Comparison of community structures of microbiota at main habitats in rice field ecosystems based on phospholipid fatty acid analysis

The present study compares the community structures of microbiota at different habitats in Japanese rice fields by comparing their phospholipid fatty acid (PLFA) compositions to understand the contribution of different habitats to microbiological diversity. The data were collected from four neighboring rice fields. Comparison was made for the PLFA compositions extracted from the floodwater, percolating water, rice soils under flooded and drained conditions, rice straw (RS) placed in flooded and drained rice soils, RS in the composting process, and RS compost placed in a flooded rice field. Average amounts of PLFAs were 33 μg L⁻¹ in the floodwater, 17.1 μg L⁻¹ in the percolating water from plow layers, 34.6 μg L⁻¹ in the percolating water from subsoil layers, 108 μg g⁻¹ dry weight basis (dw) in flooded rice soils, 382 μg g⁻¹ dw in RS materials, 2,510 μg g⁻¹ dw in RS composts, 2,850 μg g⁻¹ dw in RS composts after application to a flooded rice soil, 222 μg g⁻¹ wet weight basis (ww) in RS in drained rice soils, and 284 μg g⁻¹ ww in RS in flooded rice soils. The total amount of PLFAs to the soil depth of 10 cm was estimated to be about 12 g m⁻². The PLFA compositions were different from each other depending on the habitats. Rice soils were characterized by the predominance of actinomycetes and Gram-positive bacteria in comparison with the other habitats. In contrast, the microbial communities in the floodwater and percolating water were characterized by the predominance of Gram-negative bacteria and eukaryotes (presumably algae), and Gram-negative bacteria, respectively. The microbial community of RS materials was dominated by fungi. Gram-positive bacteria became predominant in RS after application to flooded rice soils, while RS placed in a drained rice field after harvesting rice was characterized by the predominance of Gram-negative bacteria and fungi. The community structures at respective habitats were stable and specific, irrespective of the season of sampling and the duration of decomposition of RS.     

Fungal growth and effects of different wood decomposing fungi on the indigenous bacterial community of polluted and unpolluted soils

Thirty-two different basidiomycete isolates were inoculated separately into contaminated soil and the soil colonization ability was assessed visually. Large differences in the colonization ability and growth patterns were found between the different fungi. Phospholipid fatty acids (PLFAs) were extracted from the soils of the seven isolates with the best colonizing ability. All PLFAs that were not found in pure cultures of the seven fungi were considered as bacterial PLFAs. The bacterial PLFA data were subjected to principal component analysis (PCA) to indicate changes in the indigenous bacterial community. The experiment was repeated in a sandy agricultural soil. The bacterial PLFA patterns were altered when fungi were inoculated into soil, irrespective of whether it was polluted or not. In particular the PLFA cy19:0, indicative of Gram-negative bacteria, was higher in fungal-inoculated soil than in uninoculated controls. The PLFA patterns for each fungal treatment were distributed more or less similarly in the PCA plots of both contaminated and sandy agricultural soil. Soil inoculated with Antrodia vaillantii, Hypholoma fasciculare or Recinicium bicolor was considerably different from the control along PC 1. Soil inoculated with Phanerochaete chrysosporium was characterized by different values along PC 2 compared with the other fungal soils.     

Impact of coastal wetland cultivation on microbial biomass, ammonia-oxidizing bacteria, gross N transformation and N2O and NO potential production

A ¹⁵N dilution experiment was carried out to investigate effects of cultivation on the gross N transformation rate in coastal wetland zone. Microbial community composition was estimated by phospholipid fatty acid (PLFA) analysis and abundance of soil ammonia-oxidizing bacteria (AOB) was quantified by real-time polymerase chain reaction (PCR). Soil salinity decreased significantly, while total N increased after coastal wetland was cultivated. Microbial biomass (total PLFA), bacterial biomass, fungal biomass, and actinomycete biomass of the native coastal wetland soils were significantly (p < 0.05) lower than those of the cultivated soils whereas AOB population size also significantly increased after coastal wetland cultivation. Multiple regression analysis showed that total PLFA biomass and soil total N (TN) explained 97% of the variation of gross N mineralization rate in the studied soils (gross mineralization rate = 0.179 total PLFA biomass + 5.828TN − 2.505, n = 16, p < 0.01). Gross nitrification rate increased by increasing the soil AOB population size and gross mineralization rate (M) (gross nitrification rate = 3.39AOB + 0.18 M − 0.075, R ² = 0.98, n = 16, p < 0.01). Management of salt discharge and mineral N fertilization during the cultivation of wetland soils might have changed composition of soil microflora and AOB population size, thus influencing mineralization and nitrification. Probably, the cultivation of coastal wetland soils increased the risk of N losses from soil through nitrate leaching and gas emission (e.g., N₂O and NO).     

Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques

We have compared the total microbial biomass and the fungal/bacterial ratio estimated using substrate-induced respiration (SIR) in combination with the selective inhibition technique and using the phospholipid fatty acid (PLFA) technique in a pH gradient (3.0-7.2) consisting of 53 mature broad-leaved forest soils. A fungal/bacterial biomass index using the PLFA technique was calculated using the PLFA 18:2ω6,9 as an indicator of fungal biomass and the sum of 13 bacterial specific PLFAs as indicator of the bacterial biomass. Good linear correlation (p<0.001) was found between the total microbial biomass estimated with SIR and total PLFAs (totPLFA), indicating that 1 mg biomass-C was equivalent to 130 nmol totPLFA. Both biomass estimates were positively correlated to soil pH. The fungal/bacterial ratio measured using the selective inhibition technique decreased significantly with increasing pH from about 9 at pH 3 to approximately 2 at pH 7, while the fungal/bacterial biomass index using PLFA measurements tended to increase slightly with increasing soil pH. Good correlation between the soil content of ergosterol and of the PLFA 18:2ω6,9 indicated that the lack of congruency between the two methods in estimating fungal/bacterial ratios was not due to PLFA 18:2ω6,9-related non-fungal structures to any significant degree. Several PLFAs were strongly correlated to soil pH (R² values >0.8); for example the PLFAs 16:1ω5 and 16:1ω7c increased with increasing soil pH, while i16:0 and cy19:0 decreased. A principal component analysis of the total PLFA pattern gave a first component that was strongly correlated to soil pH (R²=0.85, p<0.001) indicating that the microbial community composition in these beech/beech-oak forest soils was to a large extent determined by soil pH.     

干旱热带地区土地利用变化对土壤微生物群落组成及有机碳含量的影响

Restoration of forests poses a major challenge globally,particularly in the tropics,as the forests in these regions are more vulnerable to land-use change.We studied land-use change from natural forest (NF) to degraded forest (DF),and subsequently to either Jatropha curcas plantation (JP) or agroecosystem (AG),in the dry tropics of Uttar Pradesh,India,with respect to its impacts on soil microbial community composition as indicated by phospholipid fatty acid (PLFA) biomarkers and soil organic carbon (SOC) content.The trend of bacterial PLFAs across all land-use types was in the order:NF ＞ JP ＞ DF＞ AG.In NF,there was dominance of gram-negative bacterial (G-) PLFAs over the corresponding gram-positive bacterial (G+) PLFAs.The levels of G-PLFAs in AG and JP differed significantly from those in DF,whereas those of G+ PLFAs were relatively similar in these three land-use types.Fungal PLFAs,however,followed a different trend:NF ＞ JP ＞ DF =AG.Total PLFAs,fungal/bacterial (F/B) PLFA ratio,and SOC content followed trends similar to that of bacterial PLFAs.Across all land-use types,there were strong positive relationships between SOC content and G-,bacterial,fungal,and total microbial PLFAs and F/B PLFA ratio.Compared with bacterial PLFAs,fungal PLFAs appeared to be more responsive to land-use change.The F/B PLFA ratio,fungal PLFAs,and bacterial PLFAs explained 91％,94％,and 73％ of the variability in SOC content,respectively.The higher F/B PLFA ratio in JP favored more soil C storage,leading to faster ecosystem recovery compared to either AG or DF.The F/B PLFA ratio could be used as an early indicator of ecosystem recovery in response to disturbance,particularly in relation to land-use change.     

