Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean?

The first line of evidence is the presence of GDGTs, including crenarchaeol, in suspended particulate matter (SPM) at 83 m, the archaeal community of which is nearly exclusively composed of MG-II (>94% of archaeal reads) (table 1 in ref. 1) as determined by pyrosequencing. However, according to Lincoln et al.’s definition, all SPM samples <100 m do not contain sufficient archaeal reads (i.e., <1,000) (figure S6 and table S2 in ref. 1) to draw any conclusion. This low abundance of archaeal DNA is also evident from the absence of detectable MG-I 16S rRNA gene copies (figure 2 in ref. 1). It is, however, not surprising that GDGTs were detected in the 83-m SPM sample because the lipid tracers used are core lipids. Core lipids do not occur as such in living cells, where they contain polar sugar and phospho head groups (e.g., ref. 2). Thus, by definition core lipid GDGTs are derived from dead material. The second line of evidence is based upon relating the presence of monohexose GDGTs in two SPM samples (although not the crucial 83-m sample) with archaeal diversity data. Although this approach uses intact polar lipids, it has been shown that monohexose GDGTs are also poor tracers of living archaeal cells (3) because they have a turnover time in the order of thousands of years (4), de facto also representing dead material.This dominance of dead lipid material readily explains the absence of any correlation of total MG-I+MG-II DNA abundance with total GDGT abundance (r2 = 0.06 and 0.04 for 0.3- to 3-µm and 3- to 57-µm fractions, respectively). Furthermore, it explains the much higher abundance of GDGTs in the large particle fraction compared to the small fraction (16–490 vs. 1–20 pg/L), contrasting its lower total archaeal abundance (0.3–1.8 × 105 vs. 1–7 × 105 cells/L) (figure 2 in ref. 1). We conclude that both lines of evidence are based on a comparison of minute amounts of archaeal DNA (often below detection limit) with unsuitable lipid tracers.The dominance of dead material and low abundance of archaeal cells make it impossible to infer the lipid composition of uncultivated MG-II from these samples, let alone to extrapolate this to the global ocean. In contrast, other studies, using abundant archaeal DNA and more suitable phospholipid GDGTs, do show a good match between MG-I DNA abundance and crenarchaeol concentration and not with MG-II (3, 5). Nevertheless, members of the Marine Group III Euryarchaeota have been suggested to contribute to GDGTs 0–3 (3); thus, members of the MG-II may potentially contribute to this pool of GDGTs as well. However, based on the data and arguments of Lincoln et al. (1) this is impossible to infer. The jury is, therefore, still out

Ileal Mucosal and Fecal Pancreatitis Associated Protein Levels Reflect Severity of Salmonella Inflection in Rats

Background Microbial infections induce ileal pancreatitis-associated protein/regenerating gene III (PAP/RegIII) mRNA expression. Despite increasing interest, little is known about the PAP/RegIII protein. Therefore, ileal mucosal PAP/RegIII protein expression, localization, and fecal excretion were studied in rats upon Salmonella infection. Results Salmonella infection increased ileal mucosal PAP/RegIII protein levels in enterocytes located at the crypt-villus junction. Increased colonization and translocation of Salmonella was associated with higher ileal mucosal PAP/RegIII levels and secretion of this protein in feces. Conclusions PAP/RegIII protein is increased in enterocytes of the ileal mucosa during Salmonella infection and is associated with infection severity. PAP/RegIII is excreted in feces and might be used as a new and non-invasive infection marke

Impact of salinity and growth phase on alkenone distributions in coastal haptophytes

Batch cultures of Isochrysis galbana (strain CCMP 1323) and Chrysotila lamellosa (strain CCMP 1307) were grown at salinity values of ca. 10 to ca. 35 and the alkenone distributions determined for different growth phases. U-37(K ') values decreased slightly with salinity for C. lamellosa but were largely unaffected for I. galbana, except during the decline phase. The values decreased with incubation time in both species. The proportion of C-37:4, used as a proxy for salinity, increased in both species at 0.16-0.20% per salinity unit, except during the stationary phase for I. galbana. C-37:4 was much more abundant in C. lamellosa (30-44%) than in I. galbana (4-12%). Although our results suggest that salinity has a direct effect on alkenone distribution, growth phase and species composition should also have a marked impact, complicating the use of the distributions as a proxy for salinity in the marine environment

Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with elipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (elipid/water between -149 and -264‰) and chemoautotrophs (elipid/water between -217 and -275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature

Testing the alkenone D/H ratio as a paleo indicator of sea surface salinity in a coastal ocean margin (Mozambique Channel)

