Standardizing methylation method during phospholipid fatty acid analysis to profile soil microbial communities

Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population

Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.

Soil organic carbon regulation by pH in acidic red soil subjected to long-term liming and straw incorporation

The manipulation of soil pH through liming and straw incorporation plays a pivotal role in influencing soil organic carbon (SOC) dynamics in acidic red soil. This study aimed to assess the impact of these practices on SOC and elucidate the relationship between SOC and pH. Over a 31-year field experiment, seven different fertilization treatments were implemented: unfertilized (CK), nitrogen and potassium fertilizers (NK), NK with lime (NKCa), nitrogen, phosphorous, and potassium fertilizers (NPK), NPK with lime (NPKCa), NPK with straw (NPKS), and NPKS with lime (NPKSCa). Results revealed that liming and straw incorporation significantly elevated soil pH by 0.13-0.73 units. Lime application boosted SOC and mineral-associated organic carbon (MAOC) by 20.2% and 28.7%, respectively, in NK treatment, whereas its impact on SOC in NPK and NPKS treatments were negligible. SOC witnessed a 17.1% increase with NPKS and a 15.2% increase with NPKSCa compared to NPK alone. Notably, NPKS and NPKSCa led to a significant surge in particulate organic carbon (POC) by 19.7% and 37.7%, respectively, albeit NPKSCa reduced MAOC by 14.9% relative to NPK. Linear regression analysis unveiled a positive correlation between POC and soil pH, while SOC and MAOC exhibited an initial rise at lower pH levels followed by stabilization as pH continuously increasing. A partial least squares path model showed two pathways through which pH influenced SOC: firstly, by positively affecting SOC through increasing Fe and Al oxides contents and enhanced aggregate stability, and secondly, by negatively influencing SOC through altered ratios of fungi/bacteria and Gram-positive bacteria/Gram-negative bacteria. In conclusion, the long-term effects of lime and straw application on SOC and MAOC were contingent upon soil pH, with more pronounced positive effects observed at lower pH levels. These findings underscore the importance of considering soil pH when implementing lime and straw strategies to mitigate acidification and regulate SOC in acidic red soil.

Head Space Single Drop Micro Extraction Gas Chromatography Flame Ionization Detection (HS-SDME-GC-FID) Method for the Analysis of Common Fatty Acids

Objectives

Post-marketing/surveillance studies show that most of the many vegetable oils that are sold with health-promoting claims or statements with high nutritional values and are beneficial against diseases are off-limits of related monographs/criteria. Defining the oil with a fast, cheap, and efficient analytical method is needed to express fatty acids in any herbal product to authenticate, trace, specify, and classify the content.The majority of the after marketing/surveillance studies shows that most of the many vegetable oils that are sold with health-promoting claims or statements with high nutritional values and are beneficial against diseases are off-limits of related monographs/criteria. Defining the oil with fast, cheap and efficient analytical method to express fatty acids in any herbal product, to authenticate, trace, specify and classify the content is needed.

Materials and Methods

Here, we define a new simple tool with a headspace single drop microextraction (HS-SDME) method coupled with a gas chromatography-flame ionization detector (GC-FID) for the analysis of common fatty acids (FAs) in oils. Linolenic acid, γ-linolenic acid, and linoleic acid in olive oil, thyme oil, and fish oil were determined. Derivatization was performed with 0.2 mL of 2 mol/L KOH in methanol to transfer the FAs of oils into their methyl esters (FAMEs). Then, FAMEs were extracted using a head space single drop, which is 2.0 μL of sodium dodecyl sulfate:1-butanol (1:3, v/v) mixture.

Results

The most suitable extraction condition was that 360 μL of the FAMEs, 2.0 mL vial, 0.07 g NaCl as a salting-out effect, 45 °C extraction temperature, and 35 min extraction time. The precision of the method was below 12%, with accuracy validated by the GC-FID reference method.The most suitable extraction condition was that 360 μL of the fatty acid methyl esters (FAMEs), 2.0 mL vial, 0.07 g NaCl as a salting-out effect, 45 °C extraction temperature, and 35 min extraction time. The precision of the method was below 12% with an accuracy validated by the GC-FID reference method.