Carbon uptake by a microbial community during 30-day treatment with 13C-glucose of a sandy loam soil fertilized for 20 years with NPK or compost as determined by a GC–C–IRMS analysis of phospholipid fatty acids

To investigate the uptake by the microbial community of easily decomposable exogenous organic C and the proportion of this organic C remaining in soils under long-term fertilization schemes, ¹³C-glucose was supplied to arable soils (aquic inceptisol) following a 20-year (1989–2009) application of compost (CM) or inorganic NPK (NPK), along with a control (no fertilizer). Phospholipid fatty acids (PLFAs) were used as biomarkers for actinobacteria, bacteria and fungi. Gas chromatography–combustion–stable isotope ratio mass spectrometry (GC–C–IRMS) was used to determine the incorporation of ¹³C into individual PLFAs. The concentrations of soil microbial PLFAs significantly (P < 0.05) increased in all three soils after the addition of ¹³C-glucose. Over a 30-day incubation period, the highest PLFA concentrations were on day 7 (control) or day 15 (NPK and CM) for bacteria, and on day 30 for both fungi and actinobacteria. The added ¹³C-glucose was incorporated into bacterial PLFAs first, whilst an increase of ¹³C in fungal and actinobacterial PLFAs was measured on day 7 and 15, respectively. The mean amounts of ¹³C in bacterial, actinobacterial and fungal PLFAs in CM-treated soil during the 30-day incubation period were 0.589, 0.030 and 0.056 μg g⁻¹ soil, respectively, which were significantly (P < 0.05) higher than levels measured in the NPK and control soils. Among the bacterial groups, the amount of ¹³C in Gram-positive (G⁺) bacteria over the entire incubation ranged from 0.326 to 0.440 μg g⁻¹ soil in the CM scheme, which was significantly (P < 0.05) higher than levels detected in the NPK and control regimes. In contrast, ¹³C concentrations in monounsaturated PLFAs (aerobic microorganisms) in the CM-treated soil were 0.030–0.045 μg g⁻¹ soil, which was significantly (P < 0.05) lower than in the NPK schemes. The proportion of glucose-derived ¹³C remaining in soils was ranked as follows: CM (53%) > NPK (41%) > control (28%) after 30 days of incubation. Easily decomposable exogenous organic C was thus more effectively maintained under the CM regime, primarily because, after 20 years, CM had altered the microbial community by reducing the ratio of aerobic to anaerobic microorganisms whilst increasing levels of G⁺ bacteria in soil compared to the control and NPK soils. This study aids our understanding of the transformation and maintenance of easily decomposable organic C in soil over long-term fertilization regimes.     

Distinct microbial and faunal communities and translocated carbon in Lumbricus terrestris drilospheres

Lumbricus terrestris is a deep-burrowing anecic earthworm that builds permanent, vertical burrows with linings (e.g., drilosphere) that are stable and long-lived microhabitats for bacteria, fungi, micro- and mesofauna. We conducted the first non-culture based field study to assess simultaneously the drilosphere (here sampled as 0–2 mm burrow lining) composition of microbial and micro/mesofaunal communities relative to bulk soil. Our study also included a treatment of surface-applied ¹³C- and ¹⁵N-labeled plant residue to trace the short-term (40 d) translocation of residue C and N into the drilosphere, and potentially the assimilation of residue C into drilosphere microbial phospholipid fatty acids (PLFAs). Total C concentration was 23%, microbial PLFA biomass was 58%, and PLFAs associated with protozoa, nematodes, Collembola and other fauna were 200-to-300% greater in the drilosphere than in nearby bulk soil. Principal components analysis of community PLFAs revealed that distributions of Gram-negative bacteria and actinomycetes and other Gram-positive bacteria were highly variable among drilosphere samples, and that drilosphere communities were distinct from bulk soil communities due to the atypical distribution of PLFA biomarkers for micro- and mesofauna. The degree of microbial PLFA ¹³C enrichment in drilosphere soils receiving ¹³C-labeled residue was highly variable, and only one PLFA, 18:1ω9c, was significantly enriched. In contrast, 11 PLFAs from diverse microbial groups where enriched in response to residue amendment in bulk soil 0–5 cm deep. Among control soils, however, a significant δ¹³C shift between drilosphere and bulk soil at the same depth (5–15 cm) revealed the importance of L. terrestris for translocating perennial ryegrass-derived C into the soil at depth, where we estimated the contribution of the recent grass C (8 years) to be at least 26% of the drilosphere soil C. We conclude that L. terrestris facilitates the translocation of plant C into soil at depth and promotes the maintenance of distinct soil microbial and faunal communities that are unlike those found in the bulk soil.     

