Substrate inputs and pH as factors controlling microbial biomass, activity and community structure in an arable soil

Our aim was to determine whether the smaller biomasses generally found in low pH compared to high pH arable soils under similar management are due principally to the decreased inputs of substrate or whether some factor(s) associated with pH are also important. This was tested in a soil incubation experiment using wheat straw as substrate and soils of different pHs (8.09, 6.61, 4.65 and 4.17). Microbial biomass ninhydrin-N, and microbial community structure evaluated by phospholipid fatty acids (PLFAs), were measured at 0 (control soil only), 5, 25 and 50 days and CO₂ evolution up to 100 days. Straw addition increased biomass ninhydrin-N, CO₂ evolution and total PLFA concentrations at all soil pH values. The positive effect of straw addition on biomass ninhydrin-N was less in soils of pH 4.17 and 4.65. Similarly total PLFA concentrations were smallest at the lowest pH. This indicated that there is a direct pH effect as well as effects related to different substrate availabilities on microbial biomass and community structure. In the control soils, the fatty acids 16:1ω5, 16:1ω7c, 18:1ω7c&9t and i17:0 had significant and positive linear relationships with soil pH. In contrast, the fatty acids i15:0, a15:0, i16:0 and br17:0, 16:02OH, 18:2ω6,9, 17:0, 19:0, 17:0c9,10 and 19:0c9,10 were greatest in control soils at the lowest pHs. In soils given straw, the fatty acids 16:1ω5, 16:1ω7c, 15:0 and 18:0 had significant and positive linear relationships with pH, but the concentration of the monounsaturated 18:1ω9 PLFA decreased at the highest pHs. The PLFA profiles indicative of Gram-positive bacteria were more abundant than Gram-negative ones at the lowest pH in control soils, but in soils given straw these trends were reversed. In contrast, straw addition changed the microbial community structures least at pH 6.61. The ratio: [fungal PLFA 18:2w6,9]/[total PLFAs indicative of bacteria] indicated that fungal PLFAs were more dominant in the microbial communities of the lowest pH soil. In summary, this work shows that soil pH has marked effects on microbial biomass, community structure, and response to substrate addition.     

Linking dynamics of soil microbial phospholipid fatty acids to carbon mineralization in a C natural abundance experiment: Impact of heavy metals and acid rain

A ¹³C natural abundance experiment including GC-c-IRMS analysis of phospholipid fatty acids (PLFAs) was conducted to assess the temporal dynamics of the soil microbial community and carbon incorporation during the mineralization of plant residues under the impact of heavy metals and acid rain. Maize straw was incorporated into (i) control soil, (ii) soil irrigated with acid rain, (iii) soil amended with heavy metal-polluted filter dust and (iv) soil with both, heavy metal and acid rain treatment, over a period of 74 weeks. The mineralization of maize straw carbon was significantly reduced by heavy metal impact. Reduced mineralization rate of the added carbon likely resulted from a reduction of the microbial biomass due to heavy metal stress, while the efficiency of ¹³C incorporation into microbial PLFAs was hardly affected. Since acid rain did not significantly change soil pH, little impact on soil microorganisms and mineralization rate was found. Temporal dynamics of labelling of microbial PLFAs were different between bacterial and fungal PLFA biomarkers. Utilization of maize straw by bacterial PLFAs peaked immediately after the application (2 weeks), while labelling of the fungal biomarker 18:2ω6,9 was most pronounced 5 weeks after the application. In general, ¹³C labelling of microbial PLFAs was closely linked to the amounts of maize carbon present in the soil. The distinct higher labelling of microbial PLFAs in the heavy metal-polluted soils 74 weeks after application indicated a large fraction of available maize straw carbon still present in the soil.     

