and Pearson correlations. The highest concentrations of PLFA were found in the most water repellent samples. PCA showed that microorganism composition was more dependent of the severity of SWR than the type of plant species. In the Redundancy Analysis, SWR was the only significant factor (p<0.05) to explain PLFA distributions. The only PLFA biomarkers directly related to SWR were associated with Actinobacteria (10Me16:0, 10Me17:0 and 10Me18:0). All the results suggest that a strong dependence between SWR and microbial community composition.
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Wang, Hehua, Juan Wang, Chaorong Ge, and Huaiying Yao. "Fungi Dominated the Incorporation of 13C-CO2 into Microbial Biomass in Tomato Rhizosphere Soil under Different CO2 Concentrations." Microorganisms 9, no. 10 (October 9, 2021): 2121. http://dx.doi.org/10.3390/microorganisms9102121.
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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.
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Joergensen, Rainer Georg. "Phospholipid fatty acids in soil—drawbacks and future prospects." Biology and Fertility of Soils 58, no. 1 (December 4, 2021): 1–6. http://dx.doi.org/10.1007/s00374-021-01613-w.
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Abstract The current opinion and position paper highlights (1) correct assignation of indicator phospholipid fatty acids (PLFA), (2) specificity and recycling of PLFA in microorganisms, and (3) complete extraction and detection of PLFA. The straight-chain PLFA 14:0, 15:0, 16:0, and 17:0 occur in all microorganisms, i.e., also in fungi and not only in bacteria. If the phylum Actinobacteria is excluded from the group of Gram-positive bacteria, all remaining bacteria belong to the bacterial phylum Firmicutes, which should be considered. The PLFA 16:1ω5 should be used as an indicator for the biomass of arbuscular mycorrhizal fungi (AMF) as there is no experimental evidence that they occur in marked amounts in Gram-negative bacteria. Fungal PLFA should embrace the AMF-specific 16:1ω5. In the presence of plants, ergosterol should be used instead of the PLFA 18:2ω6,9 and 18:1ω9 as fungal indicators for Mucoromycotina, Ascomycota, and Basidiomycota. The majority of indicator PLFA are not fully specific for a certain microbial group. This problem might be intensified by recycling processes during decomposition to an unknown extent. Soil handling and extraction conditions should be further optimized. The reliability and accuracy of gas chromatographic separation need to be regularly checked against unintentional variations. PLFA analysis will still be of interest over the next decades as an important independent control of DNA-based methods.
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Ibekwe, A. Mark, Sharon K. Papiernik, Jianying Gan, Scott R. Yates, Ching-Hong Yang, and David E. Crowley. "Impact of Fumigants on Soil Microbial Communities." Applied and Environmental Microbiology 67, no. 7 (July 1, 2001): 3245–57. http://dx.doi.org/10.1128/aem.67.7.3245-3257.2001.
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ABSTRACT Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity,H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, Hincreased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. andHeliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.
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Wang, Mingyu, Xiaohong Weng, Rongtao Zhang, Libin Yang, Yingnan Liu, and Xin Sui. "The Diversity and Composition of Soil Microbial Community Differ in Three Typical Wetland Types of the Sanjiang Plain, Northeastern China." Sustainability 14, no. 21 (November 3, 2022): 14394. http://dx.doi.org/10.3390/su142114394.
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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.
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Yao, Zhiyuan, Haizhen Wang, Laosheng Wu, Jianjun Wu, Philip C. Brookes, and Jianming Xu. "Interaction between the Microbial Community and Invading Escherichia coli O157:H7 in Soils from Vegetable Fields." Applied and Environmental Microbiology 80, no. 1 (October 11, 2013): 70–76. http://dx.doi.org/10.1128/aem.03046-13.
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ABSTRACTThe survival ofEscherichia coliO157:H7 in soils can contaminate vegetables, fruits, drinking water, etc. However, data on the impact ofE. coliO157:H7 on soil microbial communities are limited. In this study, we monitored the changes in the indigenous microbial community by using the phospholipid fatty acid (PLFA) method to investigate the interaction of the soil microbial community withE. coliO157:H7 in soils. Simple correlation analysis showed that the survival ofE. coliO157:H7 in the test soils was negatively correlated with the ratio of Gram-negative (G−) to Gram-positive (G+) bacterial PLFAs (G−/G+ratio). In particular, levels of 14 PLFAs were negatively correlated with the survival time ofE. coliO157:H7. The contents of actinomycetous and fungal PLFAs in the test soils declined significantly (P, <0.05) after 25 days of incubation withE. coliO157:H7. The G−/G+ratio declined slightly, while the ratio of bacterial to fungal PLFAs (B/F ratio) and the ratio of normal saturated PLFAs to monounsaturated PLFAs (S/M ratio) increased, afterE. coliO157:H7 inoculation. Principal component analysis results further indicated that invasion byE. coliO157:H7 had some effects on the soil microbial community. Our data revealed that the toxicity ofE. coliO157:H7 presents not only in its pathogenicity but also in its effect on soil microecology. Hence, close attention should be paid to the survival ofE. coliO157:H7 and its potential for contaminating soils.