Biochemical properties of forest soils as affected by a fire retardant

Synthetic polymers are currently being used as water additives to control wildfires and prescribed burns. This laboratory study examines the effects of one of these acrylic-based polymers (Firesorb) on some biochemical properties (microbial biomass C, hydrolysis of FDA, #-glucosidase, urease and N mineralization) of two coarse textured soils (loamy sand and sandy loam) under pinewood located at Galicia (NW Spain). Firesorb was added to unheated and heated soil samples at two levels of application (1 and 3 times the recommended dose) and measurements were made after 6 and 12 weeks of aerobic incubation. The results obtained for both soils at different incubation times were found to be comparable. Except for N mineralization, which was reduced by Firesorb addition, in both unheated and heated soils, the Firesorb-treated samples showed similar or significantly higher values for the biochemical parameters analyzed than those in the untreated control soils. This finding suggests that under these assay conditions the synthetic polymer used as a fire-fighting chemical had no adverse effects on soil microbial communities.     

Identification of Metabolically Active Rhizosphere Microorganisms by Stable Isotopic Probing of PLFA in Switchgrass

Root-derived rhizodeposits of recent photosynthetic carbon (C) are the foremost source of energy for microbial growth and development in rhizosphere soil. A substantial amount of photosynthesized C by the plants is translocated to belowground and is released as root exudates that influence the structure and function of soil microbial communities with potential inference in nutrient and C cycling in the ecosystem. We applied the ¹³C pulse chase labeling technique to evaluate the incorporation of rhizodeposit-C into the phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of switchgrass (Panicum virgatum L.). Soil samples of bulk and rhizosphere were taken at 1, 5, 10 and 20 days after labeling and analyzed for ¹³C enrichment in the microbial PLFAs. Temporal differences of ¹³C enrichment in PLFAs were more prominent than spatial differences. Among the microbial PLFA biomarkers, fungi and Gram-negative (GM-ve) bacterial PLFAs showed rapid enrichment with ¹³C compared to Gram-positive (GM+ve) and actinomycetes in rhizosphere soil. The ¹³C enrichment of actinomycetes biomarker PLFA significantly increased along with sampling time in both soils. PLFAs indicative to fungi, GM-ve and GM+ve showed a significant decrease in ¹³C enrichment over sampling time in the rhizosphere, but a decrease was also observed in GM-ve (16:1ω5c) and fungal biomarker PLFAs in the bulk soil. The relative ¹³C concentration in fungal PLFA decreased on day 10, whereas those of GM-ve increased on day 5 and GM+ve remained constant in the rhizosphere soil. However, the relative ¹³C concentrations of GM-ve and GM+ve increased on days 5 and 10, respectively, and those of fungal remain constant in the bulk soil. The present study demonstrates the usefulness of ¹³C pulse chase labeling together with PLFA analysis to evaluate the active involvement of microbial community groups for utilizing rhizodeposit-C.     

Changes in the soil microbial community structure with latitude in eastern China, based on phospholipid fatty acid analysis

Phospholipid fatty acid (PLFA) profiles were measured in soils from 14 sites in eastern China representing typical geographic zones of varying latitude from north (47.4°N) to south (21.4°N). Amounts of soil microbial biomass, measured as total amounts of PLFAs, showed no regular trend with latitude, but were positively correlated with soil organic carbon content, the concentration of humic acid and amorphous iron oxide. Soil microbial community structure showed some biogeographical distribution trends and was separated into three groups in a cluster analysis and principal coordinate analysis of log transformed PLFA concentrations (mol%). Soils in the first group came from northern China with medium mean annual temperature (1.2–15.7 °C) and rainfall (550–1021 mm). Soils in the second group originated from southern China with a relatively higher mean annual temperature (15.7–21.2 °C) and rainfall (1021–1690 mm). Soils clustered in the third group originated from the most southerly region. The northern soils contained relatively more bacteria and Gram-negative PLFAs, while the southern soils had more fungi and pressure indexed PLFAs. These differences in soil microbial community structure were largely explained by soil pH, while other site and soil characteristics were less important.     