Reconstructing past ocean salinity is important for assessing paleoceanographic change and therefore past climatic dynamics. Commonly, sea water salinity reconstruction is based on planktonic foraminifera oxygen isotope values combined with sea surface temperature reconstruction. However, the approach relies on multiple proxies, resulting in rather large uncertainty and, consequently, relatively low accuracy of salinity estimates. An alternative tool for past ocean salinity reconstruction is the hydrogen isotope composition of long chain (C37) alkenones (dDalkenone). Here, we have applied dDalkenone to a 39 ka sedimentary record from the Eastern South African continental shelf in the Mozambique Channel, close to the Zambezi River mouth. Despite changes in global seawater dD related to glacial – interglacial ice volume effects, no clear changes were observed in the dDalkenone record throughout the entire 39 ka. The BIT index record from the same core, which provides information on relative contributions of soil organic matter (OM) vs. marine input, indicates high soil OM input during the glacial and low input during the Holocene. This suggests a more pronounced freshwater influence at the core location during the glacial, resulting in alkenones depleted in D during that time, thereby explaining the lack of a clear glacial-interglacial alkenone dD shift. The correlation between the BIT index and dDalkenone during the glacial period suggests that increased continental runoff potentially changed the growth conditions of the alkenone-producing haptophytes, promoting coastal haptophyte species with generally more enriched dDalkenone values. We therefore suggest that the application of dDalkenone for reconstructing past salinity in coastal settings may be complicated by changes in the alkenone-producing haptophyte community

Large effect of irradiance on hydrogen isotope fractionation of alkenones in <i>Emiliania huxleyi</i>

The hydrogen isotopic (dD) composition of long-chain alkenones produced by certain haptophyte algae has been suggested as a potential proxy for reconstructing paleo sea surface salinity. However, environmental parameters other than salinity may also affect the dD of alkenones. We investigated the impact of the level of irradiance on hydrogen isotopic fractionation of alkenones versus growth water by cultivating two strains of the cosmopolitan haptophyte Emiliania huxleyi at different light intensities. The hydrogen isotope fractionation decreased by approximately 40‰ when irradiance was increased from 15 to 200 µmol photons m-2 s-1 above which it was relatively constant. The response is likely a direct effect of photosystem I and II activity as the relationship of the fractionation factor a versus light intensity can be described by an Eilers–Peeters photosynthesis model. This irradiance effect is in agreement with published dD data of alkenones derived from suspended particulate matter collected from different depths in the photic zone of the Gulf of California and the eastern tropical North Pacific. However, haptophyte algae tend to bloom at relatively high light intensities (>500 µmol photons m-2 s-1) occurring at the sea surface, at which hydrogen isotope fractionation is relatively constant and not affected by changes in light intensity. Alkenones accumulating in the sediment are likely mostly derived from these surface water haptophyte blooms, when the largest amount of biomass is produced. Therefore, the observed irradiance effect is unlikely to affect the applicability of the hydrogen isotopic composition of sedimentary long chain alkenones as a proxy for paleosalinit

Solar city indicator: a methodology to predict city level PV installed capacity by combining physical capacity and socio-economic factors

Shifting to renewable sources of electricity is imperative in achieving global reductions in carbon emissions and ensuring future energy security. One technology, solar photovoltaics (PV), has begun to generate a noticeable contribution to the electricity mix in numerous countries. However, the upper limits of this contribution have not been explored in a way that combines both building-by-building solar resource appraisals with the city-scale socio-economic contexts that dictate PV uptake. This paper presents such a method, whereby a ‘Solar City Indicator’ is calculated and used to rank cities by their capacity to generate electricity from roof-mounted PV. Seven major UK cities were chosen for analysis based on available data; Dundee, Derby, Edinburgh, Glasgow, Leicester, Nottingham and Sheffield. The physical capacity of each city was established using a GIS-based methodology, exploiting digital surface models and LiDAR data, with distinct methodologies for large and small properties. Socio-economic factors (income, education, environmental consciousness, building stock and ownership) were chosen based on existing literature and correlation with current levels of PV installations. These factors were enumerated using data that was readily available across each city. Results show that Derby has the greatest potential of all the cities analysed, as it offers both good physical and socio-economic potential. In terms of physical capacity it was seen that over a 15 year payback period there are two plateaus, showing a marked difference in viability between small and large PV arrays. It was found that both the physical and socio-economic potential of a city are strongly influenced by the nature of the local building stock. This study also identifies areas where policy needs to be focused in order to encourage uptake and highlights factors limiting maximum PV uptake. While this methodology has been demonstrated using UK cities, it is equally applicable to any country where city data is available

