Changes in soil microbial properties and phospholipid fatty acid fractions after chloroform fumigation (original) (raw)
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FEMS Microbiology Ecology, 1991
A sensitive method for estimating living biomass, based on a direct extraction of phospholipids, was applied to soil. The variation between replicate soil samples was generally below 10%. Recovery from soil was qualitative. Estimates of biomass from the phospholipid assay were not correlated with estimates from the chloroform fumigation-incubation method (CFIM). In nonfumigated soil a significant reduction (25-57%) of biomass, as determined from phospholipid analysis, was observed during the 10-day incubation. The concentration of phospholipids was reduced by 21-54% during the 24-h chloroform fumigation, decreasing further during the 10-day incubation. Phospholipid, carbon dioxide evolution and inorganic nitrogen were followed in a growth experiment with additions of glucose and glucose +
Soil Biology and Biochemistry, 2004
Techniques developed to measure microbial biomass in mineral soils may not give reliable results in humus. We evaluated the relationships between three techniques to estimate microbial biomass in forest humus: chloroform fumigation-extraction (CFE), total extractable phospholipid fatty acids (PLFA), and extractable DNA. There was a good relationship between PLFA and CFE ðR 2 ¼ 0:96Þ; with a slope slightly different from that previously reported for mineral soils (1 nmol PLFA corresponded to a flush of 3.2 mg C released by fumigation in humus cf. 2.4 mg C in mineral soil). There was no relationship between DNA concentration and the other two measurements of microbial biomass. This may be due, in part, to the high fungal biomass in forest humus, as DNA concentration per unit biomass is much more variable for fungi than bacteria.
Soil Biology and Biochemistry, 1987
The chloroform fumigation-incubation method underestimates the amount of microbial biomass C in strongly acid soils @H < 4.5). Several explanations for the failure of the method were examined using IO forest soils that ranged in pH from 3.4 to 7.2. The hypothesis that chloroform might form compounds toxic to microbial recolonizers in strongly acid soils, but not in soils of higher pH, was tested using an alternative fumigant. carbon disulphide. CO& evolution was very similar with both fumigants and this explanation was rejected. Another possibility is that the proportion of microbial C evolved as CO& from the decomposition of microbial cells killed by fumigation (k,-) is tess in strongly acid soils than in soils of higher pH, so that low values for biomass wilt be obtained if the value of kc commonly used for near-neutral soils (0.45) is used on strongly acid soils. This was tested by measuring the "CO, evolved when "CT-labelled fungi and bacteria were added to the soils, which were then fumigated and incubated. The values of kc thus obtained were indeed less in strongly acid soils; the mean kc for soils below pH 4.5 was 0.30, compared to a mean of 0.46 in soils above pH 4.5.
Soil Biology and Biochemistry, 1992
The organic C (Ec), total N (EN), anthrone-, phenol-and orcinol-reactive C (ARC, PRC and ORC, respectively), ninhydrin-reactive N (NRN), FolinCiocalteu's reagent-reactive C and N compounds (FRC and FRN) and deoxyribose containing compounds (diphenylamine-reactive compounds, DRC) extracted by 0.5 M K,SO, before (non-fumigated extracts) and after (fumigated extracts) CHCI, fumigation were evaluated in 8 ;ery' different soils. Ali quantities were significantly linearly correlated between them and with total organic C (TOC) and total N (TN) as well. The frequency distribution of the significance levels passing from non-fumigated to fumigated extracts and y-values (fumigated minus non-fumigated values for the same class of compounds) showed a shift towards the highest significances; this may indirectlv confirm the action of chloroform in lvsina soil microbial cells. The significance levels (P) of TOC I correlated vs fumigated extracts were higher than vs non-fumigated extracts and y-values, thus indicating a release of non-biomass C organic compounds after CHCI, fumigation. Since TN vs fumigated extracts showed significance levels higher than non-fumigated extracts but equal to y-values, any release of non-biomass N probably did not occur. These considerations were confirmed by multiple regression analysis when Ec and E, (dependent variables) were reconstituted taking into account TOC and TN as additional independent variables, respectively. However, released non-biomass C organic compounds (likely sugars) compared to TOC were very low and could be considered to be negligible. A low release of ribose-containing compounds (ORC) occurred, thus indicating that the amount of RNA material released after CHCl, exposure was negligible. Deoxyribose-containing compounds rendered extractable after CHCl, fumigation were probably derived from bacterial plasmids rather than from bacterial and eukaryotic chromosomes. The possibility of characterizing soil microbial biomass C and N compounds by adopting suitable calorimetric methods, as demonstrated in this work, is a further advantage of the fumigation-extraction method when compared with the fumigation-incubation method.
Soil Biology and …, 2004
Phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME), both lipid-based approaches used to characterize microbial communities, were compared with respect to their reliable detection limits, extraction precision, and ability to differentiate agricultural soils. Two sets of soil samples, representing seven crop types from California's Central Valley, were extracted using PLFA and TSFAME procedures. PLFA analysis required 10 times more soil than TSFAME analysis to obtain a reliable microbial community fingerprint and total fatty acid content measurement. Although less soil initially was extracted with TSFAME, total fatty acid (FA) content g K1 soil (DW) was more than 7-fold higher in TSFAME-versus PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than PLFA analysis, with the coefficient of variation between replicates being as much as 4-fold higher with TSFAME extraction. There were significant differences between PLFA-and TSFAME-extracted samples when biomarker pool sizes (mol% values) for bacteria, actinomycetes, and fungi were compared. Correspondence analysis (CA) of PLFA and TSFAME samples indicated that extraction method had the greatest influence on sample FA composition. Soil type also influenced FA composition, with samples grouping by soil type with both extraction methods. However, separate CAs of PLFA-and TSFAME extracted samples depicted strong differences in underlying sample groupings. Recommendations for the selection of extraction method are presented and discussed. q
Using the chloroform fumigation-extraction (CFE) method for determining microbial biomass in soils, a presumption is followed, i.e., that chloroform becomes fully evacuated from the fumigated soil before extraction. Otherwise, the C-containing fumigant may comprise an unknown part of the extractable C flush, resulting in certain overestimation of soil microbial biomass. A quantitative assessment of extractable residual chloroform levels in fumigated soils was performed, testing soils varying in clay and organic matter contents. The tests were performed over a broad range of soil moisture conditions as to facilitate a mechanistic interpretation of possible chloroform interactions in the studied soils (i.e., dissolution, sorption). The results support the validity of the CFE method's application in agricultural soils, demonstrating the insignificance of biomass overestimation arising from residual chloroform.
Phospholipid fatty acids in soil—drawbacks and future prospects
Biology and Fertility of Soils, 2021
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 speci...
Geoderma, 2018
The chloroform fumigation-extraction method for determining soil microbial biomass is commonly applied at soil moisture (SM) levels of 40-50% water-holding capacity (WHC). Below that moisture range, restricted enzymatic autolysis might limit the fumigation flush of extractable cellular material, thus underestimating microbial biomass. Likewise, the upper range of SM (i.e., > 50% WHC) is considered problematic due to an alleged reduced fumigation efficiency when vapor diffusivity through soil is reduced. The current investigation demonstrated relatively constant fumigation flushes along a 40-90% WHC moisture gradient alongside unchanging carbon-to-nitrogen flush ratios corresponding to characteristic cellular values. This clearly refuted the proposed reduced fumigation efficiency under elevated moisture conditions, and thus validated the applicability of the method to samples collected moist.
Microbial ecology, 2011
Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on Electronic supplementary material The online version of this article (