Linking microbial community structure and allocation of plant-derived carbon in an organic agricultural soil using 13CO2 pulse-chase labelling combined with 13C-PLFA profiling

We conducted a ¹³CO₂ pulse-chase labelling experiment in a drained boreal organic (peat) soil cultivated with perennial crop, reed canary grass (RCG; Phalaris arundinacea) to study the flow of carbon from plants to soil microbes. Both limed and unlimed soils were studied, since liming is a common agricultural practice for acidic organic soils. Soil samples taken within three months after the labelling and three times in the following year were used for the δ¹³C analysis of microbial phospholipid fatty acids (PLFAs), root sugars and root lipids. We estimated the contribution of carbon from root exudates to microbial PLFA synthesis. The flow of carbon from plants to microbes was fast as the label allocation in PLFAs had a peak 1–3 days after labelling. The results showed that fungi were important in the incorporation of fresh, plant-derived carbon, including root sugars. None of the main microbial PLFA biomarker groups (fungi, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi) was completely lacking label over the measurement period. One year after the labelling, when the labelled carbon was widely distributed into plant biomass and soil, bacterial biomarkers increased their share of the label allocation. Liming had a minor effect on the label allocation rate into PLFAs. The mixing model approach used to calculate the root exudate contribution to microbial biomass resulted in a highly conservative estimate of utilization of this important C-source (0–6.5%, with highest incorporation into fungi). In summary, the results of this study provide new information about the role of various microbial groups in the turnover of plant-derived, fresh carbon in boreal organic soil.     

Soil microbial communities response to herbicide 2,4-dichlorophenoxyacetic acid butyl ester

2,4-Dichlorophenoxyacetic acid butyl ester (2,4-D butyl ester) is extensively applied for weed control in cultivation fields in China, but its effect on soil microbial community remains obscure. This study investigated the microbial response to 2,4-D butyl ester application at different concentrations (CK, 10, 100 and 1000 μg g^?1) in the soils with two fertility levels, using soil dilution plate method and phospholipid fatty acid (PLFA) analysis. Culturable microorganisms were affected by the herbicide in both soils, particularly at the higher concentration. After treating soil with 100 μg g^?1 herbicide, culturable bacteria and actinomycetes were significantly higher, compared to other treatments. Treatment of soil with 1000 μg g^?1 2,4-D butyl ester caused a decline in culturable microbial counts, with the exception of fungal numbers, which increased over the incubation time. PLFA profiles showed that fatty acids for Gram-negative (GN) bacteria, Gram-positive (GP) bacteria, total bacteria and total fungi, as well as total PLFAs, varied with herbicide concentration for both soil samples. As herbicide concentration increased, the GN/GP ratio decreased dramatically in the two soils. The higher stress level was in the treatments with high concentrations of herbicide (1000 μg g^?1) for both soils. Principal component analysis of PLFAs showed that the addition of 2,4-D butyl ester significantly shifted the microbial community structure in the two soils. These results showed that the herbicide 2,4-D butyl ester might have substantial effects on microbial population and microbial community structure in agricultural soils. In particular, the effects of 2,4-D butyl ester were greater in soil with low organic matter and fertility level than in soil with high organic matter and fertility level.     

Investigation of the effect of ammonium sulfate on populations of ambient methane oxidising bacteria by C-labelling and GC/C/IRMS analysis of phospholipid fatty acids

The oxidation of atmospheric methane by methanotrophic bacteria residing in soils constitutes an important terrestrial methane sink with previous studies having revealed the inhibition of microbially mediated methane oxidation in the presence of salt ions. The bacteria responsible for ambient methane oxidation are not amenable to currently available methods of culturing, resulting in the need for a method of in situ analysis. A combination of phospholipid fatty acid (PLFA) analysis and stable isotopic labelling has been employed in this investigation as a means of cultivation-independent bacterial analysis. Soil samples were treated with an ammonium sulfate solution at a concentration that was known to inhibit methane oxidation or with distilled water, serving as a control, and incubated with ¹³C-labelled methane. PLFAs were analysed by GC/C/IRMS in order to determine their ¹³C content and, hence, the PLFA distribution of the methane oxidising bacteria. Ammonium sulfate treatment reduced the amount of ¹³C incorporated into the majority of PLFAs except the i17:0 PLFA in the presence of high concentrations of methane. These results implied a shift in the composition of the methane oxidising bacterial community in the soils treated with ammonium ions, with the treatment appearing to suppress one group of organisms more than another.     