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Bååth, Erland, Montserrat Díaz-Raviña, Åsa Frostegård, and Colin D. Campbell. "Effect of Metal-Rich Sludge Amendments on the Soil Microbial Community." Applied and Environmental Microbiology 64, no. 1 (January 1, 1998): 238–45. http://dx.doi.org/10.1128/aem.64.1.238-245.1998.
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ABSTRACT The effects of heavy-metal-containing sewage sludge on the soil microbial community were studied in two agricultural soils of different textures, which had been contaminated separately with three predominantly single metals (Cu, Zn, and Ni) at two different levels more than 20 years ago. We compared three community-based microbiological measurements, namely, phospholipid fatty acid (PLFA) analysis to reveal changes in species composition, the Biolog system to indicate metabolic fingerprints of microbial communities, and the thymidine incorporation technique to measure bacterial community tolerance. In the Luddington soil, bacterial community tolerance increased in all metal treatments compared to an unpolluted-sludge-treated control soil. Community tolerance to specific metals increased the most when the same metal was added to the soil; for example, tolerance to Cu increased most in Cu-polluted treatments. A dose-response effect was also evident. There were also indications of cotolerance to metals whose concentration had not been elevated by the sludge treatment. The PLFA pattern changed in all metal treatments, but the interpretation was complicated by the soil moisture content, which also affected the results. The Biolog measurements indicated similar effects of metals and moisture to the PLFA measurements, but due to high variation between replicates, no significant differences compared to the uncontaminated control were found. In the Lee Valley soil, significant increases in community tolerance were found for the high levels of Cu and Zn, while the PLFA pattern was significantly altered for the soils with high levels of Cu, Ni, and Zn. No effects on the Biolog measurements were found in this soil.
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Chaudhary, Doongar R., Jyotisna Saxena, Nicola Lorenz, Linda K. Dick, and Richard P. Dick. "Microbial Profiles of Rhizosphere and Bulk Soil Microbial Communities of Biofuel Crops Switchgrass (Panicum virgatumL.) and Jatropha (Jatropha curcasL.)." Applied and Environmental Soil Science 2012 (2012): 1–6. http://dx.doi.org/10.1155/2012/906864.
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The production of biofuels from the low-input energy crops, switchgrass (Panicum virgatumL.) and jatropha (Jatropha curcasL.), is a sustainable approach that can provide more usable energy and environmental benefits than food-based biofuels. Plant rhizosphere affects the microbial community structure due to variations in root exudation rates and residue chemistry. The objective of this investigation was to determine the profiles of microbial communities associated with rhizosphere and bulk soils of switchgrass or jatropha using phospholipid fatty acid (PLFA) analysis and length heterogeneity PCR (LH-PCR). Switchgrass soil contained a significantly (P<0.05) higher abundance of Gram-positive (i14:0, i15:0, a15:0), Gram-negative (16:1ω5c, 16:1ω7c, 18:1ω5c), and saturated (14:0, 15:0) PLFAs compared to jatropha soil, whereas jatropha had a higher abundance of fungal (18:2ω6, 9c), 18:1ω9c, 20:1ω9c, and 18:0 PLFAs compared to switchgrass soil. Irrespective of plant type, rhizosphere soil contained a significantly (P<0.05) higher abundance of saturated PLFAs (16:0, 18:0, 20:0), actinomycetes (10Me17:0), and fungal (18:2ω6, 9c) PLFAs compared to bulk soil; whereas bulk soil had higher abundance of saturated (14:0), Gram-negative (16:1ω9c, 16:1ω5c, 16:1ω7c), and 18:1ω9c PLFAs compared to rhizosphere soil. Multivariate principle component analysis of PLFAs and LH-PCR percent relative peak areas successfully differentiated the microbial communities of rhizosphere and bulk soils of switchgrass and jatropha.
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Vestberg, Mauritz, Ansa Palojärvi, Timo Pitkänen, Saara Kaipainen, Elina Puolakka, and Marjo Keskitalo. "Neutral lipid fatty acid analysis is a sensitive marker for quantitative estimation of arbuscular mycorrhizal fungi in agricultural soil with crops of different mycotrophy." Agricultural and Food Science 21, no. 1 (March 12, 2012): 12–27. http://dx.doi.org/10.23986/afsci.4996.
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The impact of host mycotrophy on arbuscular mycorrhizal fungal (AMF) markers was studied in a temperate agricultural soil cropped with mycorrhizal barley, flax, reed canary-grass, timothy, caraway and quinoa and non-mycorrhizal buckwheat, dyer's woad, nettle and false flax. The percentage of AMF root colonization, the numbers of infective propagules by the Most Probable Number (MPN) method, and the amounts of signature Phospholipid Fatty Acid (PLFA) 16:1ω5 and Neutral Lipid Fatty Acid (NLFA) 16:1ω5 were measured as AMF markers. Crop had a significant impact on MPN levels of AMF, on NLFA 16:1ω5 levels in bulk and rhizosphere soil and on PLFA 16:1ω5 levels in rhizosphere soil. Reed canary-grass induced the highest levels of AMF markers. Mycorrhizal markers were at low levels in all non-mycorrhizal crops. NLFA 16:1ω5 and the ratio of NLFA to PLFA 16:1ω5 from bulk soil are adequate methods as indicators of AMF biomass in soil.
