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Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities
Abstract
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−1 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.
... Fatty acid methyl ester (FAME) analysis is potentially an alternative or complementary tool for the detection of organisms in soil. FAME analysis has been used extensively to characterize microbial community structure in soils and has also been applied as a diagnostic tool for the detection of specific organisms in environmental samples (Cavigelli, Robertson and Klug 1995;Drenovsky et al. 2004;Rastogi and Rajesh 2011;Yousef et al. 2012). In FAME analysis, total lipids are extracted from an organism or environmental sample, acyl chains are released as fatty acids and converted to their corresponding methyl esters with subsequent gas chromatography-mass spectrometry (GC-MS) analysis (Welch 1991;Drenovsky et al. 2004). ...
... FAME analysis has been used extensively to characterize microbial community structure in soils and has also been applied as a diagnostic tool for the detection of specific organisms in environmental samples (Cavigelli, Robertson and Klug 1995;Drenovsky et al. 2004;Rastogi and Rajesh 2011;Yousef et al. 2012). In FAME analysis, total lipids are extracted from an organism or environmental sample, acyl chains are released as fatty acids and converted to their corresponding methyl esters with subsequent gas chromatography-mass spectrometry (GC-MS) analysis (Welch 1991;Drenovsky et al. 2004). Organisms differ in the types and quantities of acyl chains that are components of their lipids (White et al. 2002;Ehrhardt et al. 2010). ...
... This suggests that a more detailed characterization of P. agathidicida FAMEs may provide sufficient information for distinguishing P. agathidicida from other Phytophthora species. Additionally, utilizing extraction techniques that target specific groups of lipids such as phospholipids or neutral lipids may help to further enrich target fatty acids such as 20:5ω3 and reduce background signals from complex environmental samples like soil (Drenovsky et al. 2004). These techniques and analyses could lead to a determination of the threshold of detection for Phytophthora in infected soil samples. ...
Phytophthora diseases cause devastation to crops and native ecosystems worldwide. In New Zealand, Phytophthora agathidicida is threatening the survival of kauri, an endemic, culturally and ecologically important tree species. The current method for detecting P. agathidicida is a soil bating assay that is time-consuming and requires high levels of expertise to assess, thus limiting the analytical sample throughput. Here, we characterized the fatty acid methyl ester (FAME) profile of P. agathidicida. We also compared it with the FAME profile of P. cinnamomi and assessed the efficacy of FAME analysis as a diagnostic tool for detecting the pathogen in soil samples. In FAME analysis, the total fatty acid content is isolated from a sample and converted to FAMEs for analysis, a process that takes less than a day. Unique fatty acid acyl chains can serve as biomarkers for specific organisms. We detected 12 fatty acids in P. agathidicida, two of which (20:4ω6 and 20:5ω3) show promise as potential Phytophthora specific biomarkers. Collectively, these findings advance our fundamental understanding of P. agathidicida biology and provide a promising technique to increase the rate of sample processing and the speed of pathogen detection for P. agathidicida in soil.
... Unlike total lipid analysis, PLFA analysis involves laborious fractionation steps and requires careful treatment of the highly unstable phospholipids [10]. However, it can provide direct information on the identity of membrane phospholipids, unlike total lipid analysis, which has difficulties in detecting some fatty acids that are sensitive to strong acid or high temperature [11,12]. ...
... As lipid analysis methods based on PLFA and total fatty acid analysis result in significant differences in the determination of fatty acid composition and extraction efficiency, and require different amounts of bacterial samples, since the two lipid analysis methods vary in derivatization procedures, especially in reaction temperature and pH [12], the two applied analytical methods showed totally different data. Total fatty acid extraction allowed highly sensitive detection of lipids from a small amount of samples, and could provide clear signal with relatively easy fatty acid methyl ester (FAME) derivatization, although it required high temperatures and an acidic pH for derivatization [11]. Unlike the total fatty acid extraction method, PLFA analysis has been widely used to discover and analyze biomarkers showing the composition of microbial communities in microbial and soil sciences [27]. ...
... In fact, harsh reaction conditions, such as the high temperatures and acidic pH applied in total fatty acid analysis, lead to degradation of some fatty acids, such as CFAs, via cleavage of the cyclopropane ring by the acidic methanol used in the procedure [42]. Therefore, we applied PLFA analysis as a key tool to highlight the major bacterial markers showing important changes during shifts in temperature [11]. PLFA analysis revealed that the isolated strain produced more UFAs, such as C16:1ω9c, C16:1ω9t, and C18:1ω9t (palmitoleic acid, trans-palmitoleic acid, and elaidic acid), at 10 °C than at 25 °C (Fig. 3a). ...
Psychrophilic bacteria, living at low and mild temperatures, can contribute significantly to our understanding of microbial responses to temperature, markedly occurring in the bacterial membrane. Here, a newly isolated strain, Pseudomonas sp. B14-6, was found to dynamically change its unsaturated fatty acid and cyclic fatty acid content depending on temperature which was revealed by phospholipid fatty acid (PLFA) analysis. Genome sequencing yielded the sequences of the genes Δ-9-fatty acid desaturase (desA) and cyclopropane-fatty acid-acyl-phospholipid synthase (cfa). Overexpression of desA in Escherichia coli led to an increase in the levels of unsaturated fatty acids, resulting in decreased membrane hydrophobicity and increased fluidity. Cfa proteins from different species were all found to promote bacterial growth, despite their sequence diversity. In conclusion, PLFA analysis and genome sequencing unraveled the temperature-related behavior of Pseudomonas sp. B14-6 and the functions of two membrane-related enzymes. Our results shed new light on temperature-dependent microbial behaviors and might allow to predict the consequences of global warming on microbial communities.
... Analysis and quantification of soil lipids has seen increased use in ecosystem studies as a means to address these needs (Ben-David et al., 2011;Frostegård et al., 2011;Fichtner et al., 2014;Willers et al., 2015a;Willers et al., 2015b). Because the abundance of individual fatty acids varies among organisms in soil, fatty acid profiles provide a rough community 'fingerprint' and can also be used to determine the presence and relative abundance of coarse ecological groupings (such as Gram -, Gram + , actinobacteria, and fungi) in soil communities (Frostegård and Bååth, 1996;Drenovsky et al., 2004;Balser and Firestone, 2005). Additionally, because membrane lipids turn over rapidly during metabolism and are quickly degraded following cell death, the concentration of lipids in soil is proportional to viable biomass (Vestal and White, 1989;Frostegård and Bååth, 1996). ...
... An alternate method, the fatty acid methyl-ester (FAME) procedure was introduced by Microbial ID, Inc. (Newark, CA) in 1990. With FAME analysis, all ester-linked lipids are extracted directly from samples (Haack et al., 1994;Schutter and Dick, 2000;Drenovsky et al., 2004). Because it has none of the concentration or purification steps that PLFA has, the FAME method has lower overall lipid loss, and is rapidallowing well over 100 samples to be processed in the time it takes to process 30-40 samples via PLFA. ...
... In addition, the greater throughput allowed by the FAME has potential to allow processing of sample numbers equivalent to most large-scale ecosystem studies. However, because the potential coextraction of soil organic matter, and thus subsequent profile distortion is a serious concern, researchers have continued to utilize PLFA despite its longer processing time and added complexity (Nielsen and Petersen, 2000;Bailey et al., 2002;Drenovsky et al., 2004;Balser and Firestone, 2005;Liang et al., 2008;Balser and Wixon, 2009;Herman et al., 2012;Schmidt et al., 2015;Kotas et al., 2018). ...
During the past two decades interest in linking soil microbial community composition and activity with ecosystem scale field studies of nutrient cycling or plant community response to disturbances has grown. Despite its importance there are challenges in making this linkage. Foremost is the question of analytical feasibility. In general, microbiological community-level methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. Soil lipid analysis shows potential as a middle ground between simple biomass measures and molecular profiling. However, the two protocols that have most often been followed are either rapid but indiscriminate (total lipid analysis or fatty acid methyl ester analysis; FAME), or precise but time consuming (phospholipid fatty acid analysis; PLFA). In this paper we report results from a standardized soil used test a modified extraction method (the ‘hybrid’ method) developed to balance the speed of FAME and the precision of PLFA in order to increase sample throughput. In comparing the three methods, we find that FAME and PLFA are qualitatively and quantitatively distinct. The FAME method yielded the highest fatty acid abundance, but also had high variance resulting in low precision. The PLFA method had precision, but low yield. The ‘hybrid’ method fell midway between FAME and PLFA for quantitative fatty acid yield. In addition, the hybrid extraction can be completed in a fraction of the time it takes for PLFA. The hybrid protocol appears to provide an optimal balance between effort and accuracy and therefore is a good choice for large-scale ecosystem studies.
... The alteration of the microbial community structure can significantly impact crop productivity and soil health and quality [25,26], and there are several ways to quantify this structure in agricultural soil [27]. To gain insights into the variations in the microbial composition in arable soils, the phospholipid fatty acid (PLFA) analysis technique is widely applied [28] since different organisms contain various PLFA functional groups (i.e., fungi, Gram-positive (G + ) and Gram-negative (G − ) bacteria, actinomycetes, and eukaryotes) [29,30]. Thus, interpreting variations in PLFAs delivers a quantitative picture of microbial composition, which can vary with different fertilization practices, soil types, and climate origins [31,32]. ...
It is crucial to comprehend how fertilization and cultivation management alter the composition of dissolved organic carbon (DOC) and microbial communities to regulate the biogeochemical cycling of soil nutrients and mitigate adverse impacts on soil-water quality. Based on 15 years of long-term field trials conducted in purple soil on farmland with a slope of 15° in southwestern China, the following five treatments were examined: CK (no fertilizer was applied), T1 (NPK plus organic manure and downslope cultivation), T2 (NPK and downslope cultivation), T3 (1.5-fold NPK and downslope cultivation), and T4 (NPK and contour cultivation). Soil samples were obtained from summer maize at two soil depths (0-10 and 10-20 cm) and from rhizospheric soil, and the changes in the DOC content, UV-visible (UV-Vis) absorptivity, and phospholipid fatty acids (PLFAs) were assessed. Our results revealed a significant change in the DOC content following fertilization, especially in T1, as it was 136.0%, 179.4%, and 132.2% higher, respectively, than that in CK at the 0-10 and 10-20 cm depths and rhizospheric soil. Fertilization decreased the UV-Vis absorptivity variables of DOC (i.e., SUVA 254, SUVA 260, SUVA 400, SUVA 465, SUVA 665, and C:C ratio) and raised the E4:E6 ratio (fulvic acid to humic acid in DOC), regardless of T2 and T3 at the 10-20 cm depth and in the rhizospheric soil compared with those in CK, respectively. Fertilization significantly increased the total PLFA content and selected microbial groups relative to CK. Among the treatments, T1 significantly increased the total PLFA content by 50.6%, 59.0%, and 46.2%, respectively, relative to CK, at the 0-10 and 10-20 cm depths and in the rhizospheric soil. The microbial community structure in contour cultivation (T4) was significantly greater than in downslope cultivation (T2). Random forest analysis (RFA) revealed that SOC and DOC were likely the primary variables for regulating the total PLFAs in the examined soil. Partial least squares path modeling (PLS-PM) further indicated that the DOC content and the ratio of E4:E6 among DOC compositions had greater effects on the soil microbial community structure in the examined soil. These observations suggested that long-term fertilization and cultivation management are effective approaches to regulating the soil microbial community structure by altering the composition of DOC in sloping farmland.
... The detection of phospholipid fatty acids was accomplished following methyl esterification in KOH-methanol solution, as described [25], with inclusion of nineteen-alkanoic acids (19:0) as an internal standard. Detection was performed by gas chromatography (Agilent 6850), and from the phospholipid fatty acid compositions, microbes were identified using the Sherlock Microbial Identification System (v4, Element). ...
Fire is a crucial disturbance factor for the structure and function of forest ecosystems, as it directly or indirectly affects plant growth, animal life and soil biogeochemical properties. Here, the effects of different fire severities and key driving environmental factors on soil microbial diversity and biomass were investigated in taiga forests that had undergone light, moderate or heavy fires, more recently or in the past, with unburned taiga forest included as a control (CK). The sample sites were located in the Greater Khingan mountains in the northeast of China. Critical soil parameters were determined, and bacterial and fungal content was inferred from determined phospholipid fatty acids (TPLFAs). The results showed that (1) all three fire severities significantly increased the concentrations of soil microbial carbon (MBC), moisture content (MC) and total nitrogen content (TN), but they significantly decreased soil available potassium (AK) content compared with the CK. (2) Recent light and moderate fires significantly decreased the Simpson and Shannon indices of soil microbial communities compared to CK; moderate fire did not change the Menhinick and Margalef indices. (3) Following moderate fire disturbance, there were no significant differences (p > 0.05) in relative abundance of total soil bacteria (Ba), Gram-positive bacteria (G+), Gram-negative bacteria (G−) and content of TPLFAs compared to the control, either as a result of more recent fires or earlier fires. (4) Redundancy analysis revealed that soil MC, TN, soil organic carbon (SOC), available P (AP) and alkaline N (AN) all strongly significantly affected the composition of the microbial communities, with a total explanation of 85.16% of the data. The species diversity and biomass of Ba, G+, G− and TPLFAs were in accordance with the intermediate disturbance hypothesis. The change pattern of soil fungi was in accordance with their own characteristics of reproduction and growth, which was in line with k-selection and ecological countermeasures.
... PLFA 18:2ω6,9 represent fungi, 18:1ω9 represent G − bacteria, whereas higher polyunsaturated PLFAs represent eukaryotes. Saturated straight chain fatty acids were considered as nonspecific PLFAs (Drenovsky et al., 2004;Frostegård et al., 2011;Frostegård and Bååth, 1996;Kaiser et al., 2010). ...