Estimation of conversion factors for fungal biomass determination in compost using ergosterol and PLFA 18:2ω6,9

Eleven species of common fungi from compost were analysed for their content of ergosterol and phospholipid fatty acids (PLFAs) after growth on agar media. Mean content of ergosterol was 3.1 mg g⁻¹ dw of fungal mycelium (range 1-24 mg g⁻¹ dw). Total amount of PLFAs varied between 2.6 and 43.5 μmol g⁻¹ dw of fungi (mean 14.9 μmol g⁻¹ dw). The most common PLFAs were 16:0, 18:2ω6,9 and 18:1ω9, comprising between 79 and 97 mol% of the total amount of PLFAs. The PLFA 18:2ω6,9, suggested as a marker molecule for fungi, comprised between 36 and 61 mol% of the total PLFAs in the Ascomycetes, between 45 and 57 mol% in the Basidiomycetes and 12-22 mol% in the Zygomycetes. There was a good correlation between the content of the two fungal marker molecules, ergosterol and the PLFA 18:2ω6,9, with a mean content of 1 mg ergosterol being equivalent to 2.1 μmol of 18:2ω6,9. Based on results from the fungal isolates, conversion factors were calculated (5.4 mg ergosterol g⁻¹ biomass C and 11.8 μmol 18:2ω6,9 g⁻¹ biomass C) and applied to compost samples in which both the ergosterol and the PLFA 18:2ω6,9 content had been measured. This resulted in similar estimates of fungal biomass C using the two marker molecules, but was three to five times higher than total microbial biomass C calculated using ATP content in the compost. This could partly be explained by the fact that both of the markers used for fungal biomass are cell membrane constituents. Thus, the ergosterol and the PLFA content were related to the hyphal diameter of the fungi, where fungi with thinner hyphae had higher ergosterol concentrations than fungi with thicker hyphae. This could also partly explain the large interspecific variation in content of the two marker molecules.     

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.     

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.     

Distribution of microbial biomass and phospholipid fatty acids in Podzol profiles under coniferous forest

Microbial‐derived phospholipid fatty acids (PLFAs) can be used to characterize the microbial communities in soil without the need to isolate individual fungi and bacteria. They have been used to assess microbial communities of humus layers under coniferous forest, but nothing is known of their distribution in the deeper soil. To investigate the vertical distribution we sampled nine Podzol profiles on a 100‐m‐long transect in a coniferous forest and analysed for their microbial biomass and PLFA pattern to a depth of 0.4 m. The transect covered a fertility gradient from Vaccinium vitis‐idaea forest site type to Vaccinium myrtillus forest site type. The cores were divided into humus (O) and eluvial (E) layers and below that into 10‐cm sections and designated as either illuvial (B) or parent material (C), or as a combination (BC). Two measures of microbial biomass analyses were applied: substrate‐induced respiration (SIR) to determine microbial biomass C (C_mic), and the sum of the extracted microbial‐derived phospholipid fatty acids (totPLFA). The soil fertility had no effect on the results. The C_mic correlated well with totPLFA (r= 0.86). The microbial biomass decreased with increasing depth. In addition the PLFA pattern changed with increased depth as assessed with principal component analysis, indicating a change in the microbial community structure. The composition of the PLFAs in the O layer differed from that in the E layer and both differed from the upper part of the B layer and from the rest of the BC layers. The deeper parts of the B layer (BC₁, BC₂ and BC₃) were similar to one other. The O layer had more 18:2ω6, a PLFA indicator of fungi, whereas the E layer contained relatively more of the PLFAs 16:1ω9, 18:1ω7 and cy19:0 common in gram‐negative bacteria. With increased depth the relative amount of 10Me18:0, the PLFA indicator for actinomycetes, increased. We conclude that the PLFA method is a promising discriminator between the microbial community structures of the horizons in Podzols.     

Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils

Rhizodeposit-carbon provides a major energy source for microbial growth in the rhizosphere of grassland soils. However, little is known about the microbial communities that mediate the rhizosphere carbon dynamics, especially how their activity is influenced by changes in soil management. We combined a ¹³CO₂ pulse-labeling experiment with phospholipid fatty acid (PLFA) analysis in differently managed Belgian grasslands to identify the active rhizodeposit-C assimilating microbial communities in these grasslands and to evaluate their response to management practices. Experimental treatments consisted of three mineral N fertilization levels (0, 225 and 450 kg N ha⁻¹ y⁻¹) and two mowing frequencies (3 and 5 times y⁻¹). Phospholipid fatty acids were extracted from surface (0-5 cm) bulk (BU) and root-adhering (RA) soil samples prior to and 24 h after pulse-labeling and were analyzed by gas chromatography-combustion-isotope ratio mass spectrometry (GC-c-IRMS). Soil habitats significantly differed in microbial community structure (as revealed by multivariate analysis of mol% biomarker PLFAs) as well as in gram-positive bacterial rhizodeposit-C uptake (as revealed by greater ¹³C-PLFA enrichment following pulse-labeling in RA compared to BU soil in the 450N/5M treatment). Mowing frequency did not significantly alter the relative abundance (mol%) or activity (¹³C enrichment) of microbial communities. In the non-fertilized treatment, the greatest ¹³C enrichment was seen in all fungal biomarker PLFAs (C16:1ω5, C18:1ω9, C18:2ω6,9 and C18:3ω3,6,9), which demonstrates a prominent contribution of fungi in the processing of new photosynthate-C in non-fertilized grassland soils. In all treatments, the lowest ¹³C enrichment was found in gram-positive bacterial and actinomycetes biomarker PLFAs. Fungal biomarker PLFAs had significantly lower ¹³C enrichment in the fertilized compared to non-fertilized treatments in BU soil (C16:1ω5, C18:1ω9) as well as RA soil (all fungal biomarkers). While these observations clearly indicated a negative effect of N fertilization on fungal assimilation of plant-derived C, the effect of N fertilization on fungal abundance could only be detected for the arbuscular mycorrhizal fungal (AMF) PLFA (C16:1ω5). On the other hand, increases in the relative abundance of gram-positive bacterial PLFAs with N fertilization were found without concomitant increases in ¹³C enrichment following pulse-labeling. We conclude that in situ¹³C pulse-labeling of PLFAs is an effective tool to detect functional changes of those microbial communities that are dominantly involved in the immediate processing of new rhizosphere-C.     

Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

We combined microbial community phospholipid fatty acid (PLFA) analyses with an in situ stable isotope ¹³CO₂ labelling approach to identify microbial groups actively involved in assimilation of root-derived C in limed grassland soils. We hypothesized that the application of lime would stimulate more rapid ¹³C assimilation and turnover in microbial PLFAs. Four and 8 d after label application, 18:1ω9, 18:2ω6,9 (fungal biomarkers) and 16:1ω7, 18:1ω7, 19:0cy (Gram-negative bacterial biomarkers) showed the most ¹³C enrichment and rapid turnover rates. This suggests that these microorganisms were assimilating recently-photosynthesized root C inputs to soils. Contrary to our hypothesis, liming did not affect assimilation or turnover rates of ¹³C-labelled C. ¹³C stable isotope pulse-labelling technique paired with analyses of PLFA microbial biomarkers shows promise for in situ investigations of microbial function in soils.     

Linking Microbial Community Dynamics Associated with Rhizosphere Carbon Flow in a Biofuel Crop (Jatropha curcas L.)

Photosynthetically derived rhizodeposits are an important source of carbon (C) for microbes in root vicinity and can influence the microbial community dynamics. Pulse labeling of carbon dioxide (¹³CO₂) coupled with stable isotope probing techniques have potential to track recently fixed photosynthate into rhizosphere microbial taxa. Therefore, the present investigation assessed the microbial community change associated with the rhizosphere and bulk soil in Jatropha curcas L. (a biofuel crop) by combining phospholipid fatty acid (¹³C-PLFA) profiling using a stable isotope ¹³CO₂ labeling approach. The labeling (¹³C) took place after 45 days of germination, PLFAs were extracted from both soils (rhizosphere and bulk) after 1 and 20 days pulse labeling and analyzed by gas chromatography-isotope ratio mass spectrometry. There was no significant temporal effect on the PLFA profiles in the bulk soil, but significantly increased abundance of Gram positive (i15:0) and Gram negative (16:1ω7c and 16:1ω5c) biomarkers was observed in the rhizosphere soil from day 1 to day 20 after labeling. The Gram negative (16:1ω7c) decreased and fungal (18:2ω6,9c) increased significantly in rhizospheric soil compared to bulk soil after day 1 of labeling. Whereas, after 20 days of labeling, the Gram negative biomarker (16:1ω7c and 18:1ω7c) decreased and Gram positive (a15:0) increased significantly in rhizospheric soil compared to bulk soil. One day following labeling, i15:0, a15:0, i16:0, 16:1ω5c, 16:0, i17:0, a17:0, 18:2ω6,9c, 18:1ω9c, and 18:0 PLFAs were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. Twenty days after labeling, 16:1ω5c (Gram negative) and 18:2ω6,9c (fungal) were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. These results shows the effectives of PLFA coupled using the pulse chase labeling technique to examine the microbial community changes in response to recently fixed photosynthetic C flow in rhizodeposits.     