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Ba, Duo, Duoji Qimei, Wei Zhao, and Yang Wang. "Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids." PLOS ONE 17, no. 7 (July 11, 2022): e0271101. http://dx.doi.org/10.1371/journal.pone.0271101.
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The distribution pattern of the microbial community in mountains is an important component of biodiversity research. Many environmental factors vary significantly with elevation on a relatively small scale in subalpine and alpine environments. These factors may markedly affect microbial community composition and function. In this study, we analyzed phospholipid fatty acid (PLFA) profiles and phosphorus (P) fractions in soils from 9 sites along an elevation gradient (3500–4100 m above sea level (a.s.l.)) of the Shergyla Mountain, Tibet in China. Many biomarker PLFAs indicated that there were biogeochemical trends of the microbial distribution patterns of some soil microorganisms, which were most often increasing, U-shaped and unimodal trends along the elevation gradient. A redundancy analysis (RDA) and correlations indicated that P factors (e.g., Resin-Pi, NaHCO3-Pi and NaHCO3-Po) were more important in controlling the microbial PLFA distribution pattern than other factors (e.g., MAT, MAP, pH, TOC, TN and soil moisture) in this study area. Microorganisms are strongly associated with P fractions. Our results suggested that microbial communities were subjected to P stresses and that the distribution patterns of microbial communities were shaped by bioavailable P along the elevation gradient. Our work also hints that P geochemical processes drive the microbial diversity of the Shergyla Mountains.
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Gunina, Anna, Michaela Dippold, Bruno Glaser, and Yakov Kuzyakov. "Turnover of microbial groups and cell components in soil: <sup>13</sup>C analysis of cellular biomarkers." Biogeosciences 14, no. 2 (January 18, 2017): 271–83. http://dx.doi.org/10.5194/bg-14-271-2017.
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Abstract. Microorganisms regulate the carbon (C) cycle in soil, controlling the utilization and recycling of organic substances. To reveal the contribution of particular microbial groups to C utilization and turnover within the microbial cells, the fate of 13C-labelled glucose was studied under field conditions. Glucose-derived 13C was traced in cytosol, amino sugars and phospholipid fatty acid (PLFA) pools at intervals of 3, 10 and 50 days after glucose addition into the soil. 13C enrichment in PLFAs ( ∼ 1.5 % of PLFA C at day 3) was an order of magnitude greater than in cytosol, showing the importance of cell membranes for initial C utilization. The 13C enrichment in amino sugars of living microorganisms at day 3 accounted for 0.57 % of total C pool; as a result, we infer that the replacement of C in cell wall components is 3 times slower than that of cell membranes. The C turnover time in the cytosol (150 days) was 3 times longer than in PLFAs (47 days). Consequently, even though the cytosol pool has the fastest processing rates compared to other cellular compartments, intensive recycling of components here leads to a long C turnover time. Both PLFA and amino-sugar profiles indicated that bacteria dominated in glucose utilization. 13C enrichment decreased with time for bacterial cell membrane components, but it remained constant or even increased for filamentous microorganisms. 13C enrichment of muramic acid was the 3.5 times greater than for galactosamine, showing a more rapid turnover of bacterial cell wall components compared to fungal. Thus, bacteria utilize a greater proportion of low-molecular-weight organic substances, whereas filamentous microorganisms are responsible for further C transformations. Thus, tracing 13C in cellular compounds with contrasting turnover rates elucidated the role of microbial groups and their cellular compartments in C utilization and recycling in soil. The results also reflect that microbial C turnover is not restricted to the death or growth of new cells. Indeed, even within living cells, highly polymeric cell compounds are constantly replaced and renewed. This is especially important for assessing C fluxes in soil and the contribution of C from microbial residues to soil organic matter.
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Zhang, Chuang, Xin-Yu Zhang, Hong-Tao Zou, Liang Kou, Yang Yang, Xue-Fa Wen, Sheng-Gong Li, Hui-Min Wang, and Xiao-Min Sun. "Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China." Biogeosciences 14, no. 20 (October 27, 2017): 4815–27. http://dx.doi.org/10.5194/bg-14-4815-2017.
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Abstract. The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil pH, soil organic carbon (SOC), and total N contents, but were negatively correlated with the ammonium contents. The soil enzyme activities varied seasonally, and were highest in March and lowest in October. In contrast, the contents of the microbial PLFA biomarkers were higher in October than in March and June. Ammonium may inhibit the contents of PLFA biomarkers more strongly than nitrate because of acidification. This study has provided useful information about the effects of ammonium and nitrate on soil microbial communities and enzyme activities.
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Yoshitake, Shinpei, and Takayuki Nakatsubo. "Changes in soil microbial biomass and community composition along vegetation zonation in a coastal sand dune." Soil Research 46, no. 4 (2008): 390. http://dx.doi.org/10.1071/sr07104.