Conclusion

The HS-SDME can be used effectively for extracting FAs from oils for improved analysis of other FAs. The method is of direct importance and relevance for the herbal, pharmaceutical, and cosmetics industries.The HS-SDME can be used for effectively for extracting fatty acids from oils for improved analysis of other fatty acids while the method is direct importance and relevance for herbal, pharmaceutical, cosmetics industry.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13157-023-01722-2.

Isotope-labeling in situ derivatization and HS-SPME arrow GC-MS/MS for simultaneous determination of fatty acids and fatty acid methyl esters in aqueous matrices

Fatty acids (FAs) and fatty acid methyl esters (FAMEs) co-occur in many samples, and analysis of both substance classes is frequently of high interest. To this end, this study introduces the first method for simultaneous determination of FAs and FAMEs including fully automated solvent-free solid-phase microextraction (SPME) arrow headspace extraction combined with isotope-labeling in situ FA derivatization with deuterated methanol (CD3OD). By using the chromatographic isotope effect (ΔRt = 0.03 min) and the + 3 m/z mass shift, FAs can be selectively differentiated from the FAMEs during gas chromatography tandem-mass spectrometry (GC-MS/MS) operated in the multiple reaction monitoring (MRM) aquisition mode. Additionally, an approach is presented to predict the retention times of deuterated compounds. Optimization of the derivatization conditions was accomplished by design of experiments and found to be 20 min, 50 °C, 4 v/v% CD3OD, and pH 2.1. During method validation, FAs and FAMEs were calibrated in different concentration ranges by standard addition in five real matrices and ultrapure water leading to good linearities and method detection limits for FAs ranging from 1-30 µg L-1 and for FAMEs from 0.003-0.72 µg L-1. FAs and FAMEs were detected in real samples from surface water, wastewater treatment plant effluent, and three different bioreactor samples and could be quantified in concentrations ranging from 2-1056 µg L-1 for FAs and 0.01-14 µg L-1 for FAMEs.

Effects of anthropogenic nitrogen additions and elevated CO2 on microbial community, carbon and nitrogen content in a replicated wetland

Anthropogenic deposition of nitrogen (N) and elevated CO₂ (_eaCO₂) are expected to increase continuously and rapidly in the near future and influence global carbon cycling. These parameters affect the ecosystem by regulating the microbial community and contribute to soil organic matter decomposition. The study was performed to understand the effects of N additions (4 and 6mgl^-1) and _eaCO₂ (700 ppm) on carbon (C)/nitrogen (N) content in the soil, microbial community, and plant biomass (Alternanthera philoxeroides species). The results showed that when the atmospheric CO₂ concentration was raised, the total organic carbon (TOC) in the soil statistically increased (P < 0.05) by 4% and 3% under low and high N additions respectively, while the inorganic carbon content also increased by 1% and 3% (P > 0.05) under the same conditions. The increase in the soil TOC content was a result of the movement of carbon from water to the soil due to the presence of vascular tissues of plants in the water. The redundancy analysis (RDA) results revealed that the presence of plant species was responsible for the carbon content increment in the soil. The plant biomass content increased by 30.96% (P = 0.081) and 31.36%, (P = 0.002) under low and high N addition respectively due to the increment in atmospheric CO₂. The nitrogen content in the plant species decreased (p > 0.05) by 8.62% and 6.25% at low and high N addition respectively when atmospheric CO₂ was raised. This suggests that soil microbes competed with the plants for inorganic nitrogen in the soil and the microbes used up the inorganic nitrogen before it got to the plants. The gram-positive bacteria and fungi population decreased under high N addition and _eaCO₂ while gram-negative bacteria increased, suggesting that N additions and _eaCO₂ affected the microbial function and correlated with the nitrogen reduction in the soil. The results from this study serve as a guide to researchers and stakeholders in making policies with regard to the constant increasing CO₂ concentration in the atmosphere.