Phosphorus (P) is a major limiting nutrient for plant growth implying an often-intensive competition between microorganisms and plants in the rhizosphere. Increasing the P availability in subsoils may help to mitigate potential future P fertilizer shortages and to overcome P limitations due to droughts, which mainly affect topsoils. Root exudates provide easily available carbon and energy sources for microorganisms to mobilize soil nutrients. Nonetheless, details regarding the distinct processes underlying P mobilization from various P sources (free vs. sorbed PO43−; low molecular vs. complex organic P, e.g. ATP vs. plant litter P) as affected by root exudates are poorly understood, especially in subsoils. This study aimed to identify the controlling factors and microbial processes regulating the availability of organic and inorganic P in top- and subsoils by 33P isotopic labeling. The focus was on the potential key role of root exudates in P mobilization. We found that microbial communities in top- and subsoils used high- and low-available mineral P to a similar extent, but that the subsoil communities were much more efficient in mobilizing and incorporating complex litter-derived organic P. This capability of subsoil communities was even enhanced when root exudates were present. Microbial activity and nutrient-mobilizing mechanisms (e.g., P-related enzymes) clearly increased by root exudate addition, an effect that was generally higher in sub-than in topsoils. We conclude that subsoil communities are well capable of mobilizing and using complex organic P sources, especially if root exudates accelerate overall activity and P cycling. Thus, high root exudation is highly relevant for crops, which depend on subsoil nutrients and litter-derived P. Accordingly, detritusphere P, e.g. in subsoil root channels, is likely to be plant-available because of exudate-induced microbial P (re-)cycling processes.
... The phospholipid fatty acids (PLFA) approach was used to evaluate the composition of microbial communities in the soil (Drenovsky et al., 2004). Briefly, chloroform-methanol-citrated buffer (0.05 M) was adoprted for extracting the total fatty acids (TFAs) from the freeze-dried soils (8.0 g). ...
Sequestration of soil organic carbon (SOC) is an effective means to draw atmospheric CO2. Grassland restoration is one of the fastest methods to increase soil C stocks, and particulate-associated C and mineral-associated C play critical roles in soil C stocks during restoration. Herein, we developed a conceptual mechanistic frame regarding the contributions made by mineral-associated organic matter to soil C during the restoration of temperate grasslands. Compared to 1-year grassland restoration, 30-year restoration increased mineral-associated organic C (MAOC) by 41% and particulate organic C (POC) by 47%. The SOC changed from microbial MAOC predominance to plant-derived POC predominance, as the POC was more sensitive to grassland restoration. The POC increased with plant biomass (mainly litter and root biomass), while the increase in MAOC was mainly caused by the combined effects of increasing microbial necromass and leaching of the base cations (Ca-bound C). Plant biomass accounted for 75% of the increase in POC, whereas bacterial and fungal necromass contributed to 58% of the variance in MAOC. POC and MAOC contributed to 54% and 46% of the increase in SOC, respectively. Consequently, the accumulation of the fast (POC) and slow (MAOC) pools of organic matter are important for the sequestration of SOC during grassland restoration. Overall, simultaneous tracing of POC and MAOC helps further understand the mechanisms and predict soil C dynamics combined with the input of plant C, microbial properties, and availability of soil nutrients during grassland restoration.
... As a major component of the microbial cellular membrane, phospholipid fatty acids (PLFAs) can be analyzed to determine the microbial community composition and monitor dynamic changes in membrane properties [19,20]. Unlike total lipid analysis, PLFA analysis involves laborious fractionation steps and requires careful treatment of the highly unstable phospholipids [19,21,22]. However, PLFA analysis provides more sensitive and direct information on the identity of the membrane phospholipids, as total lipid analysis was known to make identification of some fatty acids difficult [23,24]. ...
NdgR, a global regulator in soil-dwelling and antibiotic-producing Streptomyces, is known to
regulate branched-chain amino acid metabolism by binding to the upstream region of synthetic
genes. However, its numerous and complex roles are not yet fully understood. To more fully reveal
the function of NdgR, phospholipid fatty acid (PLFA) analysis with gas chromatography-mass
spectrometry (GC-MS) was used to assess the effects of an ndgR deletion mutant of Streptomyces
coelicolor. The deletion of ndgR was found to decrease the levels of isoleucine- and leucine-related
fatty acids but increase those of valine-related fatty acids. Furthermore, the defects in leucine and
isoleucine metabolism caused by the deletion impaired the growth of Streptomyces at low
temperatures. Supplementation of leucine and isoleucine, however, could complement this defect
under cold shock condition. NdgR was thus shown to be involved in the control of branched-chain
amino acids and consequently affected the membrane fatty acid composition in Streptomyces. While
isoleucine and valine could be synthesized by the same enzymes (IlvB/N, IlvC, IlvD, and IlvE), ndgR
deletion did not affect them in the same way. This suggests that NdgR is involved in the upper
isoleucine and valine pathways, or that its control over them differs in some respect.
... 60 No evidence of Cu reduction was observed when evaluating spectral quality from each (Table S2) . [64][65][66][67][68][69] Statistical Methods: Data were tested for assumptions of analysis of variance using the Shapiro-Wilk test for normality of residuals and Levene's test for homogeneity of variance. Data that did not meet these criteria were log transformed to meet the assumptions of ANOVA prior to final analysis. ...
Copper (Cu) products, including copper oxide nanoparticles (nCuO), are critically important agricultural fungicides and algaecides. Foliar application onto crops and subsequent aerosol drift of these Cu products, especially nCuO, on...
... The advantages of this method include the high separation capacity of fatty acids, good reproducibility, high sensitivity and low matrix effect (Ciucanu et al., 2020). However, this method is time-consuming and consumes homogenous acid/alkaline catalysts which are environmentally unfriendly (Drenovsky et al., 2004). Buyer et al. reported a high throughput PLFA analysis of soils developed to reduce volumes of solvents and labor intensity (Buyer and Sasser, 2012), whereas this method still requires complex acid/alkaline transesterification and multiple liquid-liquid extraction (LLE) and have lower water tolerance. ...
Phospholipid fatty acids (PLFAs) are widely used to assess soil microbial community and metabolic activity in various environmental samples. However, the transesterification of phospholipids into PLFAs still utilize homogeneous acid/alkaline catalyst, which may increase environment risk. This study developed and validated an accurate method for the determination of PLFAs in soil utilizing pyrolysis-assisted transesterification with diatomaceous earth. The thermolysis behavior of phospholipids, optimal pyrolysis conditions, tolerance against impurities, and recyclability of porous material were evaluated. Under optimal conditions, the transesterification can complete in only 8 min, with high impurity tolerance. The repeatability (relative standard deviation (RSD) between 2.59% and 12.12%), reproducibility (RSD between 5.22% and 16.22%), and linearity (r between 0.9259 and 0.9999) were excellent. This method was applied to analyze the PLFAs to evaluate microbial community of 1000-years paddy soil chronosequences and the relationships among soil chemical properties, enzyme activities and microbial community composition. Soil microbial biomass PLFAs increased significantly over time followed by slight fluctuation at 60–1000 years, but the ratios of soil fungal to bacterial and gram-positive to gram-negative PLFAs remained constant. In addition to soil total N and organic matter, soil enzyme activities related to N cycling metabolism also positively significantly influenced microbial communities. Overall, the developed PLFAs method using pyrolysis-assisted transesterification was environmentally friendly, efficient, accurate, stable, and suitable alternative to acid/alkaline transesterification of phospholipids.
... Site-level coefficient of variation (CV) averaged across absolute abundances of 43 fatty acids ranged between 5.0% and 14.1% for PLFA and between 5.2% and 15.6% for ELFA, respectively (Table 1). Drenovsky et al. [20] reported a similar precision of the PLFA method, with mean CV ranging from 4.8% to 17.9%. However, they found a much higher CV (18.1%-66.4%) ...
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.
... Various techniques have been used to investigate both endophytic and rhizospheric olive microbiota, including media culture, fatty acid methyl ester (FAME) or phospholipid fatty acid analysis (PLFA) 5 , denaturing gradient gel electrophoresis (DGGE) 6 , fluorescent terminal restriction fragment length polymorphism (FT-RFLP) 2 , and high-throughput sequencing 7 . ...
Rhizospheric soils from cultivated olive (Olea europaea) trees of Chemlali, Chetoui, Quaissi, and Djalat cultivars were assessed for their bacterial abundance and diversity and were further screened for production of exopolysaccharides and exoenzymes (cellulase, chitinase, amylase, protease, lipase, and peroxidase). The results of the present study indicate that Chetoui cultivar revealed higher diversity, followed by Chemlali > Quaissi > Djalat, wherein, bacilli, enteric bacteria, and pseudomonads were abundantly present as specific bacterial groups associated with the Chetoui rhizosphere. Moreover, the exopolysaccharide (EPS)-producing bacteria of Chetoui cultivar (68.4%) presented the highest efficiency, followed by Djalat (23.5%) > Chemlali (7 %) > Quaissi (1%). These results revealed that the Chetoui cultivar presented highest enzyme activities, followed by Chemlali > Djalat > Quaissi, with a distinct abundance of peroxidase- and chitinase-producing bacteria, which may play a pivotal role in adapting olives to the environmental stresses. From this preliminary study, we confirmed that olive rhizosphere microbial diversity is essentially driven by the geographical origin and genotype of olive cultivars. Furthermore, we recommended the Chetoui olive cultivar rhizosphere as a potential reservoir for exoenzyme- and EPS-producing bacteria useful for future biotechnological applications.
... Об актуальности проблемы поддержания равновесия биологической составляющей почвы в условиях интенсивной системы землепользования свидетельствуют отечественные и зарубежные литературные источники, рассматривающие микробиологические аспекты сохранения экологобиологического состояния различных типов почв и методы исследования биологических процессов, в том числе в условиях монокультуры [7][8][9][10][11][12][13][14][15][16]. ...
... The approximately 2-fold greater fatty acid abundance (nmol g −1 ) from EL-FAME than from PLFA was similar to results reported by other method comparisons (Drenovsky, Elliott, Graham, & Scow, 2004;Miura et al., 2017). The greater abundance with EL-FAME compared to PLFA is expected since the EL-FAME method extracts all of the lipid groups (i.e., phospholipid, glycolipid, and neutral lipid fatty acids) whereas the PLFA method used here, isolates and analyzes only the phospholipid fraction (Sharma & Buyer, 2015). ...
Fatty acid methyl ester (FAME) profiling for characterizing microbial community composition typically is conducted via phospholipid fatty acid (PLFA) or ester‐linked fatty acid methyl ester (EL‐FAME) methods. As soil health assessments aim to be utilized across the nation and globe, the robust measurement and interpretation of microbial communities across a range of soils and environments will be necessary. This study compared PLFA and EL‐FAME methods for detecting and interpreting profiles of microbial community composition in croplands across a wide geographic area using a total of 172 soil samples from 14 states representing a wide range of soil properties. Overall, PLFA and EL‐FAME provided comparable biomarkers in terms of microbial community composition. The Spearman's Rank correlation test showed positive correlations (r = 0.37–0.71) between PLFA and EL‐FAME methods for absolute abundance of total FAME and individual microbial groups including fungi (saprophytic fungi [SF], arbuscular mycorrhizal fungi [AMF], and general fungi [F]) and all bacterial groups (Gram positive [GMP], Gram negative [GMN], and Actinobacteria). In both methods, a common set of fatty acids were influential in differentiating samples. The main differences in biomarker abundances between the two methods were that fungal and Actinobacteria biomarkers (e.g., 16:1ω5c [AMF], 18:1ω9c [F], 18:3ω6c [F], and 10Me16:0 [Actinobacteria]) were more abundant or critical in EL‐FAME profiling (large variation among soil samples and sensitive to soil properties), but bacterial biomarkers such as i15:0 (GMP), 16:1ω7c (GMN), 18:1ω7c (GMN), and cy19:0ω7c (GMN) were more dominant and responsive to soil properties in PLFA profiling. The practical advantages of EL‐FAME are lower cost and simpler methodology. Although both methods produced similar microbial profile abundances for important microbial markers, PLFA was more sensitive to the wide range of soil chemical properties in this sample set including pH, clay content, soil organic matter, and active carbon.
... PLFAs are used to assess the amount of living microbial biomass in situ (Zelles, 1999;Kaur et al., 2005). The tFAs, which include the PLFAs and the FAs in the non-living OM (FAs OM ) are indicating the stabilization of FAs in the OM (Drenovsky et al., 2004;Nowak et al., 2011). The PLFAs and FAs OM thus provide information about presence of living and nonliving groups of microorganisms in situ, respectively (Zelles, 1999;Kaur et al., 2005). ...
Amendment of soils with plant residues is common practice for improving soil quality. In addition to stimulated microbial activity, the supply of fresh soluble organic (C) from litter may accelerate the microbial degradation of chemicals in soils. Therefore, the aim of this study was to test whether the maize litter enhances degradation of 4-chloro-2-methylphenoxyacetic acid (MCPA) and increases formation of non-toxic biogenic non-extractable residues (bioNERs). Soil was amended with 13C6-MCPA and incubated with or without litter addition on the top. Three soil layers were sampled with increasing distance from the top: 0–2 mm, 2–5 mm and 5–20 mm; and the mass balance of 13C6-MCPA transformation determined.Maize litter promoted microbial activity, mineralization of 13C6-MCPA and bioNER formation in the upper two layers (0–2 and 2–5 mm). The mineralization of 13C6-MCPA in soil with litter increased to 27% compared to only 6% in the control. Accordingly, maize addition reduced the amount of extractable residual MCPA in soil from 77% (control) to 35% of initially applied 13C6-MCPA. While non-extractable residues (NERs) were
... De nombreux paramètres biotiques et abiotiques, dépendants des contraintes naturelles et des modes d'usage des sols, peuvent intervenir pour modeler la structure des communautés microbiennes dans les sols dans leur diversité et leur abondance (Meyer et al., 2013;Tian et al., 2017). En effet, les paramètres pédoclimatiques telles que les variations climatiques (Lauber et al., 2013), la teneur en eau (Drenovsky et al., 2004), les teneurs en carbone organique et en azote (Fierer et al., 2007;Asuming-Brempong et al., 2008) peuvent affecter l'abondance et la diversité microbienne (Thomson et al., 2015). ...
