Phospholipid-derived Fatty Acids - The PLFA Components of Soil Microbiota

The PLFA Components of Soil Microbiota

Actinomycetes are Gram-positive bacteria that are some of the most common bacteria in soil, freshwater and marine environments. Actinomycetes are active in decomposition of organic matter and give rise to the rich “earthy” smell of freshly tilled soils. This group of bacteria produce distinctive biomarker fatty acids having a methyl branch at the 10th carbon, such as 16:0 10-methyl and 18:0 10-methyl. Some common species of soil actinomycetes include Rhodococcus, Nocardia, Corynebacterium and Streptomyces.

Gram-positive bacteria include aerobic Bacillus species especially those related to B. cereus and to B. subtilis. These bacteria are common in the bulk soil and increase in numbers in the rhizosphere. The PLFA profiles of these Gram-positive species have high percentages of biomarker branched-chain fatty acids such as 15:0 iso and 15:0 anteiso. Thus, the sum of the iso and anteiso fatty acids in a PLFA analysis may provide an estimate of the abundance of the Gram-positive bacteria (other than actinomycetes) in the sample.

Gram-negative bacteria are a major component of the plant rhizosphere and improve plant growth by increasing solubility of phosphate, producing ionophore compounds that increase uptake of iron or other minerals and may produce antifungal compounds. Gram-negative bacteria produce high levels of monounsaturated fatty acids (e.g. 16:1 omega-7 and 18:1 omega-9) during active metabolism but convert much of the unsaturated fatty acid composition to cyclopropane fatty acids (e.g. 17:0 cyclopropane and 19:0 cyclopropane) when metabolism and cell division slow due to shortage of nutrition or other stress. Thus, in PLFA analysis, the sum of monounsaturated and cyclopropane fatty acids may provide an estimate of the abundance of Gram-negative bacteria. A high ratio of cyclopropane to monounsaturated fatty acid indicates stress conditions.

Anaerobic bacteria in agriculture are primarily a factor in soils of low oxygen levels such as occur in greater depths or of wet conditions such as in rice paddies. Using PLFA analysis in early sampling, the bacteria- archaea consortia in rice paddy soil was about 44% aerobic bacteria, 32% facultatively anaerobic- bacteria and 24% archaea. Under longer term flooding, the levels were 27%, 36% and 37% respectively and with total biomass being significantly lower. Dimethyl acetals (DMA) formed during derivatization are considered to be biomarkers of anaerobic bacteria.

Archaea are universally distributed in soils and have been shown to control nitrification in acidic conditions and to contribute to ammonia oxidation in agricultural and forest soils. However, as the phospholipids of archaea are not ester linked as in bacteria, but are ether linked, they are not significantly present in routine PLFA sample preparation which is designed to cleave ester-linked fatty acids.

Arbuscular mycorrhizae fungi (AMF) penetrate the walls of cortical cells of about 80% of all vascular plant families, generating a symbiotic relationship. The fungi form membrane structures adjacent to the plant cell membrane allowing exchange of phosphorus, nitrogen compounds and minerals from the fungus and the plant provides the fungus primarily with photosynthesis-derived sugars. As the AMF are obligate symbiotic fungi, they are not free-living in the soil. The AMF hyphae in the root form lipid materials which then are transported to the hyphae that extend into the soil from the root and thus may occur in a soil sample. Vesicles are lipid storage organs of AMF and these and the hyphae in the soil contain the fatty acids 18:2 w6c (often used as an indicator of fungal content of the PLFA analysis) as well as containing the fatty acid 16:1 w5c which has been recommended as a biomarker for AMF.