Methylation procedures affect PLFA results more than selected extraction parameters

Microorganisms are key players in organic matter and nutrient cycles of terrestrial ecosystems. The analysis of microbial membrane lipids, phospholipid fatty acids (PLFAs) has strongly improved our understanding of how microbial processes contribute to these cycles. The analysis has proven to yield robust results, but adaptations of analytical parameters to laboratory needs might lead to pitfalls and impede comparability of PLFA results between different studies. Here, we show how a set of four analytical parameters (freeze-drying vs. field moist, amount of sample extracted, age of solvent mixture, and methylation methods) influence the quantitative and qualitative results of PLFA analysis. Freeze-drying vs. field moist samples and the amount of sample extracted had only minor effects on PLFA concentrations and recovery of the microbial community structure. Nevertheless, these parameters are important to consider, especially if treatment effects in an experiment are expected to be low. The use of a four weeks old extraction solution resulted in 12% lower PLFA concentrations as well as significant differences in the relative abundance of functional microbial groups. This suggests that extraction solution should be prepared on the day of extraction or that the different components of the extraction solution should be added sequentially to the sample. Most importantly, the choice of the methylation method led to differences in both, PLFA concentrations (35%) and the relative abundance of functional microbial groups, making comparisons between studies difficult. Our study provides a valuable ranking of parameters that need to be considered during PLFA method implementation in a laboratory and also highlights the fact that comparability of studies using different methylation methods might be limited.

The effect of hydrodynamics on the succession of autotrophic and heterotrophic organisms of biofilms in river ecosystems

Biofilms were cultivated for a 68-day period under different hydrodynamic conditions, and the effect of hydrodynamics on the succession of autotrophic and heterotrophic organisms of biofilms was investigated. Five obvious stages were observed during biofilm formation. At Stage I, the attachment of algae was delayed, especially under turbulent conditions. After Stage II, algal density and heterotrophic biomass of biofilms increased, which were obvious under turbulent flow. Therefore, the algal density and heterotrophic biomass of biofilms were largest under turbulent condition, followed by laminar condition, and then transitional condition. Diatoms were dominant in all flumes and were most abundant under turbulent conditions. The proportion of cyanobacteria was highest under laminar conditions. The ratio of aerobic to anaerobic bacteria decreased and their co-existence could facilitate the nitrification and denitrification in the biofilm. The ratio of monounsaturated fatty acids to saturated fatty acids was highest under turbulent conditions on the 15th day. While the ratio was highest under laminar condition on the 48th day, the high ratio indicates the high ability of biofilm to obtain nutrients, which affect the growth of algae. The regulation of hydrodynamics is a useful technology which can affect the growth of the microorganisms of biofilm, and further improve water quality.

Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time

Plant specialized metabolites play an important role in soil carbon (C) and nutrient fluxes. Through anti-microbial effects, they can modulate microbial assemblages and associated microbial-driven processes, such as nutrient cycling, so to positively or negatively cascade on plant fitness. As such, plant specialized metabolites can be used as a tool to supplant competitors. These compounds are little studied in bryophytes. This is especially notable in peatlands where Sphagnum mosses can dominate the vegetation and show strong interspecific competition. Sphagnum mosses form carpets where diverse microbial communities live and play a crucial role in Sphagnum fitness by regulating C and nutrient cycling. Here, by means of a microcosm experiment, we assessed to what extent moss metabolites of two Sphagnum species (S. fallax and S. divinum) modulate the competitive Sphagnum microbiome, with particular focus on microbial respiration. Using a reciprocal leachate experiment, we found that interactions between Sphagnum leachates and microbiome are species-specific. We show that both Sphagnum leachates differed in compound richness and compound relative abundance, especially sphagnum acid derivates, and that they include microbial-related metabolites. The addition of S. divinum leachate on the S. fallax microbiome immediately reduced microbial respiration (−95%). Prolonged exposition of S. fallax microbiome to S. divinum leachate destabilized the food web structure due to a modulation of microbial abundance. In particular, leachate addition decreased the biomass of testate amoebae and rotifers but increased that of ciliates. These changes did not influence microbial CO₂ respiration, suggesting that the structural plasticity of the food web leads to its functional resistance through the replacement of species that are functionally redundant. In contrast, S. fallax leachate neither affected S. divinum microbial respiration, nor microbial biomass. We, however, found that S. fallax leachate addition stabilized the food web structure associated to S. divinum by changing trophic interactions among species. The differences in allelopathic effects between both Sphagnum leachates might impact their competitiveness and affect species distribution at local scale. Our study further paves the way to better understand the role of moss and microbial specialized metabolites in peatland C dynamics.