La gestion des déchets constitue un problème majeur au niveau mondial. En agriculture, le retour au sol des résidus de culture est une pratique courante et constitue une opportunité intéressante pour maintenir la fertilité du sol et/ou pour stocker du carbone. La décomposition des matières végétales dans le sol est influencée par plusieurs facteurs (tels que la composition microbienne, la nature et qualité des matières végétales), et a pour acteurs principaux les microorganismes telluriques. Au-delà du retour au sol, d’autres voies de valorisation de la matière végétale non récoltée peuvent être envisagées, telle que sa transformation pour des usages non alimentaires. Dans le domaine du bâtiment, l’intérêt de l’utilisation de matériaux biosourcés (destinés à l’isolation thermique) est croissant et encouragé par les pouvoirs publics dans la construction ou la rénovation. Toutefois, à notre connaissance, la question de la gestion de la fin de vie de ces matériaux après déconstruction des bâtiments n’est pas encore abordée. Afin de mieux comprendre le retour aux sols agricoles de matières végétales de natures diversifiées (paille de blé, paille de colza et tiges de tournesol), nous avons combiné différentes caractérisations biochimiques/physicochimiques tels que le fractionnement biochimique, l’analyse thermogravimétrique et la spectroscopie infra rouge, avec l’étude de la dynamique microbienne (abondance, diversité, fonction), complétées du suivi de minéralisation du carbone et de l’azote durant 3 mois d’incubation, en microcosmes. La minéralisation des résidus de grandes cultures est principalement régie par des microbiodiversités initialement différentes, issues de la prairie permanente ou la grande culture, et dans une moindre mesure par leur qualité biochimique. Quant à la dynamique microbienne, elle est impactée par ces deux types de sols et la nature de apports. Dans le cas de coproduits contrastés de la tige de tournesol (moelle et écorce), la minéralisation du C est principalement dictée par leur qualité initiale. Concernant la mise en oeuvre d’un matériau biosourcé à base de moelle de tige de tournesol, elle semble favoriser sa minéralisation dans le sol. Le retour au sol de ce type de matériau pourrait donc constituer un moyen intéressant de gestion de sa fin de vie.
... Other studies have indicated that long-term chemical fertilization increases microbial biomass without changing microbial community structure (Zhang et al. 2012;Su et al. 2015). Overall, earlier studies mainly focused on the change of microbial biomass, richness, and diversity on the community level via phospholipid fatty acid analysis (Drenovsky et al. 2004;Williams et al. 2006), and more recently, using next-generation sequencing approach (Sugiyama et al. 2010;Chaudhry et al. 2012;Taberlet et al. 2012;Wilhelm et al. 2018). However, bacterial social interactions, particularly under different fertilizer amendments in terrestrial agro-ecosystems, are less studied. ...
Purpose
Bacterial cooperation and competition in biofilms are being recognized as important factors in regulating structure and function of microbial communities. However, knowledge about soil bacterial interactions in biofilms and how these may be influenced by different fertilization practices is still limited. This study aims to investigate interspecific interactions in biofilms and the effects of fertilization practices on these interactions.
Materials and methods
We assessed bacterial interactions according to a classification criterion proposed recently via comparing biomass of single-species biofilms with dual-species biofilms. Biofilm biomass was measured by crystal violet staining using the modified Calgary biofilm device.
Results and discussion
Increased biofilm formation was detected in 67% of co-cultures that were composed of strains isolated from unfertilized soil, indicating a high prevalence of cooperation among the strains in natural soil. In contrast, decreased biofilm formation was detected in 74% of co-cultures that contained strains isolated from soil receiving chemical fertilizer. Interestingly, combinations of bacterial isolates from soils amended with chemical fertilizer in combination with composted chicken manure or mushroom residues showed higher level of synergism and biofilm induction in dual-species biofilms than the strains from chemically fertilized soils, suggesting integrated fertilization with composted chicken manure or mushroom residues may help maintain the native microbial interaction network dominated by synergistic interactions.
Conclusions
Together, these findings indicate that social interactions, required for biofilm formation, among soil bacteria are affected by fertilization practices. Cooperation is dominant in dual-species biofilms in unfertilized soil. Organic manure could mitigate the negative impacts on bacterial social interactions caused by chemical fertilizers.
... Au sein des acides gras identifiables dans la MOD des solutions de sol, les acides gras phospholipidiques (PLFA) sont des biomarqueurs moléculaires spécifiques de l'activité des microorganismes des sols tels que les bactéries et les champignons (Bossio et Scow, 1998;Zelles et al., 1992). Certains de ces acides gras étant spécifiques de certaines espèces ou grands groupes de bactéries, leur distribution sont couramment utilisées dans le but de distinguer des changements de composition de communautés bactériennes (Drenovsky et al., 2004). ...
Les matières organiques dissoutes (MOD), en tant que sources de nutriments ou potentiels vecteurs de pollution, sont impliquées dans de nombreuses problématiques environnementales. Bien qu'elles fassent l'objet de nombreuses études depuis plusieurs décennies, les mécanismes gouvernant leur solubilisation et leur transfert depuis les sols vers les systèmes aquatiques demeurent sujets à discussion. En s'appuyant sur l'étude de la composition moléculaire des MOD par hydrolyse et méthylation assistée par température et couplée à la chromatographie en phase gazeuse et à la spectrométrie de masse (HMT-CPG-SM), cette thèse a pour objectif d'apporter une meilleure compréhension de leurs mécanismes de solubilisation et de transfert à l'échelle d'un bassin versant agricole. Ce travail s'est appuyé sur le bassin versant expérimental de Kervidy-Naizin (Morbihan, Observatoire de Recherche en Environnement AgrHys) afin d'observer les processus mis en jeux à deux échelles temporelles différentes. A l'échelle de la crue, ce travail a permis de préciser l'impact des conditions hydrologiques spécifiques sur la dynamique des MOD. A l'échelle annuelle, l'utilisation conjointe de la signature isotopique du carbone (δ13C) et de la composition moléculaire des MOD a permis de préciser les mécanismes de transfert de MOD impliqués à l'échelle du versant. L'utilisation de la HMT-CPG-SM s'est avéré un outil adéquat pour l'étude de la dynamique des MOD. L'ensemble des résultats ainsi obtenus ont permis de souligner l'importance des conditions hydrologiques et en particulier de la dynamique de nappe dans les processus de solubilisation et de transfert des MOD
... PLFAT, FPLFA and BPLFA can be viewed as indicators of total microbial biomass, fungal biomass, and bacterial biomass, respectively. Soil PLFAs analysis is a widely accepted method based on the rapid degradation of PLFAs after cell death [71]. ...
Biochar application to the soil has been recommended as a carbon (C) management approach to sequester C and improve soil quality. Three-year experiments were conducted to investigate the interactive effects of three types of amendments on microbial biomass carbon, soil dehydrogenase activity and soil microbial community abundance in luvisols of arable land in the Czech Republic. Four different treatments were studied, which were, only NPK as a control, NPK + cattle manure, NPK + biochar and NPK + combination of manure with biochar. The results demonstrate that all amendments were effective in increasing the fungal and bacterial biomass, as is evident from the increased values of bacterial and fungal phospholipid fatty acid analysis. The ammonia-oxidizing bacteria population increases with the application of biochar, and it reaches its maximum value when biochar is applied in combination with manure. The overall results suggest that co-application of biochar with manure changes soil properties in favor of increased microbial biomass. It was confirmed that the application of biochar might increase or decrease soil activity, but its addition, along with manure, always promotes microbial abundance and their activity. The obtained results can be used in the planning and execution of the biochar-based soil amendments.
... To this end, a mesocosm study was carried out to monitor changes in microbial community occurring during the degradation of anthracene and benzo[a]pyrene in soils added with either a fungal consortium or compost. Microbial community was studied through the analysis of the phospholipid fatty acid (PLFA) profile, a useful tool to investigate microbial community composition and structure (Drenovsky et al., 2004;Wei et al., 2014;Kim et al., 2016;Meena et al., 2017). ...
Microbial degradation is the main responsible for polycyclic aromatic hydrocarbons (PAHs) removal from contaminated soils, and the understanding of this process is pivotal to define effective bioremediation approaches. To evaluate the contribution of several microbial groups in soil anthracene and benzo[a]pyrene degradation, the analysis of phospholipid fatty acid (PLFA) profiles and machine learning techniques were employed. To this end, PLFAs and PAH concentrations were analysed, along 274 days of incubation in mesocosms, in soils artificially contaminated with anthracene and benzo[a]pyrene, subjected to different treatments: untreated soil and soils treated with biowaste compost or fungal consortium. Random forest models, figuring anthracene or benzo[a]pyrene concentrations as dependent variables and PLFAs as predictors, were then built to evaluate the contribution of each variable in PAH degradation. PLFA profiles varied substantially among soil treatments and along time, with the increase of Actinomycetes in soils added with fungi and other Gram+ bacteria in compost amended soils. The former, together with fungi, are primarily responsible for anthracene and benzo[a]pyrene degradation in both treated soils, a process in which also metanotrophs and other Gram+ and Gram- bacteria participate. In untreated soil, the cooperation of a multitude of different microorganisms was, instead, responsible for PAH removal, a process with lower efficiency in respect to treated soils.
... Extracted lipids afterward are separated into diverse types through solid-phase extraction method followed by transesterification catalyzed by base to yield fatty acid methyl esters (FAMEs) (Findlay 2004). This method is best suited for the fatty acid profiling of living soil microorganisms because phospholipids commence to collapse immediately after the death of the microorganisms (Drenovsky et al. 2004). This method is additionally referred to as the fatty acid methyl ester (FAME) analysis because fatty acid profiling indirectly reflects the growth behavior of bacteria (Fakruddin and Mannan 2013). ...
Soil comprises three interconnected factors responsible for its fertility including physical, chemical, and biological. The soil fertility depends upon the diversity of living microorganisms in the soil and their interaction with other physicochemical components, which accounts for their higher complexity and dynamic behavior. It has been documented as the well-understood component for soil fertility. Along with maintaining the soil fertility, soil microorganisms also impart essential roles in the nutrient biogeochemical cycles that are the fundamentals of life on the earth. A small amount of soil exhibits a great deal of microbial diversity, which includes bacteria, actinomycetes, fungi, algae, and protozoa. Bacteria comprise dominating population in the soil followed by actinomycetes, fungi, algae, and protozoa. It has been reported that one gram of soil may contain 10⁹–10¹⁰ prokaryotes including bacteria-archaea and actinomycetes, 10⁴–10⁷ protists, ∼100 m of fungal hyphae, and 10⁸–10⁹ viruses. The rhizosphere, a narrow zone influenced by plant roots, provides an active habitat for abundant microbes and is considered as one of the most complex ecosystems on the earth. To improve soil health and plant growth performance, it is important to know about the occurrence of diverse microbes and their behavior and role in the rhizosphere microbiome. Moreover, the ability of root exudates for mediating plant–microbe and plant–microbiome interactions could maintain agricultural practices sustainable. This chapter explores the utility and functioning of soil microbial diversity in terms of its agricultural relevance and subsequent increased crop production so that the growing world population scenario could conquer. The microbial population has not been promoted effectively in agricultural practices till date because several beneficial soil microbes are still not explored. So, the chapter insights the various modern molecular tools that will provide an opportunity to discover new species currently unknown to science.
... At the end of the second year of trial after harvest, representative soil samples were collected from each plot and sent to the laboratory for soil biological assessment using Phospholipid Fatty Acid (PLFA) analysis to estimate the total microbial biomass, diversity index, total bacteria biomass, total fungi biomass, arbuscular mycorrhizae fungi and total saprophytes [32]. ...
A study was conducted in an irrigated arid agroecosystem in southwestern USA, to compare two conservation tillage systems (strip tillage (ST) and no-tillage (NT)) to conventional, plow-based tillage (PT) system. Corn silage (Zea mays L.) was planted in this trial. Growth parameters (plant population and height) of corn silage were measured during the season and yield was evaluated at harvest. Soil physical measurements assessed included mean weight diameter of dry aggregates, wet aggregate stability, and penetrometer resistance. While soil biological measurements included total microbial biomass, diversity index (DI), total bacteria biomass, total fungi biomass (TFB), arbuscular mycorrhizae fungi (AMF), and total saprophytes. Results showed that plant population and silage yield at 65% moisture content were not significant with tillage during both trial years. Soil physical parameters were mostly not significant with tillage, while three out of the six biological measurements (DI, TF, and AM) were significant with tillage at p ≤ 0.05. No-tillage had higher DI and TFB than the ST, but not different from PT, while AMF was significantly higher in PT than ST, but not different from NT. The study demonstrates that farmers in the study region can adopt conservation tillage without yield losses during the early years of transition.
... Only phenotypes of V. proteolyticus were monitored in sterilized conditions. In addition, phospholipid fatty acid analysis, which can be used to analyze the composition of microbes in a community [25], indicated that both sterilized and unsterilized cultures had the same pattern and amount of the marker, 7-hexadecenoic acid (C 16:1 w9), which is found in Gram-negative bacteria and sterilized conditions, suggesting that V. proteolyticus was dominant in unsterilized conditions with 5% NaCl (Fig. 7). ...