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We used phospholipid fatty acid (PLFA) analysis to examine the relation of microbial biomass and community composition to vegetation zonation on a coastal sand dune. Soil samples were collected along 3 line transects established from the shoreline to the inland bush. Total PLFA content and PLFA composition of soils were used as indices of total microbial biomass and community composition, respectively. The microbial biomass was much higher in the inland Vitex rotundifolia zone than in the seaside plots. The microbial community composition also differed among the vegetation zones, with a higher contribution of fungal biomarkers in the inland plots. The microbial biomass increased significantly with increasing soil organic matter (SOM) content, but was not correlated with soil salinity. These results suggest that microbial biomass in the coastal sand dune was controlled primarily by the accumulation of SOM. The microbial community composition also changed with SOM content in the seaside plots, but SOM had little effect in the inland plots. These results suggest that the factors limiting the microbial community composition differed with location on the dune.
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Fan, Qiuyun, Yuguo Yang, Yuqing Geng, Youlin Wu, and Zhanen Niu. "Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai–Tibetan plateau, China." PeerJ 10 (April 4, 2022): e13188. http://dx.doi.org/10.7717/peerj.13188.
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Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400–3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai–Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions.
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Chatterjee, A., L. J. Ingram, G. F. Vance, and P. D. Stahl. "Soil processes and microbial community structures in 45- and 135-year-old lodgepole pine stands." Canadian Journal of Forest Research 39, no. 11 (November 2009): 2263–71. http://dx.doi.org/10.1139/x09-132.
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As forests develop, changes in soil organic matter quantity and quality affect both nutrient dynamics and microbial community structure. Litter decomposition and nitrogen mineralization in association with soil microbial communities were compared between 45- and 135-year-old lodgepole pine ( Pinus contorta var. latifolia (Englem.)) stands in southeastern Wyoming, USA. Compared with the 45-year-old stand, the 135-year-old stand was found to have greater live-tree biomass, litter decomposition rates (264 versus 135 mg·(g litter)–1·year–1), soil nitrification rates (0.38 versus 0.19 µg NO3–·(g soil)–1 after 265 days of field incubation), and total phospholipid fatty acid (PLFA) concentrations (25 versus 9.2 nmol·(g soil)–1 at 0–5 cm depth). Canonical correspondence analysis indicated that variation of PLFA profiles within the 45-year-old stand was explained by soil pH and bulk density, whereas soil process rates explained the distributions of PLFA profiles within the 135-year-old stand. The results of these studies indicate that stand age influences live-tree biomass and soil properties that can lead to changes in litter decomposition rates and soil microbial communities in lodgepole pine forests.
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Butler, Jessica L., Mark A. Williams, Peter J. Bottomley, and David D. Myrold. "Microbial Community Dynamics Associated with Rhizosphere Carbon Flow." Applied and Environmental Microbiology 69, no. 11 (November 2003): 6793–800. http://dx.doi.org/10.1128/aem.69.11.6793-6800.2003.
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ABSTRACT Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing 13C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using 13C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.
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Hynes, Holly M., and James J. Germida. "A chronsequential approach to investigating microbial community shifts following clearcutting in Boreal Plain forest soils." Canadian Journal of Forest Research 42, no. 12 (December 2012): 2078–89. http://dx.doi.org/10.1139/cjfr-2012-0038.
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Impacts of forest harvesting are often assessed in short-term studies that ignore the longer term changes associated with the disturbance. A chronosequence approach was taken to investigate changes in microbial community size and composition over ∼20 years post-harvest in lodgepole pine ( Pinus contorta Douglas ex Loudon) stands of the Boreal Plain. The LFH and mineral Ae horizons of Orthic Gray Luvisolic soils were sampled in six cutblocks, aged 1–19 years since harvest, in 2009 and 2010. Changes in microbial communities were assessed using phospholipid fatty acid analysis (PLFA) and 16S rDNA analysis. Physical and chemical soil parameters were measured to delineate microsite changes impacting microbial community shifts. Total microbial biomass (PLFA) was unaffected by harvesting disturbance, although fungal biomass was significantly larger in the oldest cutblock of the chronosequence. Microbial community composition did, however, differ between younger and older cutblocks as indicated by both lipid PLFA and 16S rDNA fingerprinting techniques. Forest soil microbial communities subject to clearcutting were observed to shift in overall community composition while remaining consistent in overall community size. The shift in community composition, which occurred in concert with the maintenance of biomass, indicated that the microbial community adapted sufficiently to the new post-harvest microsite conditions.
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Buyer, Jeffrey S., Bryan Vinyard, Jude Maul, Kaitlyn Selmer, Robert Lupitskyy, Clifford Rice, and Daniel P. Roberts. "Combined extraction method for metabolomic and PLFA analysis of soil." Applied Soil Ecology 135 (March 2019): 129–36. http://dx.doi.org/10.1016/j.apsoil.2018.11.012.
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Yu, Wenjuan, Huanhuan Gao, and Hongzhang Kang. "Ester Linked Fatty Acid (ELFA) method should be used with caution for interpretating soil microbial communities and their relationships with environmental variables in forest soils." PLOS ONE 16, no. 5 (May 10, 2021): e0251501. http://dx.doi.org/10.1371/journal.pone.0251501.