Soil microbial community dynamics and phenanthrene degradation as affected by rape oil application

The effects of rape oil application on soil microbial communities and phenanthrene degradation were characterized by examining phenanthrene concentrations, changes in microbial composition and incorporation of [¹³C] phenanthrene-derived carbon into phospholipid fatty acids (PLFAs). A Haplic Chernozem was incubated with and without rape oil in combination with and without phenanthrene over 60 days. High-performance liquid chromatography (HPLC) analysis showed a net reduction in extractable phenanthrene in the soils treated with rape oil but no net reduction in the soils without rape oil. Rape oil application increased the total PLFA content and changed microbial community composition predominantly due to growth of fungal groups and Gram-positive bacterial groups. Under rape oil and phenanthrene amendment all detected microbial groups grew until day 24 of incubation. The ¹³C PLFA profiles showed ¹³C enrichment for the PLFAs i14:0, 15:0, 18:0, 18:1ω5 and the fungal biomarker 18:2ω6,9 under rape oil application. Fungal PLFA growth was highest among detected all PLFAs, but its ¹³C incorporation was lower compared to the Gram-positive and Gram-negative bacteria PLFAs. Our results demonstrate the effect of rape oil application on the abundance of microbial groups in soil treated with phenanthrene and its impact on phenanthrene degradation.     

Soil microbial community structure affected by 53 years of nitrogen fertilisation and different organic amendments

The Ultuna long-term soil organic matter experiment in Sweden (59′82° N, 17′65° E) was started in 1956 to study the effects of different N fertilisers and organic amendments on soil properties. In this study, samples were taken from 11 of the treatments, including unfertilised bare fallow and cropped fallow, straw with and without N addition, green manure, peat, farmyard manure, sawdust, sewage sludge, calcium nitrate and ammonium sulphate, with n = 4 for each treatment. Samples were taken from topsoil (0–20 cm) and subsoil (27–40 cm depth) and analysed for concentrations of phospholipid fatty acids (PLFAs), organic C, total N and pH. The results showed that the subsoil samples reflected the total PLFA content of the topsoil, but not the microbial community structure. Total PLFA content was well correlated with total organic C and total N in both topsoil and subsoil. Total PLFA content in topsoil samples was highest in the sewage sludge treatment (89 ± 22 nmol PLFA g dw⁻¹). This contradicts earlier findings on microbial biomass in this sewage sludge-treated soil, which indicated inhibition of microorganisms, probably by heavy metals added with sludge. A switch towards microbial growth and faster decomposition of organic matter occurred around 2000, coinciding with lowered heavy metal content in the sludge. According to the PLFA data, the microbial community in the sewage sludge treatment is now dominated by Gram-positive bacteria. A lack of Gram-negative bacteria was also observed for the ammonium sulphate treatment, obviously caused by a drop in pH to 4.2.     

Solvent-based washing removes lipophilic contaminant interference with phospholipid fatty acid analysis of soil communities

Phospholipid fatty acid (PLFA) analysis is an informative method for characterising and quantifying changes in the phenotypic profile of the soil microbial community when soils are exposed to chemical toxicants and other xenobiotics. However, where such materials are lipophilic, a range of non-polar compounds can be co-extracted with PLFAs and can consequently mask PLFA chromatograms. We found this to be the case with the lipophilic anti-microbial compound triclosan, which can enter the soil via the addition of sewage sludge. A simple method of washing soil in solvent prior to extraction was developed in order to remove triclosan without altering the relative abundance of PLFAs. Three contrasting soils were spiked with 500 mg kg⁻¹ of triclosan before being washed with methanol (MeOH), dichloromethane (DCM), hexane or aqueous solutions of these solvents. PLFAs were then extracted and analysed. All treatments were found to remove triclosan effectively, allowing all peaks to be identifiable. Whilst the polar solvents MeOH and DCM significantly altered the relative abundance of extracted fatty acids in most of the soils tested, soil washing with a small quantity of hexane was able to remove triclosan whilst best preserving the fidelity of the PLFA profiles.     