Effects of flue gas desulfurization gypsum by-products on microbial biomass and community structure in alkaline–saline soils

Purpose

For an alkaline?Csaline region in Northwest China, we examined the responses of soil microbial communities to flue gas desulfurization gypsum by-products (FGDB), a new ameliorant for alkaline?Csaline soils. In 2009 and 2010, we collected soils from 0?C20?cm and 20?C40?cm depths along an experimental FGDB gradient (0, 0.74, 1.49, 2.25, and 3.00?kg FGDB m^?2).

Materials and methods

As a measure of microbial community composition and biomass, we analyzed phospholipid fatty acids (PLFAs). We used real-time quantitative polymerase chain reaction (qPCR) to measure abundance of bacterial 16?S rRNA copy numbers. Additionally, physicochemical soil parameters were measured by common laboratory methods.

Results and discussion

Microbial community composition differed along the FGDB gradient; however, the microbial parameters did not follow a linear response. We found that, in 2009, total PLFA concentrations, and concentrations of total bacterial and Gram-negative bacterial PLFAs were slightly higher at intermediate FGDB concentrations. In 2010, total PLFA concentrations, and concentrations of total bacterial, Gram-positive bacterial, Gram-negative bacterial, and fungal PLFAs as well as the fungal:bacterial PLFA ratio were highest at 1.49?kg FGDB m^?2 and 3.00?kg FGDB m^?2. PLFA concentrations often differed between 2009 and 2010; however, the patterns varied across the gradient and across microbial groups. For both years, PLFA concentrations were generally higher at 0?C20?cm depth than at 20?C40?cm depth. Similar results were obtained for the 16?S rRNA copy numbers of bacteria at 0?C20?cm depth. FGDB addition resulted in an increase in soil Ca²⁺ and NO ₃ ^? ?CN and a decrease in pH and electrical conductivity (EC). Shifts in PLFA-based microbial community composition and biomass could partly be explained by pH, soil organic carbon, total nitrogen (TN), soil moisture, EC, inorganic nitrogen, C/N, and Ca²⁺. Indirect effects via shifts in abiotic soil properties, therefore, seem to be an important pathway through which FGDB affect soil microbial communities.

Conclusions

Our results demonstrate that addition of FGDB leads to significant changes in soil physicochemical and microbial parameters. As such, addition of FGDB can have large impacts on the functioning of soil ecosystems, such as carbon and nitrogen cycling processes.     

Incorporation of 13C-labelled rice rhizodeposition carbon into soil microbial communities under different water status

The overall processes by which carbon is fixed by plants in photosynthesis then released into the soil by rhizodeposition and subsequently utilized by soil micro-organisms, links the atmospheric and soil carbon pools. The objective of this study was to determine the plant derived ¹³C incorporated into the phospholipid fatty acid (PLFA) pattern in paddy soil, to test whether utilization of rice rhizodeposition carbon by soil micro-organisms is affected by soil water status. This is essential to understand the importance of flooded conditions in regulating soil microbial community structure and activity in wetland rice systems. Rice plants were grown in soil derived from a paddy system under controlled irrigation (CI), or with continuous waterlogging (CW). Most of the ¹³C-labelled rice rhizodeposition carbon was distributed into the PLFAs 16:0, 18:1ω7 and 18:1ω9 in both the CW and CI treatments. The bacterial PLFAs i15:0 and a15:0, both indicative of gram positive bacteria, were relatively more abundant in the treatments without rice plants. When rice plants were present rates of ¹³C-incorporation into i15:0 and a15:0 was slow; the microbes containing these PLFAs may derive most of their carbon from more recalcitrant C (soil organic matter). PLFAs, 18:1ω7 and 16:1ω7c, indicative of gram negative bacteria showed a greater amount incorporation of labelled plant derived carbon in the CW treatment. In contrast, 18:2ω6,9 indicative of fungi and 18:1ω9 indicative of aerobes but also potentially fungi and plant roots had greater incorporation in the CI treatment. The greater root mass concomitant with lower incorporation of ¹³C into the total PLFA pool in the CW treatment suggests that the microbial communities in wetland rice soil are limited by factors other than substrate availability in flooded conditions. In this study differing soil microbial communities were established through manipulating the water status of paddy soils. Steady state ¹³C labelling enabled us to determine that the microbial community utilizing plant derived carbon was also affected by water status.     