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As an alternative for phospholipid fatty acid (PLFA) analysis, a simpler ester linked fatty acid (ELFA) analysis has been developed to characterize soil microbial communities. However, few studies have compared the two methods in forest soils where the contribution of nonmicrobial sources may be larger than that of microbial sources. Moreover, it remains unclear whether the two methods yield similar relationships of microbial biomass and composition with environmental variables. Here, we compared PLFA and ELFA methods with respect to microbial biomass and composition and their relationships with environmental variables in six oriental oak (Quercus variabilis) forest sites along a 1500-km latitudinal gradient in East China. We found that both methods had a low sample-to-sample variability and successfully separated overall community composition of sites. However, total, bacterial, and fungal biomass, the fungal-to-bacterial ratio, and the gram-positive to gram-negative bacteria ratio were not significantly or strongly correlated between the two methods. The relationships of these microbial properties with environmental variables (pH, precipitation, and clay) greatly differed between the two methods. Our study indicates that despite its simplicity, the ELFA method may not be as feasible as the PLFA method for investigating microbial biomass and composition and for identifying their dominant environmental drivers, at least in forest soils.
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Li, Hailiang, Yang Yang, M. James C. Crabbe, and Haikui Chen. "The Characteristics of Dissolved Organic Matter and Soil Microbial Communities in the Soils of Larix principis-rupprechtii Mayr. Plantations in the Qinling Mountains, China." Sustainability 14, no. 19 (September 22, 2022): 11968. http://dx.doi.org/10.3390/su141911968.
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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.
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Hahn, Aria S., and Sylvie A. Quideau. "Shifts in soil microbial community biomass and resource utilization along a Canadian glacier chronosequence." Canadian Journal of Soil Science 93, no. 3 (August 2013): 305–18. http://dx.doi.org/10.4141/cjss2012-133.
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Hahn, A. S. and Quideau, S. A. 2013. Shifts in soil microbial community biomass and resource utilization along a Canadian glacier chronosequence. Can. J. Soil Sci. 93: 305–318. We aimed to describe soil microbial community composition and functional diversity as well as determine the influence of Engelmann spruce (Picea engelmannii Parry) and yellow mountain avens (Dryas drummondii Rich.) on soil microbial community succession along a Canadian glacier chronosequence. Soil microbial composition and functional activity were assessed using phospholipid fatty acid (PLFA) analysis, substrate-induced respiration and enzyme activity analysis. To the best of our knowledge, this is the first study investigating peroxidase and phenol oxidase activities, indicators of fungal activity, along any glacial chronosequence. While no difference in soil microbial community composition along the chronosequence was detected from the PLFA analysis, both total microbial biomass and fungal activity increased with time since deglaciation. Yellow mountain avens, a plant known to support microbial nitrogen fixation in mid- and late successional stages, increased soil microbial biomass, although this effect took 40 yr after deglaciation to emerge. Additionally, significant correlations between microbial respiration of N-acetyl-glucosamine, protocatechuic acid, glucose and percent soil N were found along the chronosequence, indicating that the soil microbial community was influencing changes in the soil environment.
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Petersen, S�ren O., Peter Roslev, and Roland Bol. "Dynamics of a Pasture Soil Microbial Community after Deposition of Cattle Urine Amended with [13C]Urea." Applied and Environmental Microbiology 70, no. 11 (November 2004): 6363–69. http://dx.doi.org/10.1128/aem.70.11.6363-6369.2004.
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ABSTRACT Within grazed pastures, urine patches are hot spots of nitrogen turnover, since dietary N surpluses are excreted mainly as urea in the urine. This short-term experiment investigated 13C uptake in microbial lipids after simulated deposition of cattle urine at 10.0 and 17.1 g of urea C m−2. Confined field plots without or with cattle urine amendment were sampled after 4 and 14 days, and soil from 0- to 5-cm and 10- to 20-cm depths was analyzed for content and composition of phospholipid fatty acids (PLFAs) and for the distribution of urea-derived 13C among individual PLFAs. Carbon dioxide emissions were quantified, and the contributions derived from urea were assessed. Initial changes in PLFA composition were greater at the lower level of urea, as revealed by a principal-component analysis. At the higher urea level, osmotic stress was indicated by the dynamics of cyclopropane fatty acids and branched-chain fatty acids. Incorporation of 13C from [13C]urea was low but significant, and the largest amounts of urea-derived C were found in common fatty acids (i.e., 16:0, 16:1ω7c, and 18:1ω7) that would be consistent with growth of typical NH4 +-oxidizing (Nitrosomonas) and NO2 −-oxidizing (Nitrobacter) bacteria. Surprisingly, a 20‰ depletion of 13C in the cyclopropane fatty acid cy17:0 was observed after 4 days, which was replaced by a 10 to 20‰ depletion of that in cy19:0 after 14 days. Possible reasons for this pattern are discussed. Autotrophic nitrifiers could not be implicated in urea hydrolysis to any large extent, but PLFA dynamics and the incorporation of urea-derived 13C in PLFAs indicated a response of nitrifiers which differed between the two urea concentrations.