Influences of past application rates of nitrogen and a catch crop on soil microbial communities between an intensive rotation

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

Methanotrophic communities in a landfill cover soil as revealed by [13C] PLFAs and respiratory quinones: Impact of high methane addition and landfill leachate irrigation

The soil microbial communities of a landfill cover substrate, which was treated with landfill gas (100 l CH₄ m^?2 d^?1) and landfill leachate for 1.5 years, were investigated by phospholipid fatty acid (PLFA), ergosterol and respiratory quinone analyses. The natural ¹³C depletion of methane was used to assess the activity of methanotrophs and carbon turnover in the soil system. Under methane addition, the soil microbial community was dominated by PLFAs (14:0 and 16:1 isomers) and quinones (ubiquinone-8 and 18-methylene-ubiquinone-8) related to type I methanotrophs, and 18:1 PLFAs contained in type II methanotrophs. While type I methanotrophic PLFAs were ¹³C depleted, i.e. type I methanotrophs were actively oxidising and assimilating methane, ¹³C depletion of 18:1 PLFAs was low and inconsistent with their abundance. This, possibly reflects isotopic discrimination, assimilation of carbon derived from type I methanotrophs and a high contribution of non-methanotrophic bacteria to the 18:1 isomers. Landfill leachate irrigation caused the methanotrophic community to shift closer to the soil surface. It also decreased 18:1 PLFAs, while type I methanotrophs were probably stimulated. Gram positive bacteria, but not fungi, were also ¹³C depleted and consequently involved in the secondary turnover of carbon originating from methanotrophic bacteria. Cy17:0 PLFA was ¹³C depleted in deep soil layers, indicating anaerobic methane oxidation.     

The microbial PLFA composition as affected by pH in an arable soil

The influence of soil pH on the phospholipid fatty acid (PLFA) composition of the microbial community was investigated along the Hoosfield acid strip, Rothamsted Research, UK - a uniform pH gradient between pH 8.3 and 4.5. The influence of soil pH on the total concentration of PLFAs was not significant, while biomass estimated using substrate induced respiration decreased by about 25%. However, the PLFA composition clearly changed along the soil pH gradient. About 40% of the variation in PLFA composition along the gradient was explained by a first principal component, and the sample scores were highly correlated to pH (R² = 0.97). Many PLFAs responded to pH similarly in the Hoosfield arable soil compared with previous assessments in forest soils, including, e.g. monounsaturated PLFAs 16:1ω5, 16:1ω7c and 18:1ω7, which increased in relative concentrations with pH, and i16:0 and cy19:0, both of which decreased with pH. Some PLFAs responded differently to pH between the soil types, e.g. br18:0. We conclude that soil pH has a profound influence on the microbial PLFA composition, which must be considered in all applications of this method to detect changes in the microbial community.     

Seasonal Patterns of Microbial Community Structure and Enzyme Activities in Coastal Saline Soils of Perennial Halophytes

Perennial halophytes are known to be one of the most influential parameters in coastal ecosystem affecting ecosystem processes. The aim of this study was to investigate the changes in soil microbial community structure and enzyme activities in different halophyte‐covered soils (Arthrocnemum indicum , Aeluropus lagopoides , Heleochloa setulosa and Suaeda nudiflora ) with control soil (un‐vegetated) that were collected in three seasons (rainy, winter and summer) from intertidal coastal soils of Gujarat, India. Soil microbial community structure was assessed using phospholipid fatty acid (PLFA) profiling. Halophytes influenced significantly soil micro‐environment by exerting effects on the soil chemical characteristics, enzyme activities and microbial community structure. The activities of β‐glucosidase, urease and alkaline phosphatase were significantly higher in halophyte‐covered soils than in control soil. Among four halophyte‐covered soils, the highest amounts of total, bacterial, actinomycetes and fungal PLFAs were observed in Arthrocnemum soil. The concentrations of total, bacterial, actinomycetes and fungal PLFAs were also significantly higher in summer and winter seasons than in rainy season, whereas enzyme activities also vary with seasons. The non‐metric multidimensional scaling analysis PLFA profiling revealed that the structure of microbial community significantly differed in all seasons as well as between control and halophyte‐covered soils. These shifts in microbial community were due to the higher abundance of Gram‐positive, total bacterial and actinomycetes PLFAs in summer and winter seasons than in rainy season, whereas abundance of fungal biomarker was significantly higher in rainy season than in other seasons. Among halophytes, significantly higher abundance of Gram‐positive, Gram‐negative and total bacteria was observed in Arthrocnemum , Heleochloa and Suaeda whereas the lowest in control soil. Halophytes exhibited improved soil microbial activities, which is important for healthy ecosystem. Copyright © 2017 John Wiley & Sons, Ltd.