Soil organic carbon and microbial communities respond to vineyard management

The farming practices in vineyards vary widely, but how does this affect vineyard soils? The main objective of this study was to evaluate the effects of vineyard management practices on soil organic matter and the soil microbial community. To this end, we investigated three adjacent vineyards in the Traisen valley, Austria, of which the soils had developed on the same parent material and under identical environmental/site conditions but were managed differently (esp. tillage, fertilizer application, cover crops) for more than 10 yrs. We found that topsoil bulk density (BD) decreased with increasing tillage intensity, while subsoil BD showed the opposite trend. Soil organic carbon (SOC) stocks in 0–50 cm depth increased from 10 kg m^?2 in an unfertilized and frequently tilled vineyard to 17 kg m^?2 in a regularly fertilized but less intensively tilled vineyard. Topsoil microbial biomass per unit SOC, estimated by the sum of microbial phospholipid fatty acids (PLFAs), followed this trend, albeit not statistically significantly. Principal component analysis of PLFA patterns revealed that the microbial communities were compositionally distinct between different management practices. The fungal PLFA marker 18:2ω6,9 was highest in the vineyard with the lowest amount of extractable Cu (by 0.01 m CaCl₂), and the bacterial‐to‐fungal biomass ratio was positively correlated with extractable Cu. Our results indicate that tillage and fertilizer application of vineyards can strongly affect vineyard soil properties such as BD and SOC stocks and that the application of Cu‐based fungicides may impair soil fungal communities.     

Impact of cattle grazing and inorganic fertiliser additions to managed grasslands on the microbial community composition of soils

A study was undertaken to determine if cattle grazing on managed grasslands had an impact on the microbial community composition of soils. Microbial community molecular profiles of bacteria, actinomycetes, pseudomonads and fungi were generated by polymerase chain reaction (PCR) amplification of rDNA sequences from community DNA isolated from soils. PCR products were profiled using denaturing gradient gel electrophoresis (DGGE) and analysed by principal co-ordinate analysis. PCR–DGGE profiles indicated that cattle grazing had an impact on the pseudomonad community structure only, and that the addition of inorganic nitrogen (N) fertiliser impacted on bacterial, actinomycete and pseudomonad community structure. There was no difference in the community profiles of fungi from grazed and N fertilised grassland plots. Analysis of phospholipid fatty acid (PLFA) profiles revealed that both cattle grazing and N fertiliser impacted on microbial community structure. The abundance of individual PLFAs differed between treatments, with bacterial (15:0), actinomycete (10Me18:0) and fungal (18:2ω6) PLFAs not affected directly by grazing cattle and N fertiliser, however, there were significant grazing–fertiliser interactions. Bacterial plate counts were highest in the N fertilised plots and fungal plate counts were highest in the cattle grazed plots. Analysis of molecular microbial community profiles with PLFA and background soil data revealed several significant correlations. Notably, soil pH was positively correlated with PCO1 of the pseudomonad community profiles and negatively correlated with the fungal PLFA 18:2ω6. Fungal DGGE profiles were negatively correlated with the fungal PLFA 18:2ω6, and bacterial and fungal plate counts positively correlated with each other. Correlation analysis using PC1 from PLFA profile data showed no significant relationship with soil organic matter, pH, total C and total N. The results indicate that cattle grazing and N fertiliser addition to grasslands impact on the community composition of specific groups of micro-organisms. The consequences of such changes in population structure may have implications regarding the dynamics of nutrient turnover in soils.     

Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9

The phospholipid fatty acid biomarkers 18:1ω9, 18:2ω6,9 and 18:3ω3,6,9 are commonly used as fungal biomarkers in soils. They have, however, also been found to occur in plant tissues, such as roots. Thus, the use of these PLFAs as fungal biomarkers in sieved soil, which may still contain small remains of roots, has been questioned. We used data from a recent beech tree girdling experiment to calculate the contribution of roots to these biomarkers and were able to demonstrate that not more than 0.61% of 18:1ω9 and 18:2ω6,9 in sieved soil samples originated from roots (but 4% of 18:3ω3,6,9). Additionally, the abundance of the biomarker 18:2ω6,9 in the soil was found to be highly correlated to ectomycorrhizal root colonization, which further corroborates its fungal origin. PLFA biomarkers were substantially reduced in vital roots from girdled trees compared to roots of control trees (by up to 76%), indicating that the major part of PLFAs measured in roots may actually originate from ectomycorrhizal fungi growing inside the roots. We calculated, that even a near to 50% reduction in fine root biomass - as observed in the girdling treatment - accounted for only 0.8% of the measured decrease of 18:2ω6,9. Our results demonstrate that both 18:1ω9 and 18:2ω6,9 are suitable biomarkers for detecting fungal dynamics in soils and that especially 18:2ω6,9 is a reliable biomarker to study mycorrhizal dynamics in beech forests.     

Microbial community composition and activity in different Alpine vegetation zones

In alpine environments, climate change may alter vegetation composition as well as the quantity and quality of plant litter, which in turn may affect microbial community composition and functioning. In this study, we analyzed soil microbial community composition and its activity along a vegetation gradient (900-1900 m above sea level (a.s.l.)) in the Austrian Limestone Alps. Soil pH and C:N ratios were significantly different under different plant communities and ranged from 3.9 to 6.1 and from 29 to 17, respectively. The highest amounts of microbial biomass, estimated by the sum of microbial phospholipid fatty acids (total PLFAs), were found at sites with high pH and low C:N ratio, i.e. in alpine grassland and beech forest sites (3.9 ± 0.05 and 3.4 ± 0.7 μmol per g organic carbon (OC), respectively), and the lowest amounts were found at sites with low pH and high C:N ratio, i.e. sites with high percentage of conifers and acidophilic vegetation (around 2 μmol (g OC)⁻¹). Total and bacterial PLFAs as well as microbial activity (dimethyl sulphoxide reduction) did not show consistent altitudinal trends. The fungal PLFA 18:2ω6,9 was significantly higher in the forest sites (between 9.2 and 6.7 mol%) compared to the shrubland and grassland sites (between 4.5 and 2.3 mol%). A similar trend was found for ergosterol contents. As a consequence, the bacterial to fungal biomass ratio increased significantly from forest sites to shrubland and grassland sites. Expected future upward migration of the tree line in alpine environments in response to climate warming will therefore increase the abundance of fungi in these ecosystems.     

Effects of short-term conservation management practices on soil organic carbon fractions and microbial community composition under a rice-wheat rotation system

The objective of this study was to investigate the effects of short-term (less than 2 years) conservation managements [no-tillage (NT) and crop residue returning] on top soil (0–5 cm) microbial community composition and soil organic C (SOC) fractions under a rice-wheat rotation at Junchuan town of Hubei Province, China. Treatments were established following a split-plot design of a randomized complete block with tillage practices [conventional tillage (CT) and NT] as the main plot and residue returning level [no residue returning (0) and all residues returned to fields from the preceding crop (S, 2,146 kg C ha^?1)] as the subplots. The four treatments were CT with or without residue returning (CT0 and CTS) and NT with or without residue returning (NT0 and NTS). The abundances of microbial groups [total FLFAs, fungal biomass, bacterial biomass, fungal biomass/bacterial biomass (F/B), monounsaturated fatty acids/saturated fatty acids (MUFA/STFA), and microbial stress] were determined by phospholipid fatty acid (PLFA) analysis of soil. The ratio of MUFA/STFA reflects aeration of soil and greater MUFA/STFA means better aeration condition of soil. Moreover, the microbial stress, the ratio of cy19:0 to 18:1ω7, was regarded as an indicator of physiological or nutritional stress of microbial community. PLFA profiles were dominated by the fatty acids iC15:0 (9.8 %), C16:0 (16.5 %), 10Me17:0 (9.9 %), and Cyc19:0 (8.3 %), together accounting for 44.6 % of the total PLFAs. Compared with CT, NT significantly increased microbial biomass C (MBC) by 20.0 % but did not affect concentrations of total organic C (TOC), dissolved organic C (DOC), easily oxidizable C (EOC), and SOC of aggregates. Residue returning significantly increased MBC by 18.3 % and SOC content of 2–1-mm aggregate by 9.4 %. NT significantly increased total PLFAs by 9.8 % and fungal biomass by 40.8 % but decreased MUFA/STFA by 15.5 %. Residue returning significantly enhanced total PLFAs, bacterial biomass, fungal biomass, F/B, and MUFA/STFA by 31.1, 36.0, 95.9, 42.5, and 58.8 %, respectively, but decreased microbial stress by 45.9 %. Multivariate analysis (redundancy analysis and partial correlation analysis) indicated that SOC of 2–1-mm aggregate was related to changes in the composition of soil microbial groups, suggesting that SOC of 2–1-mm aggregate was sensitive to changes in soil microbial community composition affected by short-term conservation management practices in our study.     