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Rinklebe, Jörg, and Uwe Langer. "Relationship between soil microbial biomass determined by SIR and PLFA analysis in floodplain soils." Journal of Soils and Sediments 10, no. 1 (November 25, 2009): 4–8. http://dx.doi.org/10.1007/s11368-009-0155-0.
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Yu, Xuan, Lin Yang, Shixuan Fei, Zitong Ma, Ruqian Hao, and Zhong Zhao. "Effect of Soil Layer and Plant–Soil Interaction on Soil Microbial Diversity and Function after Canopy Gap Disturbance." Forests 9, no. 11 (October 29, 2018): 680. http://dx.doi.org/10.3390/f9110680.
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Gaps by thinning can have different microclimatic environments compared to surrounding areas, depending on the size of the gap. In addition, gaps can play important roles in biological dynamics, nutrient cycling, and seedling regeneration. The impacts of gap size on soil microbial communities and enzyme activities in different soil layers in Chinese pine plantations are not well understood. Here, we created gaps of 45 m2 (small, G1), 100 m2 (medium, G2), and 190 m2 (large, G3) by thinning unhealthy trees in an aged (i.e., 50 years old) monoculture Chinese pine plantation in 2010. Soil samples were collected in 2015. The total, bacterial, Gram-positive (G+), and Gram-negative (G−) phospholipid fatty acid (PLFA) profiles were highest in medium gaps in both the organic and mineral layers. These indicesdecreased sharply as gap size increased to 190 m2, and each of the detected enzyme activities demonstrated the same trend. Under all the gap size managements, abundances of microbial PLFAs and enzyme activities in the organic layers were higher than in the mineral layers. The soil layer was found to have a stronger influence on soil microbial communities than gap size. Redundancy analysis (RDA) based on the three systems with different gap sizes showed that undergrowth coverage, diversity, soil total nitrogen (TN), total organic carbon (TOC), and available phosphorus (AT) significantly affected soil microbial communities. Our findings highlighted that the effect of gap size on soil microenvironment is valuable information for assessing soil fertility. Medium gaps (i.e., 100 m2) have higher microbial PLFAs, enzyme activity, and soil nutrient availability. These medium gaps are considered favorable for soil microbial communities and fertility studied in a Chinese pine plantation managed on the Loess Plateau.
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Roslev, Peter, Peter L. Madsen, Jesper B. Thyme, and Kaj Henriksen. "Degradation of Phthalate and Di-(2-Ethylhexyl)phthalate by Indigenous and Inoculated Microorganisms in Sludge-Amended Soil." Applied and Environmental Microbiology 64, no. 12 (December 1, 1998): 4711–19. http://dx.doi.org/10.1128/aem.64.12.4711-4719.1998.
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ABSTRACT The metabolism of phthalic acid (PA) and di-(2-ethylhexyl)phthalate (DEHP) in sludge-amended agricultural soil was studied with radiotracer techniques. The initial rates of metabolism of PA and DEHP (4.1 nmol/g [dry weight]) were estimated to be 731.8 and 25.6 pmol/g (dry weight) per day, respectively. Indigenous microorganisms assimilated 28 and 17% of the carbon in [14C]PA and [14C]DEHP, respectively, into microbial biomass. The rates of DEHP metabolism were much greater in sludge assays without soil than in assays with sludge-amended soil. Mineralization of [14C]DEHP to 14CO2 increased fourfold after inoculation of sludge and soil samples with DEHP-degrading strain SDE 2. The elevated mineralization potential was maintained for more than 27 days. Experiments performed with strain SDE 2 suggested that the bioavailability and mineralization of DEHP decreased substantially in the presence of soil and sludge components. The microorganisms metabolizing PA and DEHP in sludge and sludge-amended soil were characterized by substrate-specific radiolabelling, followed by analysis of 14C-labelled phospholipid ester-linked fatty acids (14C-PLFAs). This assay provided a radioactive fingerprint of the organisms actively metabolizing [14C]PA and [14C]DEHP. The14C-PLFA fingerprints showed that organisms with different PLFA compositions metabolized PA and DEHP in sludge-amended soil. In contrast, microorganisms with comparable 14C-PLFA fingerprints were found to dominate DEHP metabolism in sludge and sludge-amended soil. Our results suggested that indigenous sludge microorganisms dominated DEHP degradation in sludge-amended soil. Mineralization of DEHP and PA followed complex kinetics that could not be described by simple first-order equations. The initial mineralization activity was described by an exponential function; this was followed by a second phase that was described best by a fractional power function. In the initial phase, the half times for PA and DEHP in sludge-amended soil were 2 and 58 days, respectively. In the late phase of incubation, the apparent half times for PA and DEHP increased to 15 and 147 days, respectively. In the second phase (after more than 28 days), the half time for DEHP was 2.9 times longer in sludge-amended soil assays than in sludge assays without soil. Experiments with radiolabelled DEHP degraders suggested that a significant fraction of the 14CO2 produced in long-term degradation assays may have originated from turnover of labelled microbial biomass rather than mineralization of [14C]PA or [14C]DEHP. It was estimated that a significant amount of DEHP with poor biodegradability and extractability remains in sludge-amended soil for extended periods of time despite the presence of microorganisms capable of degrading the compound (e.g., more than 40% of the DEHP added is not mineralized after 1 year).