Polyhydroxybutyrates (PHB) are biodegradable polymers that are produced by various microbes, including Ralstonia, Pseudomonas, and Bacillus species. In this study, a Vibrio proteolyticus strain, which produces a high level of polyhydroxyalkanoate (PHA), was isolated from the Korean marine environment. To determine optimal growth and production conditions, environments with different salinity, carbon sources, and nitrogen sources were evaluated. We found that the use of a medium containing 2% (w/v) fructose, 0.3% (w/v) yeast extract, and 5% (w/v) sodium chloride (NaCl) in M9 minimal medium resulted in high PHA content (54.7%) and biomass (4.94 g/L) over 48 h. Addition of propionate resulted in the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)
(P(HB-co-HV)) copolymer as propionate acts as a precursor for the HV unit. In these conditions, the bacteria produced poly(3-hydroxybutyrate-co-3-hydroxyvalerate) containing a 15.8% 3HV fraction with 0.3% propionate added as the substrate. To examine the possibility of using unsterilized media with high NaCl content for PHB production, V. proteolyticus was cultured in sterilized and unsterilized conditions. Our results indicated a higher growth, leading to a dominant population in unsterilized conditions and higher PHB production. This study showed the conditions for halophilic PHA producers to be later implemented at a larger scale.
... The PLFA method has an advantage that both living fungi and bacteria can be determined in the same sample using the same technique (Frostegård and Bååth, 1996). In general, PLFA analysis can provide a general fingerprint of the microbial community over direct microscopy or DNA methods due to the high precision between replicate samples (Drenovsky et al., 2004(Drenovsky et al., , 2010Ramsey et al., 2006;Frostegård et al., 2011;Contosta et al., 2015). Most importantly, PLFA analysis may have the lowest Type II error rate of common methods used to detect changes in microbial community composition with experimental treatments (Ramsey et al., 2006). ...
... Transects of sampling locations along the engineered (E1-E10) and standard (S1-S10) covers at an oil sands reclamation area. decanoate (19:0) (Drenovsky et al. 2004;Helgason et al. 2010b). ...
Microbial communities that colonize plant rhizosphere and the root interior can ameliorate plant stress and promote growth. These plant-microbe associations are being investigated to assist in reclamation soils in northern Alberta. This study assessed the diversity of bacterial species associated with barley plants growing at different cover managements and slope positions in an oil sands reclamation area. Microbial communities assessed by phospholipid fatty-acid analysis (PLFA) indicated that both cover type and slope, in addition to soil total and organic carbon, NH<sup>4+</sup> and organic matter, were a significant determinant of microbial community composition. However, analysis of denaturing gel gradient electrophoresis (DGGE) banding patterns revealed that while most bulk and rhizosphere soils differentiated by cover management, no clustering was observed in endophytes. In addition, culture dependent techniques assessing endophytic bacteria revealed a dominance of the class Gamaproteobacteria , in which Enterobacteriaceae (44%), Xanthomonaceae (30%) and Pseudomonaceae (26%) were the most abundant families in this class. Several endophytic isolates also matched those from DGGE profiles. The results of this study therefore suggest that plants growing on oil sands reclamation covers host a wide range of bacterial endophytes, which should be assessed as to their potential to assist plant establishment and growth at such sites.
... When 13 C is combined with analysis of phospholipidlinked fatty acids (PLFAs), it becomes possible to trace C transfer into individual microbial groups that account for the living biomass within sediment organic C (OC) (Drenovsky et al., 2004;Hardison et al., 2011;Oakes et al., 2012;Oakes and Eyre, 2014;Spivak, 2015). This allows for the quantification of microbial transfers of newly produced algal C between MPB and bacteria and the relative contributions of MPB and bacteria to microbial biomass in sediment OC. ...
Shallow coastal waters in many regions are subject to nutrient enrichment.
Microphytobenthos (MPB) can account for much of the carbon (C) fixation in
these environments, depending on the depth of the water column, but the
effect of enhanced nutrient availability on the processing and fate of
MPB-derived C (MPB-C) is relatively unknown. In this study, MPB was labeled
(stable isotope enrichment) in situ using 13C-sodium bicarbonate. The
processing and fate of the newly fixed MPB-C was then traced using ex situ
incubations over 3.5 days under different concentrations of nutrients
(NH4+ and PO43−: ambient, 2 × ambient, 5 ×
ambient, and 10 × ambient). After 3.5 days, sediments incubated with
increased nutrient concentrations (amended treatments) had increased loss of
13C from sediment organic matter (OM) as a
portion of initial uptake (95 % remaining in ambient vs. 79–93 % for
amended treatments) and less 13C in MPB (52 % ambient, 26–49 %
amended), most likely reflecting increased turnover of MPB-derived C
supporting increased production of extracellular enzymes and storage
products. Loss of MPB-derived C to the water column via dissolved organic C
(DOC) was minimal regardless of treatment (0.4–0.6 %). Loss due to
respiration was more substantial, with effluxes of dissolved inorganic C
(DIC) increasing with additional nutrient availability (4 % ambient,
6.6–19.8 % amended). These shifts resulted in a decreased turnover time
for algal C (419 days ambient, 134–199 days amended). This suggests that
nutrient enrichment of estuaries may ultimately lead to decreased retention
of carbon within MPB-dominated sediments.
... A simple approach to characterize microbial communities is the extraction and subsequent methylation of lipids from soils to release their respective fatty acid methyl esters (FAMEs). Because the extracted lipids derive not only from cellular storage compounds and membranes of living organisms, but also from plant tissues in various stages of decomposition, it is difficult to draw conclusions about changes in soil microbial community structure from these patterns (Drenovsky et al., 2004). However, FAME analysis is more rapid than phospholipid fatty acids (PLFA) analysis and has been applied to describe microbial communities in agricultural soils. ...
Die 17. Auflage dieses renommierten Lehrbuches vermittelt ein umfassendes Wissen über Böden und deren Schutz. Böden bilden eine der wichtigsten Grundlagen für das terrestrische Leben. Für einen effektiven Schutz und Erhalt dieses Lebensraums braucht es ein grundlegendes Verständnis der Prozesse, die Böden formen, sowie der Eigenschaften der Böden selbst. Dieses Buch fasst den neusten Kenntnisstand der Forschung zusammen und vermittelt ein umfassendes Wissen der Bodenkunde. Im Detail werden behandelt:
die Vorgänge der Bodenbildung und -entwicklung,
die physikalischen, chemischen und biologischen Eigenschaften und Prozesse,
Nähr- und Schadstoffe,
die verschiedenen Bodensystematiken,
die wichtigsten Böden und Bodenlandschaften,
die Nutzungsbewertung der Böden,
Grundsätze des Bodenschutzes.
Die 17. Auflage wurde überarbeitet und ergänzt. Neu ist ein Kapitel zu dem aktuellen Thema Nanopartikel als Schadstoffe im Boden.
Durch seine Ausführlichkeit ist dieses Buch ein Must-Have für alle, die sich mit Böden befassen.
Die Autoren
Alle Autoren und Autorinnen sind international renommierte Fachwissenschaftler und Fachwissenschaftlerinnen an den Universitäten Bonn, Hohenheim, Kiel, der TU München, der TU Berlin und der ETH Zürich.
... The supernatant was used for protein quantification after centrifugation (Eppendorf 5415D, 12,000 rpm, 5 min). Lipid extraction and determination of BioSeNPs were used the method described by Drenovsky et al. 55 . ...
... The supernatant was used for protein quantification after centrifugation (Eppendorf 5415D, 12,000 rpm, 5 min). Lipid extraction and determination of BioSeNPs were used the method described by Drenovsky et al. 55 . ...
Elemental selenium nanoparticles (SeNPs) are useful in medicine, environmental remediation and in material science. Biosynthesized SeNPs (BioSeNPs) by bacteria are cheap, eco-friendly and have a lower cytotoxicity in comparison with chemically synthesized ones. Organic matters were found to cap on the surface of BioSeNPs, but the functions were still not entirely clear. The purified BioSeNPs were coated in a thick layer of organic substrates observed by transmission electron microscopy (TEM). Fourier Transform Infrared (FT-IR) and quantitative detection of the coating agents showed that one gram of purified BioSeNPs bound 1069 mg proteins, 23 mg carbohydrates and only very limited amounts of lipids. Proteomics of BioSeNPs showed more than 800 proteins bound to BioSeNPs. Proteins enriched in charged amino acids are the major factor thought to govern the formation process and stabilization of BioSeNPs in bacteria. In view of the results reported here, a schematic model for the molecular mechanism of BioSeNPs formation in bacteria is proposed. These findings are helpful for the artificial green synthesis of stable SeNPs under specific condition and guiding the surface modification of SeNPs for medicine application.
... Host specificity of root-associated fungi varies between species, but generally the different fungal species are specialized to form only one type of association (ECM, ERM, endophytic or pathogenic) with certain plant species (Brundrett, 2002;Drenovsky et al., 2004;Bougoure et al., 2007;Ishida & Nordin, 2010;Tedersoo et al., 2013). However, different fungal species with ECM, ERM or endophytic nature are found to coexist and possibly compete in plant root systems (Toju et al., 2016a,b). ...
Root‐colonizing fungi can form mycorrhizal or endophytic associations with plant roots, the type of association depending on the host. We investigated the differences and similarities of the fungal communities of three boreal ericoid plants and one coniferous tree, and identified the community structure of fungi utilizing photosynthates from the plants studied.
The fungal communities of roots and soils of Vaccinium myrtillus , Vaccinium vitis‐idaea , Calluna vulgaris and Pinus sylvestris were studied in an 18‐month‐long experiment where the plants were grown individually in natural substrate. Photosynthates utilizing fungi were detected with DNA stable‐isotope probing using ¹³ CO 2 ( ¹³ C‐ DNA ‐ SIP ).
The results indicated that the plants studied provide different ecological niches preferred by different fungal species. Those fungi which dominated the community in washed roots had also the highest ¹³ C‐uptake. In addition, a common root endophyte without confirmed mycorrhizal status also obtained ¹³ C from all the plants, indicating close plant‐association of this fungal species.
We detect several fungal species inhabiting the roots of both ericoid mycorrhizal and ectomycorrhizal plants. Our results highlight that the ecological role of co‐occurrence of fungi with different life styles (e.g. mycorrhizal or endophytic) in plant root systems should be further investigated.
... SIP combined with phospholipid fatty acid (PLFA) analysis is often used to separate C flow into different soil microorganisms (Butler et al. 2003;Treonis et al. 2004;Paterson et al. 2008). PLFAs can be used as proxies for total viable microbial biomass in soils (Frostegård et al. 1991), because rapid degradation of PLFAs occurs directly after cell death (Zelles et al. 1992;Drenovsky et al. 2004). Furthermore, group-specific PLFAs provide insights into the soil microbial community because terminally branched fatty acids are specifically associated with, variously, Grampositive bacteria (i15:0, i16.0 etc.), cyclopropyl saturated fatty acids (cy17:0, cy19:0) or monounsaturated fatty acids (16:1ω7) to Gram-negative bacteria, and the polyunsaturated PLFA 18:2ω6,9 to saprotrophic fungi (Ruess & Chamberlain 2010;Willers et al. 2015). ...