Ongoing biodegradation of Deepwater Horizon oil in beach sands: Insights from tracing petroleum carbon into microbial biomass

Heavily weathered petroleum residues from the Deepwater Horizon (DwH) disaster continue to be found on beaches along the Gulf of Mexico as oiled-sand patties. Here, we demonstrate the ongoing biodegradation of weathered Macondo Well (MW) oil residues by tracing oil-derived carbon into active microbial biomass using natural abundance radiocarbon (¹⁴C). Oiled-sand patties and non-oiled sand were collected from previously studied beaches in Mississippi, Alabama, and Florida. Phospholipid fatty acid (PLFA) analyses illustrated that microbial communities present in oiled-sand patties were distinct from non-oiled sand. Depleted ¹⁴C measurements of PLFA revealed that microbes on oiled-sand patties were assimilating MW oil residues five years post-spill. In contrast, microbes in non-oiled sand assimilated recently photosynthesized carbon. These results demonstrate ongoing biodegradation of weathered oil in sand patties and the utility of ¹⁴C PLFA analysis to track the biodegradation of MW oil residues long after other indicators of biodegradation are no longer detectable.

Phospholipid fatty acid (PLFA) analysis for profiling microbial communities in offshore produced water

A method based on phospholipid fatty acid (PLFA) analysis for profiling microbial communities in offshore produced water was optimized. The operation parameters affecting final PLFA profiling performance from the solid phase extraction (SPE) purification and fatty acid methyl esters (FAMEs) yielding process were investigated. Under the selected conditions, 92.9%, 96.3% and 92.8% of the spiked phospholipid standards C16:1 (cis-9) PC, C18:1 (cis-9) PC, and C19:0 PC were recovered, respectively, using 10mL methanol as elution solvent on a non-commercial SPE column. Over 90% of spiked C19:0 PC was recovered before sample transesterification. Four parameters including alkaline reagent, volume of acid for neutralization, time and temperature for FAMEs derivatization were examined. Gas Chromatography-Mass Spectrometry (GC-MS) was used to analyze FAMEs and the method linearities, recoveries of 29 FAMEs during transesterification, detection limits, relative standard deviations were presented. The results provided valuable information for biological reservoir souring control.

Soil microbial community structure and catabolic activity are significantly degenerated in successive rotations of Chinese fir plantations

This study examined the hypotheses that soil microbial community composition and catabolic activity would significantly degenerated by consecutive monoculture in Chinese fir plantations. The phospholipid fatty acids (PLFA) and community level physiological profiles (CLPP) methods were used to assess the variations of soil microbial community among the first rotation Chinese fir plantation (FCP), the second rotation plantation (SCP) and the third rotation plantation (TCP). The total content of PLFA biomarkers was highest in FCP, followed by SCP, and TCP was the least detected. Conversely, the fungi/bacteria ratio significantly increased in the SCP and TCP soils. The average well-color development (AWCD) values significantly decreased (FCP > SCP > TCP). However, the sum of AWCD values of amino acids, carboxylic acids and phenolic compounds were higher significantly in the SCP and TCP soils than FCP soils, suggesting that the microflora feeding on acids gradually became predominant in the continuous monoculture plantation soils. Soil C/N ratio was one of the most important factors to soil microbial diversity. Both the PLFA and CLPP results illustrated the long-term pure plantation pattern exacerbated the microecological imbalance in the rhizospheric soils of Chinese fir, and markedly decreased the soil microbial community diversity and metabolic activity.

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors.

The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis.

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations.