Changes In Phospholipid Fatty Acid Profiles Research Articles

Toward conceptual clarity: PLFA in warmed soils

Studies assessing shifts in soil nutrient cycling with warming benefit from microbial data collection with clear ecological hypotheses. However, the fact that many organisms alter their lipids to adjust to temperature complicates interpretation of the widely-used method of phospholipid fatty acid (PLFA) analysis. Changes in PLFA profiles may reflect shifts in community composition (i.e. relative abundance of microbial groups) or physiological change (i.e. the same groups after membrane optimization) or both. The various approaches presently used to interpret results from warming studies expose a need for greater conceptual clarity. We compile the various data metrics commonly used for PLFA and discuss their interpretations in the context of temperature-based studies. We propose that certain lipid ratios are likely to at least partially reflect decreased unsaturation and other warming-induced physiological shifts. A change in community composition may underlie warming results for both whole-community ordination and certain indicator lipids, provided that the effect of lipids commonly re-synthesized to maintain membrane fluidity are considered. Overall, conclusions in warming studies would be strengthened by explicit consideration of temperature-dependent lipid effects in data analysis. Further research is needed toward substantiating the interpretation of PLFA-based temperature response data as indicating community compositional or physiological change.

Root controls on soil microbial community structure in forest soils

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Microbial responses to simulated tillage in cultivated and uncultivated soils

Tillage is known to have long-term effects on organic matter and labile pools of nutrients in soil, but the short-term changes in microbial dynamics and activity after tillage are less well understood. We investigated the immediate effects of simulated tillage on microbial community structure as determined by phospholipid fatty acid (PLFA) profiles, microbial activity, and carbon (C) and nitrogen (N) pools. Intact cores were obtained from Chualar sandy loam soils under grassland and vegetable production. The top 15 cm of soil was sieved to simulate tillage, then the cores were incubated in the greenhouse. Sampling took place 1 day before the tillage simulation and throughout the next 2 weeks. In the grassland soil, multivariate analysis showed changes in PLFA profiles within hours, indicating rapid changes in microbial community structure. Specific PLFA markers indicated a reduction in microeukaryotic biomass as well as an increase in a microbial stress marker after sieving. Respiration (as determined by soil incubation in sealed containers) decreased immediately after sieving and continued to decline through the next 14 days. Sieving was followed by a continuous accumulation of nitrate. In the vegetable soil, the changes in PLFA profiles were slow and gradual. The PLFA stress indicator rose only slightly. Microbial activity and biomass were low, and only small changes occurred in most variables. A decline in respiration and an increase in nitrate occurred several days after sieving. In both soils, decreased soil moisture may have contributed to changes in soil responses after sieving. Short-term responses to tillage may be less pronounced in soils with a long history of cultivation because of a relatively resilient microbial community and/or because lower initial microbial biomass and nutrient pools preclude a strong response to disturbance.

Distribution and Composition of Microbial Populations in a Landfill Leachate Contaminated Aquifer (Grindsted, Denmark).

> Abstract To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use of the acridine orange direct count method (AODC). Numbers of dominant, specific groups of bacteria and total numbers of protozoa were measured by use of the most probable number method (MPN). Viable biomass estimates were obtained from measures of ATP and ester-linked phospholipid fatty acid (PLFA) concentrations. The estimated numbers of total bacteria by direct counts were relatively constant throughout the aquifer, ranging from a low of 4.8 x 10(6) cells/g dry weight (dw) to a high of 5.3 x 10(7) cells/g dw. Viable biomass estimates based on PLFA concentrations were one to three orders of magnitude lower with the greatest concentrations (up to 4 x 10(5) cells/g dw) occurring at the border of the landfill and in samples collected from thin lenses of clay and silt with sand streaks. Cell number estimates based on ATP concentrations were also found to be lower than the direct count measurements (<2.2 x 10(6) cells/g dw), and with the greatest concentrations close to the landfill. Methanogens (Archaea) and reducers of sulfate, iron, manganese, and nitrate were all observed in the aquifer. Methanogens were found to be restricted to the most polluted and reduced part of the aquifer at a maximum cell number of 5.4 x 10(4) cells/g dw. Populations of sulfate reducers decreased with an increase in horizontal distance from the landfill ranging from a high of 9.0 x 10(3) cells/g dw to a low of 6 cells/g dw. Iron, manganese, and nitrate reducers were detected throughout the leachate plume all at maximum cell numbers of 10(6) cells/g dw. Changes in PLFA profiles indicated that a shift in microbial community composition occurred with increasing horizontal distance from the landfill. The types and patterns of lipid biomarkers suggested that increased proportions of sulfate- and iron-reducing bacteria as well as certain microeukaryotes existed at the border of the landfill. The presence of these lipid biomarkers correlated with the MPN results. There was, however, no significant correlation between the abundances of the specific PLFA biomarkers and quantitative measurements of redox processes. The application of AODC, MPN, PLFA, and ATP analyses in the characterization of the extant microbiota within the Grindsted aquifer revealed that as distance increased from the leachate source, viable biomass decreased and community composition shifted. These results led to the conclusion that the landfill leachate induced an increase in microbial cell numbers by altering the subsurface aquifer so that it was conducive to the growth of methanogens and of iron-and sulfate-reducing bacteria and fungi.

Changes in Ester-Linked Phospholipid Fatty Acid Profiles of Subsurface Bacteria during Starvation and Desiccation in a Porous Medium

Ester-linked phospholipid fatty acid (PLFA) profiles of a Pseudomonas aureofaciens strain and an Arthrobacter protophormiae strain, each isolated from a subsurface sediment, were quantified in a starvation experiment in a silica sand porous medium under moist and dry conditions. Washed cells were added to sand microcosms and maintained under saturated conditions or subjected to desiccation by slow drying over a period of 16 days to final water potentials of approximately - 7.5 MPa for the P. aureofaciens and - 15 MPa for the A. protophormiae. In a third treatment, cells were added to saturated microcosms along with organic nutrients and maintained under saturated conditions. The numbers of culturable cells of both bacterial strains declined to below detection level within 16 days in both the moist and dried nutrient-deprived conditions, while direct counts and total PLFAs remained relatively constant. Both strains of bacteria maintained culturability in the nutrient-amended microcosms. The dried P. aureofaciens cells showed changes in PLFA profiles that are typically associated with stressed gram-negative cells, i.e., increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl fatty acids to their monoenoic precursors. P. aureofaciens starved under moist conditions showed few changes in PLFA profiles during the 16-day incubation, whereas cells incubated in the presence of nutrients showed decreases in the ratios of both saturated fatty acids to unsaturated fatty acids and cyclopropyl fatty acids to their monoenoic precursors. The PLFA profiles of A. protophormiae changed very little in response to either nutrient deprivation or desiccation. Diglyceride fatty acids, which have been proposed to be indicators of dead or lysed cells, remained relatively constant throughout the experiment. Only the A. protophormiae desiccated for 16 days showed an increase in the ratio of diglyceride fatty acids to PLFAs. The results of this laboratory experiment can be useful for interpreting PLFA profiles of subsurface communities of microorganisms for the purpose of determining their physiological status.