SOIL MICROBIAL COMMUNITY ANALYSIS

Soil Testing

We understand your soil’s microbial health is important to you. Whether you’re optimizing soil for crop production, amending soil to its baseline after a forest fire, or researching the effects of climate change on soil, Microbial ID’s cutting-edge soil analysis services provide the answers you need.

Our soil microbial community analysis services include phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) analysis: 

  • Phospholipid fatty acid (PLFA) analysis identifies fatty acids from the “living” microbial biomass, including arbuscular mycorrhizal fungi (AMF) hyphae.
  • Neutral lipid fatty acid (NLFA) analysis identifies fatty acids from AMF spores.

AMF abundance can only be measured accurately through PLFA + NLFA analysis.

Unsure if soil testing can benefit you? Keep reading to learn how Microbial ID can help you meet your goals.

The Soil Microbiota: The Biological Engine of the Earth

Soil bacteria and fungi are responsible for many ecosystem functions, including plant growth regulation, nutrient cycling, and carbon sequestration.

These bacteria and fungi — including arbuscular mycorrhizal fungi (AMF) — are highly sensitive to soil-altering processes both degradative and beneficial. Changes can guide appropriate management procedures for either conservation or restoration.

Using the information provided by soil lipid analysis studies, you can take the appropriate steps to maintain and improve overall ecosystem health.

Microbial Lipids: Major Soil Health Quality Indicators

Phospholipids are an essential structural component of all microbial cell membranes, including those found in soil. Unlike DNA, which can be present in living or dead cells, phospholipids are present only in living soil microbes. Phospholipid fatty acids (PLFAs) are the main structural component of the phospholipid molecule. They serve as useful biomarkers to determine the living microbial types and abundance in the soil (e.g., branched chain fatty acids are a biomarker for Gram-positive bacteria).

Neutral lipids (mainly in the form of triglycerides) are an essential energy storage component of eukaryotic organisms. Neutral lipid fatty acids (NLFAs) are the main structural component of the neutral lipid molecule. In microbial community analysis, NLFAs are used to measure the abundance of arbuscular mycorrhizal fungi (AMF), the most widespread symbiont fungus, involved with 85% of land plants and many important crops.

Soil lipid analysis is crucial for soil microbial community analysis and plant productivity studies. Through PLFA + NLFA analysis, you can measure the “living” biomass, broad microbial community structure, and environmental stress impacts on soil in near real-time — meaning you can quickly measure the impact of various inputs on soil health.

The United States Department of Agriculture, Natural Resources Conservation Service (USDA-NRCS) recommends PLFA analysis as a key measure of soil health.

A High-Throughput Soil Lipid Extraction Method

However, before soil lipids can be analyzed, a long extraction process must take place. This isolates the phospholipid and neutral lipid fractions from the other plant and animal lipids present in the soil, and it isolates the fatty acids from those respective lipid fractions.

Soil lipid analysis is typically time-consuming and labor-intensive, requiring a large volume of reagents. With traditional PLFA analysis (not including NLFA), it can take 1.5 – 3 days to prepare a small batch (i.e., 20 – 24 samples and blanks), depending on the equipment used in the laboratory. Extraction requires considerable experience, and contamination is a potential major issue that must be minimized.

However, Microbial ID’s service lab uses a high-throughput PLFA extraction method co-developed by our sister company MIDI, Inc. and the USDA-ARS Sustainable Agriculture Systems Laboratory to isolate and analyze PLFAs and NLFAs. This method yields a 500% increase in throughput and tenfold reduction in reagent use versus traditional PLFA and NLFA extraction methods, and the results are equivalent to traditional methods.

Expert Analysis of Soil PLFA & NLFA

Even after the extraction method, many different gas chromatography (GC) and gas chromatography–mass spectroscopy (GC/MS) methods and instrument platforms are used for PLFA & NLFA analysis. However, most of them require great expertise and time to interpret the complex data. Recognizing and separating out background contamination from the microbial lipid information of interest is also a challenge.

At Microbial ID, we use a platform that we co-developed — one that has been optimized for soil PLFA and NLFA extraction and analysis. We coupled a proven high-throughput soil lipid extraction method to the well-established MIDI Sherlock™ PLFA Analysis System.

Our protocol objectively names PLFAs and NLFAs, quantitates them with the appropriate internal standard, and provides you with a detailed report of all fatty acids in the sample. The Sherlock software even removes background contamination from the extraction process, leading to more accurate, reproducible, and cleaner results.

Our reports provide customers with the raw data, total microbial biomass (nmol/g), biomass of each fatty acid (nmol/g) and key biomass ratios (e.g., fungi:bacteria).