Intestinally secreted C-type lectin Reg3b attenuates salmonellosis but not listeriosis in mice

The Reg3 protein family, including the human member designated pancreatitis-associated protein (PAP), consists of secreted proteins that contain a C-type lectin domain involved in carbohydrate binding. They are expressed by intestinal epithelial cells. Colonization of germ-free mice and intestinal infection with pathogens increase the expression of Reg3g and Reg3b in the murine ileum. Reg3g is directly bactericidal for Gram-positive bacteria, but the exact role of Reg3b in bacterial infections is unknown. To investigate the possible protective role of Reg3b in intestinal infection, Reg3b knockout (Reg3b-/-) mice and wild-type (WT) mice were orally infected with Gram-negative Salmonella enteritidis or Gram-positive Listeria monocytogenes. At day 2 after oral Listeria infection and at day 4 after oral Salmonella infection, mice were sacrificed to collect intestinal and other tissues for pathogen quantification. Protein expression of Reg3b and Reg3g was determined in intestinal mucosal scrapings of infected and noninfected mice. In addition, ex vivo binding of ileal mucosal Reg3b to Listeria and Salmonella was investigated. Whereas recovery of Salmonella or Listeria from feces of Reg3b-/- mice did not differ from that from feces of WT mice, significantly higher numbers of viable Salmonella, but not Listeria, bacteria were recovered from the colon, mesenteric lymph nodes, spleen, and liver of the Reg3b-/- mice than from those of WT mice. Mucosal Reg3b binds to both bacterial pathogens and may interfere with their mode of action. Reg3b plays a protective role against intestinal translocation of the Gram-negative bacterium S. enteritidis in mice but not against the Gram-positive bacterium L. monocytogenes

Seasonal variability in the abundance and stable carbon-isotopic composition of lipid biomarkers in suspended particulate matter from a stratified equatorial lake (Lake Chala, Kenya/Tanzania): Implications for the sedimentary record

We studied the distribution and stable carbon-isotopic (δ13C) composition of various lipid biomarkers in suspended particulate matter (SPM) from the water column of Lake Chala, a permanently stratified crater lake in equatorial East Africa, to evaluate their capacity to reflect seasonality in water-column processes and associated changes in the lake's phytoplankton community. This lake has large seasonal variation in water-column dynamics (stratified during wet seasons and mixing during dry seasons) with associated phytoplankton succession. We analyzed lipid biomarkers in SPM collected monthly at 5 depths (0–80 m) from September 2013 to January 2015. Seasonal variation in total phytoplankton biovolume is strongly reflected in the concentration of phytadienes, a derivative of the general photosynthetic pigment chlorophyll. The wax and wane of several specific biomarker lipids between June and December 2014 reflect pronounced phytoplankton succession after deep mixing, starting with a long and sustained chlorophyte bloom (reflected by C23:1, C25:1 and Cn-alkenes, and C21 and C23n-alkanes), followed by a peak in diatoms between July and October (loliolide and isololiolide), and then eustigmatophytes (C30 and C32 1,15 diols) once stratification resumes in October. Peak abundance of the C19:1n-alkene during shallow mixing of the water column in January–February 2014 can be tentatively linked to the seasonal distribution of cyanobacteria. The concentration, seasonal variability, and low δ13C values of the C28 fatty acid in the SPM suggest that this biomarker is produced in the water column of Lake Chala instead of having the typically assumed vascular plant origin. The δ13C signature of particulate carbon and all aquatic biomarkers become increasingly more negative (by up to 16‰) during mixing-induced episodes of high productivity, whereas enrichment would be expected during such blooms. This reversed fractionation may be attributed to chemically enhanced diffusion, which generates depleted HCO3− under high pH (>9) conditions, as occur in the epilimnion of Lake Chala during periods of high productivity. The influence of this process can potentially explain previously observed 13C-depleted carbon signatures in the paleorecord of Lake Chala, and should be considered prior to paleorecord interpretation of organic-matter δ13C values derived (partially) from aquatic organisms in high-pH, i.e. alkaline, lake

Structure and isotopic composition of bacterial lipids: insights into distribution and carbon acquisition mechanisms of bacteria in hot spring microbial mats

The results described in this thesis thus support the possibility that Precambrian organic matter enriched in l3C relative to what would be expected for organic matter produced by the Calvin cycle could be due to organisms using carbon fixation pathways other than the Calvin cycle