Der Abbau von organischer Bodensubstanz (OBS) ist ein wichtiger Prozess des globalen Kohlenstoffkreislaufes (C-Kreislaufes), der im Wesentlichen von Bodenmikroorganismen durchgeführt wird. Trotz der großen Bedeutung der mikrobiellen Aktivität für die globale C-Bilanz, ist der Einfluss von Substratqualität und -verfügbarkeit auf Bodenmikroorganismen wenig erforscht. Ein Großteil des pflanzenbürtigen C wird indirekt durch den Einbau in Mikroorganismen der OBS zugeführt, aber über das darauffolgende Schicksal von C in der mikrobiellen Gemeinschaft ist wenig bekannt. Die mikrobielle Biogeochemie ist deswegen in Erdsystemmodellen nur unzureichend implementiert. Die im 5. Kapitel präsentierte Studie nutzte ein im Jahr 2009 angelegtes Feldexperiment um den C-Eintrag in drei Bodentiefen nach einem C3-C4 Pflanzenwechsel in fünf aufeinanderfolgenden Jahren zu untersuchen. Hierbei wurde durch den Anbau von Maispflanzen wurzelbürtiger C (unterirdischer C-Kanal), sowie durch die Applikation von Maisstreu auf die Bodenoberfläche sproßbürtiger C (oberirdischer C-Kanal) in den Boden eingetragen. Der prozentuale Anteil von maisbürtigem C variierte in den Bodenpools: geringere Einträge fanden sich in der OBS und im extrahierbaren organischen C (EOC) und höhere Einträge in den mikrobiellen Gruppen. Eine Versorgung mit beiden Pflanzensubstraten zeigte im Oberboden einen additiven Effekt in fast allen untersuchten Bodenpools. Sowohl wurzel- als auch sproßbürtiger C wurde bis in eine Tiefe von 70 cm transferiert. In allen drei Tiefen assimilierten Pilze die angebotenen C-Substrate im größeren Umfang als Gram-positive und Gram-negative Bakterien. Nach der fünften Wachstumsperiode konnte ein Einbau von bis zu 78 % Mais-C in die pilzliche Biomasse nachgewiesen werden, was auf verstärkte Nutzung des Mais-C durch saprotrophe Pilze hindeutet. Die zweite Studie untersuchte den Einfluss abnehmender Substratqualität auf Bodenmikroorganismen an der Boden-Streu Grenzschicht in einem Mikrokosmenexperiment. Ein reziproker Austausch von markierter 13C und unmarkierter 12C Maisstreuauflage auf Bodenkerne erlaubte es, den C-Eintrag von Pflanzenresten in die Hauptakteure (Bakterien und Pilze) des detritivoren Nahrungsnetzes und den darauffolgenden C-Umsatz in der mikrobiellen Biomasse zu drei unterschiedlichen Zeiten während des Streuabbaus zu bestimmen. Die Qualität (d. h. das Alter) der Maisstreu beeinflusste hierbei die Aufnahme von C in Bakterien und Pilze. Einfach verfügbarer C aus kürzlich eingetragener Streu wurde von beiden Mikroorganismengruppen genutzt, während saprotrophe Pilze zusätzlich noch komplexeres C-Substrat im fortgeschrittenen Abbaustadium nutzten. Bakterien reagierten unterschiedlich auf die angebotene Streu, indem sie entweder den Streu-C in ihren Phospholipidfettsäuren (PLFAs) über die Zeit umsetzten, es dauerhaft speicherten und/oder zusätzlich noch mikrobiell freigesetzten C aufnahmen. Saprotrophe Pilze hingegen zeigten einen deutlichen Abbau von Mais-C in der pilzlichen PLFA. Die mittlere Verweildauer von C in der pilzlichen Biomasse betrug 32 bis 46 Tage und wurde genauso schnell oder sogar schneller als in den bakteriellen PLFAs umgesetzt. Für die in Kapitel 7 präsentierte Studie wurde ein weiteres Feldexperiment genutzt, um die Mitglieder der Herbivoren- und Detritivorennahrungskette über zwei aufeinanderfolgende Jahre zu untersuchen. Drei Behandlungen wurden etabliert um wurzelbürtiges, sproßbürtiges und autochthones organisches Material als verfügbares C-Substrat zur Verfügung zu stellen: Anbau von Maispflanzen, Ausbringen von Maisstreu und Brachflächen. Entgegen den Erwartungen zeigte die veränderte C-Versorgung durch Entfernen der Ackerpflanze nur wenig Einfluss auf die mikrobielle Gemeinschaftsstruktur des Bodennahrungsnetzes. Bakterien und Pilze zeigten eine ausgeprägte Anpassungsfähigkeit an die geringere C-Verfügbarkeit. In der ersten Vegetationsperiode war die Nematodenabundanz unter Pflanzenkultivierung vergleichbar mit denen der Streu- und Brachflächen. Nach der zweiten Ernte wurden hingegen die Mitglieder der Detritivorennahrungskette durch den Abbau von Wurzelbiomasse gefördert. Die Ergebnisse dieser Studie zeigen eine ausgeprägte Widerstandsfähigkeit des Bodenmikronahrungsnetzes auf Substrat- und Nährstoffverfügbarkeit und deuten darauf hin, dass älteres organisches Material genutzt wird, um C-Mangel auszugleichen. Zusammenfassend hat die vorliegende Arbeit dazu beigetragen neue Erkenntnisse zu mikrobiellen Abbauprozessen mit unterschiedlicher zeitlicher und räumlicher Auflösung zu erlangen. Die Nutzung von stabilen Isotopen in Kombination mit PLFA-Biomarkeranalysen ermöglichte es, den C-Fluss zwischen abiotischen und mikrobiellen C-Pools im Boden zu untersuchen und den Anteil von Bakterien und Pilzen am C-Umsatz im Boden zu bestimmen. Die vorliegenden Ergebnisse können als Basis für ein empirisches Modell des C-Flusses durch das gesamte Bodennahrungsnetz genutzt werden.
... When 13 C is combined with analysis of phospholipidlinked fatty acids (PLFAs), it becomes possible to trace C transfer into individual microbial groups that account for the living biomass within sediment organic C (OC) (Drenovsky et al., 2004;Hardison et al., 2011;Oakes et al., 2012;Oakes and Eyre, 2014;Spivak, 2015). This allows for the quantification of microbial transfers of newly produced algal C between MPB and bacteria and the relative contributions of MPB and bacteria to microbial biomass in sediment OC. ...
Shallow coastal waters in many regions are subject to nutrient over-enrichment. Microphytobenthos (MPB) can account for much of the carbon (C) fixation in these environments, depending on the depth of the water column, but the effect of enhanced nutrient availability on the processing and fate of MPB-derived C is relatively unknown. In this study, MPB were labeled (stable isotope enrichment) in situ using ¹³C-sodium bicarbonate. The processing and fate of the newly-fixed MPB-C was then traced using ex situ incubations over 3.5 d under different concentrations of nutrients (NH4⁺ and PO43−: ambient, 2× ambient, 5× ambient, and 10× ambient). After 3.5 d, sediments incubated with increased nutrient concentrations (amended treatments) had increased loss of ¹³C from sediment organic matter as a portion of initial uptake (95 % remaining in ambient vs 79–93 % for amended treatments) and less ¹³C in MPB (52 % ambient, 26–49 % amended), most likely reflecting increased turnover of MPB-derived C supporting increased production of extracellular enzymes and storage products. Loss of MPB-derived C to the water column via dissolved organic C was minimal regardless of treatment (0.4–0.6 %). Loss due to respiration was more substantial, with effluxes of dissolved inorganic C increasing with additional nutrient availability (4 % ambient, 6.6–19.8 % amended). These shifts resulted in a decreased turnover time for algal C (419 d ambient, 134–199 d amended). This suggests that nutrient enrichment of estuaries may ultimately lead to decreased retention of carbon within MPB-dominated sediments.
... carbons are found in both plant material and microbes, making it difficult to determine their origin. Also, PLFA is an effective method because it provides a snapshot of the living microbial community (Drenovsky et al. 2004) and it is useful for detecting broad changes among treatments (Bossio and Scow 1998). ...
Understanding the role of species interactions as regulatory mechanisms for ecosystem processes presents a challenge to ecologists working in systems with high species diversity and habitat complexity. Recent studies suggest that interactions among intraguild predators, such as terrestrial salamanders and large arthropods, might be important for the regulation of detritivores, fungivores, and perhaps detritus within terrestrial webs. A key prediction is that interactions among predators weaken trophic cascades. Our research examined this prediction by removing predators for 4 yr from unfenced field plots to investigate the effects on litter arthropods, the microbial community, and rates of leaf litter decomposition. We manipulated predator abundance in three treatments (salamander removal, centipede removal, and multiple predator removal) compared to a control in which no predators were removed. Despite difficulties in suppressing centipede numbers, we observed increases in salamanders, millipedes, isopods, slugs, numbers of ant colonies, and gamasid mites in the centipede removal plots. Additionally, several phospholipid fatty acid markers for bacteria were suppressed in plots where salamanders were most abundant. Finally, we detected treatment effects on the rate of litter disappearance from leaf bags in our field plots: those with the most salamanders had the lowest levels of litter decomposition. Overall, we found some evidence for top-down effects of predators in a temperate forest-floor web. Our study is one of few that have employed an unfenced field design and the only study examining the effects of salamanders on forest soil microbes. The results contribute to a growing body of evidence indicating that territorial predators, such as terrestrial salamanders, can be strong regulators of species composition at lower trophic levels in a system that is commonly thought to be regulated primarily through bottom-up effects of organic matter supply.
... carbons are found in both plant material and microbes, making it difficult to determine their origin. Also, PLFA is an effective method because it provides a snapshot of the living microbial community (Drenovsky et al. 2004) and it is useful for detecting broad changes among treatments (Bossio and Scow 1998). ...
Understanding the role of species interactions as regulatory mechanisms for ecosystem processes presents a challenge to ecologists working in systems with high species diversity and habitat complexity. Recent studies suggest that interactions among intraguild predators, such as terrestrial salamanders and large arthropods, might be important for the regulation of detritivores, fungivores, and perhaps detritus within terrestrial webs. A key prediction is that interactions among predators weaken trophic cascades. Our research examined this prediction by removing predators for 4 yr from unfenced field plots to investigate the effects on litter arthropods, the microbial community, and rates of leaf litter decomposition. We manipulated predator abundance in three treatments (salamander removal, centipede removal, and multiple predator removal) compared to a control in which no predators were removed. Despite difficulties in suppressing centipede numbers, we observed increases in salamanders, millipedes, isopods, slugs, numbers of ant colonies, and gamasid mites in the centipede removal plots. Additionally, several phospholipid fatty acid markers for bacteria were suppressed in plots where salamanders were most abundant. Finally, we detected treatment effects on the rate of litter disappearance from leaf bags in our field plots: those with the most salamanders had the lowest levels of litter decomposition. Overall, we found some evidence for top-down effects of predators in a temperate forest-floor web. Our study is one of few that have employed an unfenced field design and the only study examining the effects of salamanders on forest soil microbes. The results contribute to a growing body of evidence indicating that territorial predators, such as terrestrial salamanders, can be strong regulators of species composition at lower trophic levels in a system that is commonly thought to be regulated primarily through bottom-up effects of organic matter supply.
... Phospholipid fatty acids are major cell membrane constituents, and their polar head groups and ester-linked side chains (i.e. FAs) vary in composition between eukaryotes and prokaryotes, as well as among many prokaryotic groups (Drenovsky et al., 2004). These compounds rapidly degrade upon cell death (Pinkart et al., 2002). ...
It has been predicted that the precipitation and atmospheric nitrogen (N) deposition will increase in northern China. Though a variety of publications have documented the effects of increased precipitation and N deposition on aboveground plant community, the responses of soil microbial community composition and function to these possible global changes still remain largely unknown. In this study, we take advantage of a long-term (9-year) field experiment that was established in a typical steppe in Inner Mongolia, China. The responses of microbial community composition and soil enzymatic activities to simulated N deposition and increased precipitation were examined. It was found that the low level of N addition showed no influence on the relative abundance of bacteria, but the relatively high N deposition increased the relative abundance of bacteria. The increased precipitation in combination with N addition, estimated at all N levels, significantly decreased the relative abundance of fungi and fungi/bacteria ratio. Increased precipitation played important roles in enhancing microbial activity in this semi-arid region. It was observed that water supply increased the activities of the five of the enzymes determined, including peroxidase (PER), polyphenol oxidase (PPO), β-Glucosidase (BG), protease (PRO) and alkaline phosphomonoesterase (alkaline PME). The activity of cellulase was reduced by long-term increased precipitation treatment, but was stimulated by simulated N deposition, which may due to the changes in litter components under projected climate change. The influences of N deposition on the microbial enzymatic activities might be alleviated (such as PER), strengthened (acid PME), or not affected by the projected precipitation increment. We also found that the overall changes in soil enzymatic activity patterns are more sensitive to environmental changes than the variations in soil microbial community composition, which may be explained by the microbial function redundancy and the limitations of research method. By all accounts, in future scenarios of increased precipitation in combination with N deposition, the proportion of soil fungi would be reduced, and the microbial community composition might be shifted to be bacteria-dominant. We also predicted that with the increasing of N deposition level, the activities of cellulolase would be enhanced, whereas the activities of ligninolytic enzymes (PER and PPO) would be reduced sharply.
... At the local and regional scale, influences such as recent site history, land use, and plant community composition likely play an important role in structuring communities (Martiny et al. 2006, Drenovsky et al. 2009). Indeed, although the PLFA method has been a robust fingerprinting technique for comparing microbial communities among plant communities, soils, land uses, and climates (B a ath and Anderson 2003, Drenovsky et al. 2004, Brockett et al. 2012, Welc et al. 2012), we could not strongly differentiate microbial communities by land use or soil type (see Appendix S1). But given the large area covered by our transects, and the variability at that scale, perhaps that is not a surprising result. ...
Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities versus those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM that shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils. This article is protected by copyright. All rights reserved.
... Briefly, branched PLFAs represent Gram-positive, while monounsaturated PLFAs mostly represent Gram-negative bacteria. Actinobacteria produce 10-methyl-branched PLFAs, whereas polyunsaturated PLFAs represent eukaryotes and the PLFA 18:2ω6,9 fungi (Drenovsky et al. 2004;Fierer et al. 2003;Frostegård and Bååth 1996;Harwood and Russell 1984;Zelles 1997). ...
Biopores are hotspots of nutrient mobilisation and shortcuts for carbon (C) into subsoils. C processing relies on microbial community composition, which remains unexplored in subsoil biopores. Phospholipid fatty acids (PLFAs; markers for living microbial groups) and amino sugars (microbial necromass markers) were extracted from two subsoil depths (45–75 cm ; 75–105 cm) and three biopore types: (I) drilosphere of Lumbricus terrestris L., (II) 2-year-old root biopores and (III) 1.5-year-old root biopores plus six 6 months of L. terrestris activities. Biopore C contents were at least 2.5 times higher than in bulk soil, causing 26–35 times higher Σ PLFAs g⁻¹ soil. The highest Σ PLFAs were found in both earthworm biopore types; thus, the highest soil organic matter and nutrient turnover were assumed. Σ PLFAs was 33% lower in root pores than in earthworm pores. The treatment affected the microbial community composition more strongly than soil depth, hinting to similar C quality in biopores: Gram-positives including actinobacteria were more abundant in root pores than in earthworm pores, probably due to lower C bioavailability in the former. Both earthworm pore types featured fresh litter input, promoting growth of Gram-negatives and fungi. Earthworms in root pores shifted the composition of the microbial community heavily and turned root pores into earthworm pores within 6 months. Only recent communities were affected and they reflect a strong heterogeneity of microbial activity and functions in subsoil hotspots, whereas biopore-specific necromass accumulation from different microbial groups was absent.
