Acyl chain selection couples the consumption and synthesis of phosphoinositides

Phosphoinositides (PIPn) in mammalian tissues are enriched in the stearoyl/arachidonoyl acyl chain species ("C38:4"), but its functional significance is unclear. We have used metabolic tracers (isotopologues of inositol, glucose and water) to study PIPn synthesis in cell lines in which this enrichment is preserved to differing relative extents. We show that PIs synthesised from glucose are initially enriched in shorter/more saturated acyl chains, but then rapidly remodelled towards the C38:4 species. PIs are also synthesised by a distinct 're-cycling pathway', which utilises existing precursors and exhibits substantial selectivity for the synthesis of C38:4-PA and -PI. This re-cycling pathway is rapidly stimulated during receptor activation of phospholipase-C, both allowing the retention of the C38:4 backbone and the close coupling of PIPn consumption to its resynthesis, thus maintaining pool sizes. These results suggest that one property of the specific acyl chain composition of PIPn is that of a molecular code, to facilitate 'metabolic channelling' from PIP2 to PI via pools of intermediates (DG, PA and CDP-DG) common to other lipid metabolic pathways.

Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP

Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H₂ ¹⁸ O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.

Stable Isotope Probing of Microorganisms in Environmental Samples with H218O

We describe a protocol for investigating microbial growth in environmental samples via stable isotope probing (SIP) with H₂¹⁸O. Water is a universal substrate for all microorganisms and replication is required for DNA to become labeled with ¹⁸O. By measuring how much the DNA of each taxon becomes enriched with ¹⁸O when an environmental sample is incubated with H₂¹⁸O, it is feasible to quantify that population's DNA replication rate, which is a proxy for growth.

[Temporal Dynamics of Stable Isotopic Composition in Lake Taihu and Controlling Factors]

The composition of hydrogen and oxygen stable isotopes in lake water is important to the researches in hydrology, meteorology and paleoclimatology. In this study, long-term and continuous measurement on the compositions of HDO and H₂¹⁸O in lake water (δD_L and δ¹⁸O_L) was conducted over Lake Taihu, the deuterium excess (d_L) was calculated, and the temporal variability and controlling factors were analyzed. The results indicated that ① the variation of isotopic enrichment in lake water was significant, ranging from -59.8‰ to -24.2‰ for δD_L, from -8.6‰ to -2.6‰ for δ¹⁸O_L, and from -7.9‰ to 12.9‰ for d_L, respectively. In comparison to cold season, δD_L and δ¹⁸O_L were higher and d_L was lower during warm season. ② On monthly time-scale, lake evaporation and the ratio of total water inputs lost by evaporation controlled the isotopic enrichment in lake water. When lake evaporation or the ratio increased, δD_L and δ¹⁸O_L increased, but d_L decreased. ③ Over Lake Taihu, the isotopic composition in precipitation and water temperature did not control the isotopic enrichment. The results provide scientific reference for isotope hydrology and the researches related to the isotopic enrichment in lake water in meteorology and paleoclimate.

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218 O

Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.