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Anders, Elena, Andrea Watzinger, Franziska Rempt, Barbara Kitzler, Bernhard Wimmer, Franz Zehetner, Karl Stahr, Sophie Zechmeister-Boltenstern, and Gerhard Soja. "Biochar affects the structure rather than the total biomass of microbial communities in temperate soils." Agricultural and Food Science 22, no. 4 (December 18, 2013): 404–23. http://dx.doi.org/10.23986/afsci.8095.
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Biochar application is a promising strategy for sequestering carbon in agricultural soils and for improving degraded soils. Nonetheless, contradictory and unsettled issues remain. This study investigates whether biochar influences the soil microbial biomass and community structure using phospholipid fatty acid (PLFA) analysis. We monitored the effects of four different types of biochar on the soil microbial communities in three temperate soils of Austria over several months. A greenhouse experiment and two field experiments were conducted. The biochar application did not significantly increase or decrease the microbial biomass. Only the addition of vineyard pruning biochar pyrolysed at 400°C caused microbial biomass to increase in the greenhouse experiment. The biochar treatments however caused shifts in microbial communities (visualized by principal component analysis). We concluded that the shifts in the microbial community structure are an indirect rather than a direct effect and depend on soil conditions and nutrient status.
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Ruban, Yu V., K. E. Shavanova, V. V. Illenko, K. D. Korepanova, D. O. Samofalova, S. B. Nikonov, N. F. Spyrka, N. G. Nesterova, and O. Yu Parenyuk. "PLFA analysis of the microbial community structure at the points of the temporary localization of radioactive waste." Faktori eksperimental'noi evolucii organizmiv 26 (September 1, 2020): 149–53. http://dx.doi.org/10.7124/feeo.v26.1258.
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Aim. PTLRW are the trenches and bursts for the localization of radioactive waste that were created during the first priority measures for elimination of the Chornobyl accident. The aim of the presented work was to characterize the microbial community structure on PTLRW. Methods. To describe the influence of environmental factors on the soil microflora, the agrochemical parameters of soil (pH, carbon, nitrogen, mobile potassium and phosphorus) were evaluated. Dose loading was calculated using the ERICA tool software package. The total lipid fraction was extracted with a modified Bligh-Dyer method. Results. The pH of the soil ranged from 3.0 to 3.9. The carbon content ranged from 0.95% to 2.11%. The exception was Red Forest from the trench/outside the trench where the carbon content was 2.52 and 1.98% and with a pH 4.5. Nitrogen content ranged from 33.6 mg / kg to 74.2 mg / kg. The PLFA content ranged from 15 μg / g to 18.9 μg / g, except Novoshepelychi and Zalissia (33.3 μg / g and 23 μg / g). Conclusions. In terms of the structural composition of the microorganisms, the PTLRW points were more homogeneous compared to the contaminated radionuclide ecosystems. In natural ecosystems, gram-positive bacteria were the main dominant group, unlike PTLRW where there were several groups.
Keywords: PTLRW, microbial community structure, PLFA, biomarkers, ERICA tool.
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Pennanen, Taina, Hannu Fritze, Pekka Vanhala, Oili Kiikkilä, Seppo Neuvonen, and Erland Bååth. "Structure of a Microbial Community in Soil after Prolonged Addition of Low Levels of Simulated Acid Rain." Applied and Environmental Microbiology 64, no. 6 (June 1, 1998): 2173–80. http://dx.doi.org/10.1128/aem.64.6.2173-2180.1998.
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ABSTRACT Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.
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Tang, H. M., Y. L. Xu, X. P. Xiao, C. Li, W. Y. Li, K. K. Cheng, X. C. Pan, and G. Sun. "Impacts of long-term fertilization on the soil microbial communities in double-cropped paddy fields." Journal of Agricultural Science 156, no. 7 (September 2018): 857–64. http://dx.doi.org/10.1017/s0021859618000825.
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AbstractThe response of soil microbial communities to soil quality changes is a sensitive indicator of soil ecosystem health. The current work investigated soil microbial communities under different fertilization treatments in a 31-year experiment using the phospholipid fatty acid (PLFA) profile method. The experiment consisted of five fertilization treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice (Oryza sativaL.) straw residue and chemical fertilizer (RF), low manure rate and chemical fertilizer (LOM), and high manure rate and chemical fertilizer (HOM). Soil samples were collected from the plough layer and results indicated that the content of PLFAs were increased in all fertilization treatments compared with the control. The iC15:0 fatty acids increased significantly in MF treatment but decreased in RF, LOM and HOM, while aC15:0 fatty acids increased in these three treatments. Principal component (PC) analysis was conducted to determine factors defining soil microbial community structure using the 21 PLFAs detected in all treatments: the first and second PCs explained 89.8% of the total variance. All unsaturated and cyclopropyl PLFAs except C12:0 and C15:0 were highly weighted on the first PC. The first and second PC also explained 87.1% of the total variance among all fertilization treatments. There was no difference in the first and second PC between RF and HOM treatments. The results indicated that long-term combined application of straw residue or organic manure with chemical fertilizer practices improved soil microbial community structure more than the mineral fertilizer treatment in double-cropped paddy fields in Southern China.
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Yang, Fengshan, Yanbo Wang, Yanan Huang, Yuning Wei, Mingrui Yuan, Haiyan Fu, Weimin Zeng, and Chunguang Liu. "Microbial Community’s Dynamic Response to Fomesafen Usage in Chernozems of Northeast China." Diversity 13, no. 8 (July 26, 2021): 340. http://dx.doi.org/10.3390/d13080340.
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The main purpose of this study was to explore the effects of the recommended usage level and twice the recommended usage level of the long-acting herbicide fomesafen on the soil enzymes and microbial community structure in chernozems of soybean fields. Culturable microbial biomass and phospholipid fatty acids (PLFA) were used as the main references for this evaluation. The digestion curve of fomesafen in soil conforms to the law of a single exponential function. The activities of four soil enzymes decreased significantly when exposed to twice the recommended amount, and then returned to the control level. The inhibition of the fungal and bacterial biomass section of culturable microorganisms in soil at twice the recommended usage level was greater than that under the recommended usage level, and this dosage also stimulated the rapid recovery of the initial level of fungal biomass before the application of fomesafen. The PLFA analysis showed that the ratio of GN/GP decreased significantly, and soil pressure increased significantly. Compared with the recommended usage level, the effect of twice the recommended usage level of fomesafen on soil microbial community structures was more significant. This provides a reference for environmental location recommendations, environmental safety assessments, and the rational use of herbicides.
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Romaniuk, Romina, Lidia Giuffré, Alejandro Costantini, Norberto Bartoloni, and Paolo Nannipieri. "A comparison of indexing methods to evaluate quality of soils: the role of soil microbiological properties." Soil Research 49, no. 8 (2011): 733. http://dx.doi.org/10.1071/sr11147.
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The study evaluates and compares two procedures for selecting soil quality indicators (used for the construction of soil quality indices, SQI) by using diverse chemical, physical, and biological properties, and evaluates the role of soil microbiological properties in the construction of SQI. Different soil environments were selected from an extensive agricultural production site in the rolling pampa, Buenos Aires, Argentina. The plots included an undisturbed soil, a grassland soil, and continuous tilled soils with four different surface horizon depths (25, 23, 19, and 14 cm). Various properties were measured, and a minimum dataset was chosen by principal component analysis (PCA) considering all measured soil properties together (procedure A), or the PCA was performed separately according to classification as physical, chemical, or biological soil properties (procedure B). The measured soil properties involved physical, chemical, and biochemical properties determined by standard protocols used in routine laboratory analysis (simple SQI, SSQI) or more laborious protocols to determine microbial community structure and function by phospholipid fatty acid (PLFA) and catabolic response profile (CRP), respectively (complex SQI, CSQI). The selected properties were linearly normalised and integrated by the weight additive method to calculate SSQI A, SSQI B, CSQI A, and CSQI B indices. Two microbiological SQI (MSQI) were also calculated; MSQI 1 considered only biological properties according to the procedure used for calculating SQI; MSQI 2 was calculated by considering three selected microbiological parameters representing the size (microbial biomass carbon), activity (soil basal respiration), and functional diversity (evenness, determined by CRP) of the microbial communities. All of the constructed indices show the same differences among the study sites. The inclusion of CRP and PLFA data in the indices slightly increased, or did not increase, the index sensitivity. Microbiological indices had the same sensitivity as the indices integrated by physical, chemical, and biological properties. An evaluation of the SQI constructed by both procedures found no difference in sensitivity. However, SQI constructed by procedure B allowed evaluation of the effects of management practices on physical, chemical, and biological soil properties.
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Viana, Laura Tillmann, Mercedes Maria da Cunha Bustamante, Marirosa Molina, Alexandre de Siqueira Pinto, Keith Kisselle, Richard Zepp, and Roger A. Burke. "Microbial communities in Cerrado soils under native vegetation subjected to prescribed fire and under pasture." Pesquisa Agropecuária Brasileira 46, no. 12 (December 2011): 1665–72. http://dx.doi.org/10.1590/s0100-204x2011001200012.
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The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerrado stricto sensu" and "campo sujo"), under different fire regimes, and a 20-year-old active palisadegrass pasture in the Central Plateau of Brazil. Microbial biomass was higher in the native plots than in the pasture, and the highest monthly values were observed during the rainy season in the native plots. No significant differences were observed between fire regimes or between communities from the two native vegetation types. However, the principal component (PC) analysis separated the microbial communities by vegetation cover (native x pasture) and season (wet x dry), accounting for 45.8% (PC1 and PC3) and 25.6% (PC2 and PC3), respectively, of the total PLFA variability. Changes in land cover and seasonal rainfall in Cerrado ecosystems have significant effects on the total density of soil microorganisms and on the abundance of microbial groups, especially Gram-negative and Gram-positive bacteria.