Soil phosphorus (P) can be divided into inorganic P (Pi) and organic P (Po). Microorganisms play essential roles in soil P transformation. However, there are many ways to detect P transformation, and the relationship between P forms and microorganisms under long-term fertilization is largely unclear. In this study, soil P forms were analyzed by a chemical sequential fractionation method and solution 31P nuclear magnetic resonance (31P-NMR) technique. Phospholipid fatty acid (PLFA) contents were measured by gas chromatography as the characterization of soil microbial community structures. The objective was to determine the changes of soil P forms and associated microbial community composition in mollisol with long-term fertilization. We sampled soil from a field experiment with 26-year-old continuous maize (Zea mays L.) cropping in Northeastern China. Three fertilization treatments were selected as chemical fertilization (NPK), NPK with crop straw (NPKS), and NPK with manure (NPKM). As shown in 31P-NMR spectra, orthophosphate accounted for 62.8–85.8% of total extract P. Comparison to NPK and NPKS treatments, NPKM application notably increased the concentrations of Po, Olsen-P, orthophosphate, orthophosphate monoester, and total P. Soil P fractions including resin-Pi, NaHCO3-P, NaOH-P, and HCl-P, especially Pi fractions, were enhanced by NPKM. The amounts of total PLFAs and PLFAs in bacteria, Gram-positive (G+) and Gram-negative (G−) bacteria, actinomycetes, and fungi were high in NPKM-treated soil. The percentages of PLFAs in bacteria and fungi in total soil PLFAs were 56.8% and 9.7%, respectively, which did not show any significant difference among the treatments. NPKM increased the proportions (%) of PLFAs in G+ bacteria, and NPKS increased the proportions (%) of G− bacteria in total PLFAs. The composition of soil microbial community was found to be significantly affected by soil total carbon and pH. There was a close relationship between HCl-Pi, NaHCO3-Po, orthophosphate, and pyrophosphate with anaerobe, aerobes, and G+. Manure addition directly increased soil available P concentrations, and indirectly acted through the alterations of anaerobe, aerobes, and G+. It is concluded that long-term NPKM application would lead to the accumulation of labile P and moderately labile P in mollisol through the activity of soil microbes.
The differences between aquatic and terrestrial habitats could change microbial community composition and regulate litter decomposition in a subtropical forest, but the linkage remains uncertain. Using microbial phospholipid fatty acids (PLFAs), the litter decomposition associated with microbial organisms was monitored to characterize the differences of microbial communities in the forest floor, headwater stream, and intermittent stream. Habitat type did not significantly affect the concentrations of total PLFA. However, microbial community composition (fungi, G+ bacteria, and eukaryote) was significantly affected by the microenvironment among habitats. Compared with which in headwater stream, more individual PLFAs were identified in the natural forest floor and the intermittent stream during the whole decomposition period. The differences in individual PLFA concentrations were reflected in the forest floor and aquatic system in the early stage of litter decomposition, but they mainly reflected in the headwater stream and the intermittent stream in the later stage of litter decomposition. We linked the relationships between microbial community and litter decomposition and found that communities of decomposers drive differences in litter decomposition rate among habitats. Intriguingly, the microbial community showed the greatest correlation with the decomposition rate of litter in streams. These findings could contribute to the understanding of habitats difference on the microbial community during litter decomposition.
In 21st century, food safety has become a global concern. Over the decades several efforts have been made in order to amplify the agricultural proficiency, mainly through the use of pesticides and chemical fertilizers leading to build-up of these chemical entities in the soil and depleting soil quality and fertility. These xenobiotic compounds can also accumulate in animal systems and cause serious health issues making it necessary to develop safer and eco-friendly alternatives for prolific agricultural production. Microorganisms are the omnipresent community, which are found in association of all other life forms in several different ways. Plant Growth Promoting Rhizobacteria (PGPR), a group of soil rhizospheric microbes, augment nutrient accessibility and persuade tolerance against biotic and abiotic stress to plants. PGPR are diversified phytostimulators providing multiple assets to plants in forms of available nutrients and follows the elimination of competition strategy by operating several biocontrol activities making them suitable as an eco-friendly approach for pest control. However when such isolates, which are promising candidates in- vitro, are applied to field, their effect tends to be non-significant due to complex community dynamics of the rhizosphere. To answer this situation, scientists have come up with idea of applying a synthesized consortium of microorganisms which act in synergy and are capable of overcoming the indigenous community barrier. Nowadays, application of PGPR consortium (two or more microbes together) as microbial biostimulants is gaining attention worldwide due to the multifaceted advantages these microbial consortia can offer for improving plant growth, yield and crop quality. The selection of microorganisms for consortia amongst the large array of individually screened potent PGPR is very critical. This chapter discusses the basic and general understanding of biostimulants, the marketing strategies employed by different microbes in microbe-microbe interactions and microbe-PGPR as plant probiotics and/or phytostimulators accounting to the wide array of beneficiary traits. The primary focus of this chapter is the employment of microbial consortia as biostimulant for augmentation of plant growth. Here the authors discuss multiple consortia used in various researches aimed towards enhanced quality, yield or protection of specific host plants. These consortia are composed of two, three or multiple members, where strain mixtures of the same or two different genera are used in combination to attain phytostimulatory attributes. The development of more complex co-culture encompassing multiple genera can prove more advantageous; however, it is difficult to mimic natural environmental conditions pertaining to the fact that a large population of soil flora is still uncultivable in lab. Use of advanced molecular techniques can aid analyzing the community sustainability of the developed consortia. MiL-FISH, pyrosequencing, etc. can be used to study multi-partner consortia and help identify and localize hard-to-detect taxa. Further the use of multi omics approach in developing biostimulatory microbial consortia is discussed.
Soil contamination as a result of oil spills is a serious issue due to the global demand for diesel fuel. As an alternative to diesel, biodiesel has been introduced based on its high degradability rates and potential for reducing of greenhouse gases emissions. This study assessed the impacts diesel and biodiesel contamination on soil microbial community activity and structure. Our results suggest higher microbial activity in biodiesel contaminated soils and analysis of PLFA profiles confirmed shifts in microbial community structure in response to contamination. High-throughput 16S rRNA amplicon sequencing also revealed a lower bacterial richness and diversity in contaminated soils when compared to control samples, supporting evidence of the detrimental effects of hydrocarbons on soil microbiota. Control samples comprised mostly of Actinobacteria, whereas Proteobacteria were predominantly observed in diesel and biodiesel contaminated soils. At genus level, diesel and biodiesel amendments highly selected for Rhodococcus and Pseudomonas spp., respectively. Moreover, predicted functional profiles based on hydrocarbon-degrading enzymes revealed significant differences between contaminated soils mostly due to the chemical composition of diesel and biodiesel fuel. Here, we also identified that Burkholderiaceae, Novosphingobium, Anaeromyxobacter, Pseudomonas and Rhodococcus were the main bacterial taxa contributing to these enzymes. Together, this study supports the evidence of diesel/biodiesel adverse effects in soil microbial community structure and highlights microbial taxa that could be further investigated for their biodegradation potential.
Kauri (Agathis australis), which is one of the world's largest and longest‐living conifer species, is under threat from a root and collar dieback disease caused by the oomycete pathogen Phytophthora agathidicida. The noted incidence of kauri dieback has increased in the past decade, and even trees >1000 years old are not immune. This disease has profound effects on both forest ecosystems and human society, particularly indigenous Māori, for whom kauri is a “taonga” or treasure of immense significance. This review brings together existing scientific knowledge about the pathogen and the devastating disease it causes, as well as highlighting important knowledge gaps and potential approaches for disease management. The life cycle of P. agathidicida is similar to those of other soil‐borne Phytophthora pathogens, with roles for vegetative hyphae, zoospores and oospores in the disease. However, there is comparatively little known about many aspects of the biology of P. agathidicida, such as its host range and disease latency, or about the impact on the disease of abiotic and biotic factors such as soil health and co‐occurring Phytophthora species. We discuss current and emerging tools and strategies for surveillance, diagnostics and management, including a consideration of genomic resources, and the role these play in understanding the pathogen and how it causes this deadly disease. Key aspects of indigenous Māori knowledge, which include rich ecological and historical knowledge of kauri forests and a holistic approach to forest health, are highlighted.
Given the wide range of factors influencing soil microbial communities, the aim of our study was to investigate how these communities respond to changes in plant inputs, litter, and removal of soil organic layers, in a subalpine forest. Our study site was located on the slopes of Yulong Snow Mountain, Yunnan, China. We analyzed the effect of litter, tree roots, and the organic horizon on soil microbial communities, using phospholipid fatty acid (PLFA) analysis and by monitoring any changes in soil properties, over two months. Our results showed that the gram-positive bacteria and gram-negative bacteria ratio (G⁺/G⁻), after the second month of all treatments, was significantly higher than after the first month of treatment. The biomass of the soil microbial community is sensitive to response to variation of the soil environment. Removal of the organic horizon and additional litter coverage significantly decreased the biomass of fungi, fungi/bacteria and total PLFA, and significantly increased the G⁺/G⁻ ratio compared with the control and other treatments after two months. Organic horizon and litter layer removal significantly increased the G⁺/G⁻ ratio. Litter removal significantly increased the biomass of arbuscular mycorrhizal fungi. Contrary to our expectations, root removal had no effect on the biomass of the soil microbial communities during two months' treatment.
Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition.
An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil.
This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.
Growers converting from conventional to low-input and organic farming systems must
rely on organic sources for adequate soil fertility. At the Sustainable Agriculture
Farming Systems (SAFS) project at UC Davis, we measured soil fertility and biological
parameters in four farming systems. By the end of the first 4 years, pH and percent
nitrogen were consistently higher in organic and low-input than conventional plots
for all crops. Levels of organic matter, phosphorus and potassium were significantly
higher in the organic than conventional 2-year plots. Microbial biomass levels were
consistently higher in organic and low-input systems, while plant parasitic nematode
numbers were consistently lower. Nitrogen deficiency appeared to be a problem in organic
tomatoes during the transition period. More research is needed into the dynamics of
soil nutrient availability in low-input systems. For instance, we may need to develop
new methods of assessing soil fertility in organically fertilized systems.
In 1989, a group of researchers, farmers and farm advisors initiated an interdisciplinary study of the transition from conventional to low-input and organic management of a 4-year, five-crop rotation. Crop yields initially varied among systems, but now appear to be approaching each other after a transition period that included the development of practices and equipment most appropriate for each system. Farming practices and crop production costs are carefully documented to compare the various systems' economic performance and biological risks. Supplying adequate N and managing weeds were challenges for the low-input and organic systems during the first rotation cycle, and experiments are being conducted on an 8-acre companion block to find solutions to these and other problems. Leading conventional and organic growers provide a much-needed farmer perspective on cropping practices and economic interpretations, because we try to provide “best farmer” management of each system. Research groups within the project are focusing on soil microbiology, economics, pest management, agronomy and cover crop management.
Soil microbiological parameters may be the earliest predictors of soil quality changes. Recently, molecular techniques such
as fatty acid methyl ester (FAME) profiles have been used to characterize soil microbial communities. Fatty acid methyl ester
(FAME) from whole soil may be derived from live cells, dead cells, humic materials, as well as plant and root exudates. Our
objective was to verify differences in FAME profiles from two agricultural soils with different plants. Soil samples were
collected from Ritzville and Palouse silt loams for fatty acid analysis. Soil samples from wheat (Triticum aestivum L.), barley
(Hordeum vulgare L.), pea (Pisum sativum L.), jointed goatgrass ( Aegilops cylindrica L.) and downy brome (Bromus tectorum
L.) rhizospheres were also collected for fatty acid analysis. Principal component analysis (PCA) of the two soils explained
42% of the variance on PC1, which accounted for Palouse soil. Ritzville soil accounted for 19% of the variance on PC2. Factor
analysis showed that rhizosphere microbial communities from various plant species may differ depending on the plant species.
Presence of Gram-positive bacteria as identified by a15:0, i15:0, a17:0 and i17:0 peaks were similar between rhizosphere and
nonrhizosphere soils. Gram-negative bacteria characterized by short chain hydroxy acids (10:03OH and 12:03OH) as well as cyclopropane
acids (cy17:0) were higher in rhizosphere soil than nonrhizosphere. This indicates a possible shift in the bacterial community
to more Gram-negative bacteria and fewer Gram-positive bacteria in the rhizospheres of the plants species studied.
Analysis of fatty acid methyl ester (FAME) profiles extracted from soils is a rapid and inexpensive procedure that holds great promise in describing soil microbial community structure without traditional reliance on selective culturing, which seems to severely underestimate community diversity. Interpretation of FAME profiles from environmental samples can be difficult because many fatty acids are common to different microorganisms and many fatty acids are extracted from each soil sample. We used principal components (PCA) and cluster analyses to identify similarities and differences among soil microbial communities described using FAME profiles. We also used PCA to identify particular FAMEs that characterized soil sample clusters. Fatty acids that are found only or primarily in particular microbial taxa-marker fatty acids-were used in conjunction with these analyses. We found that the majority of 162 soil samples taken from a conventionally-tilled corn field had similar FAME profiles but that about 20% of samples seemed to have relatively low, and that about 10% had relatively high, bacterial:fungal ratios. Using semivariance analysis we identified 21:0 iso as a new marker fatty acid. Concurrent use of geostatistical and FAME analyses may be a powerful means of revealing other potential marker FAMEs. When microbial communities from the same samples were cultured on R2A agar and their FAME profiles analyzed, there were many differences between FAME profiles of soil and plated communities, indicating that profiles of FAMEs extracted from soil reveal portions of the microbial community not culturable on R2A. When subjected to PCA, however, a small number of plated communities were found to be distinct due to some of the same profile characteristics (high in 12:0 iso, 15:0 and 17:1 ante A) that identified soil community FAME profiles as distinct. Semivariance analysis indicated that spatial distributions of soil microbial populations are maintained in a portion of the microbial community that is selected on laboratory media. These similarities between whole soil and plated community FAME profiles suggest that plated communities are not solely the result of selection by the growth medium, but reflect the distribution, in situ, of the dominant, culturable soil microbial populations.
Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with
measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced
by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs
(EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the
soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation,
being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter)
only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total
N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO2-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil.
Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids
in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community
in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding
community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect
on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences
in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated
community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of
the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy
analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P
were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH4-N, CO2-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy
analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated
with the variation in Biolog substrate utilization patterns.
Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury
were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury
methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations,
and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially
attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment
PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of Desulfobacter andDesulfovibrio groups of sulfate-reducing bacteria suggests that Desulfobacter-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.
The assumption that carbon and soil water content are major determinants of microbial community structure and function is rarely questioned because of substantial evidence of the impacts of these variables on specific populations and functions. The significance of carbon and water for metabolic diversity at the microbial community level was tested on the field scale in agricultural plots varying in carbon inputs and in whether they were flooded. Surface soils in which rice straw was incorporated or burned and which were flooded or unflooded were sampled at monthly intervals three times during the flooded winter period (January to March) and again 1 month postdraining. Biomass carbon and nitrogen were not affected by treatments, active bacterial counts showed slight increases, and respiration rates were increased by carbon inputs and flooding. Biolog microplates were inoculated with soil extracts to quantify the metabolic diversity of the soil microbial community. Canonical correspondence analysis and the Monte Carlo permutation testing showed that differences in substrate utilization patterns were significantly related (P < 0.001) to carbon and flooding treatments. Biolog substrates whose metabolism was altered by the treatments were consistent across dates and tended to be positively related (utilization enhancement) to carbon inputs and negatively related to winter flooding. The importance of carbon as an environmental variable increased over time after straw treatment, whereas the importance of water became evident after flooding and decreased after drainage. The effect of long-term rice straw incorporation on substrate utilization patterns at another field site was consistent with these results despite the dissimilarities of the two soils.
Little is known about the short-term effects (hours to days) of tillage on labile pools of C and N, or microbial activity and community composition. We examined the effects of rototillage on microbial biomass C (MBC) and N (MBN), respiration (i.e., soil CO2 production in 1-h incubations), CO2 efflux from the soil surface, inorganic N, nitrification potential, denitrification rate, and phospholipid fatty acids (PLFA), A fallow silt loam soil was rototilled in the field and soil cores were immediately obtained from tilled and adjacent control soils. The soil cores were then incubated at constant temperature and sampled throughout a 2-wk period, Tilled soil had higher CO2 efflux than the control soil, This increase occurred immediately after tillage and lasted for 4 d. Respiration was similar in both soils until the fourth day after tillage, and then declined in the tilled soil. Tilled soil showed increases in MEN, nitrate, and denitrification rates, suggesting that tillage makes available previously protected organic N. The overall reduction in respiration together with the lack of response in B;IBC, however, suggests that tillage did not make available significant amounts of readily decomposable C. These combined C and N dynamics suggest that low C/N ratio compounds may have been mineralized following tillage. Denitrification rates increased in the tilled soil even though the bulk of the soil had reduced respiration and bulk density, Tillage caused temporary changes in PLFA profiles, suggesting changes in soil microbial community structure. Phospholipid fatty acid 18:1 omega 7t, which marks the presence of eubacteria, decreased in the tilled soil. In contrast, 19:0 cy, a marker for anaerobic eubacteria, increased in the tilled soil. Our results show that tillage causes shortterm changes in nutrient dynamics that may potentially result in N losses through denitrification and nitrate leaching, as well as C losses through degassing of dissolved CO2. These changes are accompanied by concomitant shifts in microbial community structure, suggesting a possible relationship between microbial composition and ecosystem function.
Lipid decomposition studies in frozen fish have led to the development of a simple and rapid method for the extraction and purification of lipids from biological materials. The entire procedure can be carried out in approximately 10 minutes; it is efficient, reproducible, and free from deleterious manipulations. The wet tissue is homogenized with a mixture of chloroform and methanol in such proportions that a miscible system is formed with the water in the tissue. Dilution with chloroform and water separates the homogenate into two layers, the chloroform layer containing all the lipids and the methanolic layer containing all the non-lipids. A purified lipid extract is obtained merely by isolating the chloroform layer. The method has been applied to fish muscle and may easily be adapted to use with other tissues.
Rapid methods for characterizing soil microbial communities are essential to assess responses to perturbations and to improved management practices. This study compared the composition of microbial communities in 47 agricultural soil and adjacent land use samples collected in the San Joaquin Valley, CA. Microbial communities were characterized by DNA fingerprinting of the Intergenic Transcribed Spacer (ITS) region, using primers universal for bacteria or eucarya. Bacterial DNA fingerprints were more complex (containing 25–30 bands) than were eucaryotic fingerprints (8–15 bands). Field replicates from within an agricultural field were more similar to one another than samples collected in different fields under the same crop type or in close proximity to one another. Microbial communities in almond, grape, and tomato soils across different locations were more similar to one another than communities in cotton and safflower soils. Bacterial DNA fingerprints were significantly correlated with soil electrical conductivity, soil texture, inorganic carbon, and nitrogen content but not with pH and organic carbon content. The grouping of soil samples based on their soil reflectance properties was similar to the grouping based on the bacterial ITS analysis. Despite similarities among communities under some crops and at some locations, there is tremendous unexplained diversity within agricultural soil microbial communities. More extensive sampling is needed to better understand the driving forces underlying microbial community composition.
stress on bacterial isolates (Kieft et al., 1994, 1997), of root exudates on rhizosphere microorganisms (Griffiths Fatty acid profiling is a popular method for characterizing microbial method, respectively, but unique FAMEs generally were found in only minute amounts. Soils extracted with the MIDI method yielded proven extremely useful, the methods involved are time more hydroxy FAMEs and short-chain saturated and branched consuming. Microbial lipids are extracted from environ- FAMEs. Conversely, EL-extracted soils generally produced more mental samples in a phase-mixture of chloroform, meth- long-chain saturated and branched FAMEs, unsaturated FAMEs, and anol (MeOH), and water (Bligh and Dyer, 1959). Lipids FAMEs with cyclopropane and methyl groups. Both extraction meth- associated with the organic phase are then fractionated ods were able to differentiate among communities of different soil into neutral, glyco-, and phospholipids on silicic acid types, regardless if soils were fresh or stored. Changes in FAME columns, while the residue at the organic:aqueous in- profiles did occur in stored soils, but the effectiveness of each storage terphase can be separated into lipopolysaccharides, protocol for preserving FAME patterns over time was different among teichoic acids, and muramic acid (Vestal and White, the four soils. While community analyses should be conducted on 1989). Finally, the phospholipids are subjected to alka- fresh soil, overall effects of storage were slight compared with those of extraction method and soil type. line methanolysis to produce fatty acid methyl esters (FAMEs) for analysis by gas chromatography (GC). Recently, a simpler method has been developed to extract microbial fatty acids directly from soils. The
Abstract Phospholipid fatty acid (PLFA) profiles provide a robust measure that can be used to fingerprint the structure of soil microbial communities, and measure their biomass. A replicated field trial, with gradients in substrate and O2 availability created by straw incorporation and flooding was used to test the ability of PLFA to discriminate soil microbial communities in different management regimes. Another objective was to test the usefulness, on a large scale, of some of the proposed interpretations of PLFA biomarkers. Using a direct gradient statistical analysis method, PLFA profiles were found to be very sensitive to flooding and straw treatments. Relative abundances of monounsaturated fatty acids were reduced with flooding and increased with added carbon, consistent with their proposed interpretations as indicators of aerobic conditions and high substrate availability. The cyclopropyl fatty acids were not useful as taxonomic indicators of respiratory type, although their responses were consistent with their proposed use as growth condition indicators. Branched fatty acids decreased, as a group, in response to high substrate conditions. A specific biomarker for Type II methanotrophs was not found in this rice soil, even under high carbon, low O2 conditions, which resulted in methane exposure in the soil. Direct comparison of PLFA and substrate utilization patterns indicated that Biolog patterns are highly selective, and do not reflect compositional changes in soil communities.
The measurement of lipid phosphate is proposed as an indicator of microbial biomass in marine and estuarine sediments. This relatively simple assay can be performed on fresh, frozen or frozen-lyophilized sediment samples with chloroform methanol extraction and subsequent phosphate determination. The sedimentary lipid phosphate recovery correlates with the extractible ATP and the rate of DNA synthesis. Pulse-chase experiments show active metabolism of the sedimentary phospholipids. The recovery of added 14C-labeled bacterial lipids from sediments is quantitative. Replicate analyses from a single sediment sample gave a standard deviation of 11%. The lipid extract can be fractionated by relatively simple procedures and the plasmalogen, diacyl phospholipid, phosphonolipid and non-hydrolyzable phospholipid content determined. The relative fatty acid composition can be readily determined by gas-liquid chromatography.
The lipid composition can be used to define the microbial community structure. For example, the absence of polyenoic fatty acids indicates minimal contamination with benthic micro-eukaryotes. Therefore the high content of plasmalogen phospholipids in these sediments suggests that the anaerobic prokaryotic Clostridia are found in the aerobic sedimentary horizon. This would require anaerobic microhabitats in the aerated zones.
Phospholipid fatty acid (PLFA) profiles were measured in soils from organic, low-input, and conventional farming systems that
are part of the long term Sustainable Agriculture Farming Systems (SAFS) Project. The farming systems differ in whether their
source of fertilizer is mineral or organic, and in whether a winter cover crop is grown. Sustained increases in microbial
biomass resulting from high organic matter inputs have been observed in the organic and low-input systems. PLFA profiles were
compared to ascertain whether previously observed changes in biomass were accompanied by a change in the composition of the
microbial community. In addition, the relative importance of environmental variables on PLFA profiles was determined. Redundancy
analysis ordination showed that PLFA profiles from organic and conventional systems were significantly different from April
to July. On ordination plots, PLFA profiles from the low-input system fell between organic and conventional systems on most
sample dates. A group of fatty acids (i14:0, a15:0, 16:1ω7c, 16:1ω5c, 14:0, and 18:2ω6c) was enriched in the organic plots
throughout the sampling period, and another group (10Me16:0, 2OH 16:1 and 10Me17:0) was consistently lower in relative abundance
in the organic system. In addition, another group (15:0, a17:0, i16:0, 17:0, and 10Me18:0) was enriched over the short term
in the organic plots after compost incorporation. The relative importance of various environmental variables in governing
the composition of microbial communities could be ranked in the order: soil type > time > specific farming operation (e.g.,
cover crop incorporation or sidedressing with mineral fertilizer) > management system > spatial variation in the field. Measures
of the microbial community and soil properties (including microbial biomass carbon and nitrogen, substrate induced respiration,
basal respiration, potentially mineralizable nitrogen, soil nitrate and ammonium, and soil moisture) were seldom associated
with the variation in the PLFA profiles.
This review discusses the analysis of whole-community phospholipid fatty acid (PLFA) profiles and the composition of lipopolysaccharides
in order to assess the microbial biomass and the community structure in soils. For the determination of soil microbial biomass
a good correlation was obtained between the total amount of PLFAs and the microbial biomass measured with methods commonly
used for determinations such as total adenylate content and substrate-induced respiration. Generally, after the application
of multivariate statistical analyses, whole-community fatty acid profiles indicate which communities are similar or different.
However, in most cases, the organisms accounting for similarity or difference cannot be determined, and therefore artefacts
could not be excluded. The fatty acids used to determine the biomass vary from those which determine the community structure.
Specific attention has to be paid when choosing extraction methods in order to avoid the liberation of fatty acids from non-living
organic material and deposits, and to exclude the non-target selection of lipids from living organisms, as well. By excluding
the fatty acids which were presumed to be common and widespread prior to multivariate statistical analysis, estimates were
improved considerably. Results from principal component analysis showed that determining the levels of fatty acids present
in both low and high concentrations is essential in order to correctly identify microorganisms and accurately classify them
into taxonomically defined groups. The PLFA technique has been used to elucidate different strategies employed by microorganisms
to adapt to changed environmental conditions under wide ranges of soil types, management practices, climatic origins and different
perturbations. It has been proposed that the classification of PLFAs into a number of chemically different subgroups should
simplify the evaluating procedure and improve the assessment of soil microbial communities, since then only the subgroups
assumed to be involved in key processes would be investigated.
This paper summarises our recent field studies on the microbial communities of boreal coniferous forest humus exposed to environmental stress, heavy metals and changes in humus pH. The microbial community was measured using the phospholipid fatty acid (PLFA) and Biolog® analyses, and the actual factor in the environment exerting the selective pressure on the bacterial community was estimated with the help of tolerance determinations using the 3H-thymidine incorporation technique. The field experiments showed that the structure of the microbial community inhabiting the boreal coniferous forest humus was influenced by changes in humus pH and heavy metal concentrations at levels where no, or only small, effects on the microbial biomass or carbon mineralization rate were seen. The alterations in the humus PLFA patterns were related to the abundance of the major groups of microorganisms, bacteria and fungi. Changes in the relative proportions of Gram-negative and Gram-positive bacteria, including actinomycetes, were also shown. With the help of the 3H-thymidine incorporation technique, it was demonstrated that forest humus bacterial communities exposed to heavy metals or alterations in humus pH were able to adapt to the environmental disturbance in question. When combining the results from the PLFA and 3H-thymidine analyses, it was revealed that the increased tolerance of the humus bacterial community to heavy metals or to altered pH resulted at least partly from a change in microbial species composition. Coniferous forest humus seemed to contain a bacterial group, consisting mainly of Gram-positive bacteria, which were adapted more easily to the acidifying environment and a group of bacteria, mainly Gram-negative ones, which were more easily adapted to the humus with a higher pH. The Biolog® technique, which determines the community level physiological profile (CLPP) of the bacterial community was less sensitive and less suitable than the PLFA analysis to detect the characteristics of the forest humus microbial community. The 3H-thymidine incorporation technique was the most sensitive of the techniques used in this study to detect the influence of environmental disturbances on the microbial community. In addition, a gradient of coniferous forest stands having naturally different humus pH because of the different site properties was studied to compare these natural microbial communities with the communities subjected to anthropogenic change in humus pH. In order to reveal the similarity of the humus samples with respect to their community structure, the PLFA patterns from all the field studies were subjected to multivariate cluster analysis. The structure of the forest humus microbial community was shown to be strongly influenced by the indigenous fertility of the coniferous forest site type, which was in turn related to humus nutritional status, pH, moisture, tree species and ground vegetation. Thus, a prerequisite for successful determination of the impacts of environmental stress on forest humus microbial community is the homogeneity of the forest site types between the experimental plots.