Temperature and substrate controls on microbial phospholipid fatty acid composition during incubation of grassland soils contrasting in organic matter quality

Soil incubations are often used to investigate soil organic matter (SOM) decomposition and its response to increased temperature, but changes in the activity and community composition of the decomposers have rarely been included. As part of an integrated investigation into the responses of SOM components in laboratory incubations at elevated temperatures, fungal and bacterial phospholipid fatty acids (PLFAs) were measured in two grassland soils contrasting in SOM quality (i.e. SOM composition), and changes in the microbial biomass and community composition were monitored. Whilst easily-degradable SOM and necromass released from soil preparation may have fuelled microbial activity at the start of the incubation, the overall activity and biomass of soil microorganisms were relatively constant during the subsequent one-year soil incubation, as indicated by the abundance of soil PLFAs, microbial respiration rate (r), and metabolic quotient (qCO₂). PLFAs relating to fungi and Gram-negative bacteria declined relative to Gram-positive bacteria in soils incubated at higher temperatures, presumably due to their vulnerability to disturbance and substrate constraints induced by faster exhaustion of available nutrient sources at higher temperatures. A linear correlation was found between incubation temperatures and the microbial stress ratios of cyclopropane PLFA-to-monoenoic precursor (cy17:0/16:1ω7c and cy19:0/18:1ω7c) and monoenoic-to-saturated PLFAs (mono/sat), as a combined effect of temperature and temperature-induced substrate constraints. The microbial PLFA decay patterns and ratios suggest that SOM quality intimately controls microbial responses to global warming.     

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 flow from C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions

To better understand how residue quality and seasonal conditions influence the flow of C from both root and straw residues into the soil microbial community, we followed the incorporation of ¹³C-labeled crimson clover (Trifolium incarnatum) and ryegrass (Lolium multiflorum) root and straw residues into the phospholipid fatty acids (PLFA) of soil microbial biomass. After residue incorporation under field conditions in late summer (September), the ¹³C content of soil PLFA was measured in September, October, and November, 2002, and April and June, 2003. Multivariate non-metric multidimensional scaling techniques showed that the distribution of ¹³C among microbial PLFA differed among the four primary treatments (ryegrass straw and roots, clover straw and roots). Regardless of treatment, some PLFA remained poorly labeled with ¹³C throughout much of the study (16:1ω5, 10Me17:0; 0-5%), whereas other PLFA consistently contained a larger percentage of residue-derived C (16:0; 18:1ω9, 18:2ω6,9; 10-25%). The distribution of residue ¹³C among individual PLFA differed from the relative contributions of individual PLFA (mol%) to total PLFA-C, suggesting that a subset of the soil biomass was primarily responsible for assimilating residue-derived C. The distribution of ¹³C among soil PLFA differed between the sampling times, indicating that residue properties and soil conditions influenced which members of the community were assimilating residue-derived C. Our findings will provide the foundation for further studies to identify the nature of the community members responsible for residue decomposition at different times of the year, and what factors account for the dynamics of the community involved.     

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.