Humus phospholipid fatty acid (PLFA) analysis was used in clear-cut, wood-ash fertilized (amounts applied: 1000, 2500, and 5000 kg ha−1), or prescribed burned (both in standing and clear-cut) coniferous forests to study the effects of treatments on microbial biomass and community structure. The microbial biomass (total PLFAs) decreased significantly due to the highest rate of wood-ash fertilization, clear-cutting, and the two different fire treatments when compared to control amounts. Fungi appeared more seriously reduced by these treatments than bacteria, as revealed by a decreased index of fungal:bacterial PLFAs when compared to the controls. The community structure was evaluated using the PLFA pattern. The largest treatment effect was due to burning in both areas studied, which resulted in increases in 16:1ω5 and proportional decreases in 18:2ω6. Clear-cutting and the different amounts of ash application resulted in similar changes in the PLFA pattern to the burning treatments, but these were less pronounced. Attempts to correlate the changes in the PLFA pattern to soil pH, bacterial pH response patterns (measured using thymidine incorporation), or substrate quality (measured using IR spectroscopy) were only partly successful. Instead, we hypothesize that the changes in the PLFA pattern of the soil organisms were related to an altered substrate quantity, that is the availability of substrates after the treatments.
Soil management practices that result in increased soil C also impact soil microbial biomass and community structure. In this study, the effects of dairy manure applications and inorganic N fertilizer on microbial biomass and microbial community composition were determined. Treatments examined were a control with no nutrient additions (CT), ammonium nitrate at 218 kg N ha−1 (AN), and manure N rates of 252 kg manure-N ha−1 (LM) and 504 kg manure-N ha−1 (HM). All plots were no-till cropped to silage corn (Zea mays, L. Merr) followed by a Crimson clover (Trifolium incarnatum, L.)/annual ryegrass (Lolium multiflorum, Lam.) winter cover crop. Treatments were applied yearly, with two-thirds of the N applied in late April or early May, and the remainder applied in September. Soil samples (0–5, 5–10, and 10–15 cm) were taken in March 1996, prior to the spring nutrient application. Polar lipid fatty acid (PLFA) analysis was used to assess changes in microbial biomass and community structure. Significantly greater soil C, N and microbial biomass in the 0–5 cm depth were observed under both manure treatments than in the CT and AN treatments. There was also a definable shift in the microbial community composition of the surface soils (0–5cm). Typical Gram-negative bacteria PLFA biomarkers were 15 and 27% higher in the LM and HM treatments than in the control. The AN treatment resulted in a 15% decrease in these PLFA compared with the control. Factor analysis of the polar lipid fatty acid profiles from all treatments revealed that the two manure amendments were correlated and could be described by a single factor comprised of typical Gram-negative bacterial biomarkers. The AN treatments from all three depths were also correlated and were described by a second factor comprised of typical Gram-positive bacterial biomarkers. These results demonstrate that soil management practices, such as manuring, that result in accumulations of organic carbon will result in increased microbial biomass and changes in community structure.
Two methods for the characterization of microbial communities in field soil samples were compared. Experimental subplots were established in the Farming Systems Trial at the Rodale Institute Research Center in Kutztown, PA, USA. In the legume system, plots receiving green manure (hairy vetch) were compared to those receiving corn stover and a small amount of rye residue. In the conventional system, samples were collected in plots where corn stover was incorporated. Carbon source utilization profiles were developed using Biolog plates, while total soil fatty acids were determined by fatty acid methyl ester analysis. Principal component analysis and canonical discriminate analysis were used to analyze the data. The two methods gave similar but not identical results. Management history had more effect than specific crop residue, but temporal effects were greater than treatment effects. Certain shifts in microbial communities were detected by fatty acid analysis but not by carbon utilization assay, suggesting that changes in microbial species composition occurred that were not accompanied by changes in microbial community function.
Analyses of polar lipid fatty acids isolated from soil are frequently used for characterization of microbial communities, and any interference from fatty acids derived from dead organic material is assumed to be negligible. We studied the initial extraction of lipid material from eight different soils and from purified humic acids using four different combinations of solvent (chloroform or dichloromethane), methanol and buffer (potassium phosphate, pH 7.4 or sodium citrate, pH 4). The quantitative yields of polar lipid fatty acids (PLFA) and PLFA composition of soils and humic acids were compared with absorbance spectra (200–850 nm) of lipid extracts for evaluation of extraction efficiency and potential interference. Chloroform + citrate buffer generally gave the highest, and dichloromethane + phosphate buffer the lowest PLFA yields, and it was estimated that <20% of the yield difference between extraction methods could be explained by interference from humic acids. Principal component analyses of PLFA composition suggested an effect of extraction method for several soils, but when all soils were analyzed together the differences between soils were much more important than the choice of extraction method. Co-extraction of lipids from living cells during preparation of humic acids was quantified and, correcting for this, it was estimated that the interference from non-microbial sources in PLFA analyses was probably not more than 5–10% with the extraction methods employed.
Fatty acid methyl esters (FAMEs) were used to ‘fingerprint’ soil microbial communities that evolved during 25 years of wheat-fallow cropping following native mixed prairie sod at Sidney, Nebraska, USA. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs) were compared for their ability to discriminate between plots remaining in sod and those cropped to wheat or left fallow under no-till, sub-till or plow management. Cropped plots were higher in microbial biomass than their fallowed counterparts, and did not differ significantly with tillage for the 0–15 cm depth. Under fallow, microbial biomass was greatest in no-till and least in plow. Both cluster and discriminant analysis of PL- and EL-FAMEs clearly separated the remaining native sod plots from the existing wheat-fallow plots. This separation was particularly pronounced for the EL-FAMEs and was largely driven by high amounts in sod of a single FAME, C16:1(cis11), which has been cited as a biomarker for arbuscular mycorrhizal (AM) fungi. Within wheat-fallow, C16:1(cis11) declined significantly from no-till to plow, which supports the origin of C16:1(cis11) from extraradical mycelium and spores of AM fungi known to be sensitive to soil disturbance. Although discriminant analysis of PL- and EL-FAMEs differentiated wheat and fallow systems by tillage, discrimination among tillage treatments was expressed most strongly during fallow. FAME profiles from fallow plow were most dissimilar from cropped soils which suggests a relationship between tillage management and the long-term resiliency of the microbial community developed under the wheat crop.
To explore the spatial variation of the soil microbial community within a mixed Norway spruce–birch stand, and to test if the spatial patterns of the microbial community are related to the position of trees, we sampled the forest floor at two spatial scales and used the phospholipid fatty acid (PLFA) patterns as indicators of the microbial community structure. Of the 32 most common PLFAs, 20 (62%) were clearly spatially autocorrelated, and the limit of spatial dependence (range) varied between 1 m and 11 m. The variation in the community structure was examined by subjecting the PLFAs to a principal component analysis. The first two principal components described variation structured at two different spatial scales. The range of the microbial community for the first component was 4.6 m, whereas for the second component it was only 1.5 m. The microbial community was influenced by the position of the trees. Spruce trees had a much stronger influence on PLFA patterns than birch trees, and the first principal component, as well as 12 PLFAs, was influenced by spruce trees. Several branched PLFAs, characteristic of Gram-positive bacteria, loaded negatively on the second principal component. These PLFAs represent a complex of associated microorganisms that aggregated in small patches away from birch trees. A comparison with a laboratory experiment suggests that although the tree species differ in their influence on soil moisture and ground vegetation, their influence on the microbial community were, to a large extent, connected to the quality of soil organic matter associated with the two trees.
Dynamics of microbial communities during two growing seasons were compared in soils under tomatoes managed by conventional (2- and 4-y rotations), low input, or organic practices. Fumigation extractable carbon (FEC) and nitrogen (FEN), potentially mineralizable N, arginine ammonification and substrate induced respiration (SIR) were significantly higher in organic and low input than conventional systems on most sample dates. Microbial variables were significantly negatively correlated with amounts of soil mineral N in the conventional 4 y system, whereas they were positively correlated with mineral N in the organic system. The C-to-N ratios of material released after fumigation extraction were significantly higher in the conventional than organic soils. In all farming systems, soil moisture was positively correlated with FEC or FEN, but negatively correlated with the C-to-N ratio of the microbial biomass and SIR. Soil temperature was negatively correlated with FEC and FEN, but positively correlated with the C-to-N ratio of microbial biomass.
Spatial characteristics of soil microbial community structure and selected soil chemical factors were analyzed in soil surrounding Agropyron smithii (Western wheatgrass) and Artemisia tridentata (Wyoming big sagebrush) plants in sites reclaimed after surface mining and adjacent undisturbed sites in Wyoming. Microbial biomass C (MBC) and fatty acid methyl ester (FAME) biomarkers for total biomass, bacteria, and fungi were used as indicators of soil microbial community abundance and structure. In soil 20 years after reclamation FAME total microbial biomass, bacterial and fungal biomarkers, MBC and soil organic matter (SOM) averaged only 20, 16, 28, 44 and 36% of values found in undisturbed soils. In contrast to undisturbed soils, FAME biomarkers and MBC of reclaimed soils exhibited spatial correlation up to 42 cm. Reclaimed soils also exhibited localized enrichment of bacterial, fungal, and total microbial biomass, as well as depletion of inorganic N concentrations, around plant bases (<10 cm), suggesting relatively poor soil exploration by roots and microorganisms compared to the undisturbed ecosystem. Strong spatial stratification of undisturbed SOM and soil NH4+ pools was found with highest concentrations on the leeward side of shrubs, likely due to localized changes in microclimate and plant litter deposition. This indicates that shrub cover plays a central role in the establishment of site heterogeneity and regulation of ecological processes, such as C and N mineralization and immobilization, which has important implications for reclamation.
"Little is konwn abou thte short-term effects (hours to days) of tillage on labile pools of C and N, or microbial activity and community composition. We examined the effects of rototillage on microbial biomass C (MBC) and N (MBN), respiratoin (i.e., soil CO2 production in 1-h incubations), CO2 efflux from the soil surface, inorganic N, nitriication potential, denitrification rate, and phospholipid fatty acids (PLFA).
We do not know how many bacterial species exist in the world, or in any particular environment, because bacteria cannot be differentiated under the microscope; we do not even know the right order of magnitude. Thus, up to a few years ago, discussions of bacterial diversity were unwarranted. However, the development of a phylogenetic system based on rRNA sequences has provided tools to approach bacterial diversity and ecology in situ for the first time.
The usefulness of measuring neutral lipid fatty acids (NLFAs) and phospholipid fatty acids (PLFAs) separately in order to interpret perturbation effects on soil and compost microorganisms has been studied. Initially the NLFA/PLFA ratios were studied in different soils. Low ratios were found for fatty acids common in bacteria, especially for cyclopropane fatty acids. Higher ratios were found for fatty acids common in eukaryotic organisms such as fungi (18:1omega9 and 18:2omega6,9) or in saturated fatty acids, common to many types of organisms. Adding glucose to a forest soil increased the amounts of the fungal NLFAs 18:1omega9 and 18:2 omega6,9 up to 60 and 10 times, respectively, after 10 days, followed by a gradual decrease. After 3 months incubation, higher levels of these NLFAs were still found compared with the control samples. Adding glucose together with nitrogen (N) and phosphorus (P) resulted in no increase in NLFAs but a 10-fold increase in the PLFAs 18:1omega9 and 18:2omega6,9. Thus, the NLFA/PLFA ratios for these fatty acids were lower than in the no-addition control when glucose was added together with N and P, but higher when glucose was added alone, even 3 months after the addition. Adding N+P without glucose did not affect the NLFA/PLFA ratio for any fatty acid. Increasing NLFA/PLFA ratios for the fungal fatty acids were also found with time after the thermophilic phase in a compost, indicating increased availability of easily available carbon.
Lipid decomposition studies in frozen fish have led to the development of a simple and rapid method for the extraction and purification of lipids from biological materials. The entire procedure can be carried out in approximately 10 minutes; it is efficient, reproducible, and free from deleterious manipulations. The wet tissue is homogenized with a mixture of chloroform and methanol in such proportions that a miscible system is formed with the water in the tissue. Dilution with chloroform and water separates the homogenate into two layers, the chloroform layer containing all the lipids and the methanolic layer containing all the non-lipids. A purified lipid extract is obtained merely by isolating the chloroform layer. The method has been applied to fish muscle and may easily be adapted to use with other tissues.Lipid decomposition studies in frozen fish have led to the development of a simple and rapid method for the extraction and purification of lipids from biological materials. The entire procedure can be carried out in approximately 10 minutes; it is efficient, reproducible, and free from deleterious manipulations. The wet tissue is homogenized with a mixture of chloroform and methanol in such proportions that a miscible system is formed with the water in the tissue. Dilution with chloroform and water separates the homogenate into two layers, the chloroform layer containing all the lipids and the methanolic layer containing all the non-lipids. A purified lipid extract is obtained merely by isolating the chloroform layer. The method has been applied to fish muscle and may easily be adapted to use with other tissues.
We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid "signatures" in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI-FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.
The analysis of microbial interactions and communities in situ
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Changes in soil fertility and biology during the transition from conventional to low-input and organic cropping systems
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Changes in soil fertility and biology during the transition from conventional to low-input and organic cropping systems
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