Depth-related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota

The distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature-dependent in world oceans. Depth-related differences in the ammonia monooxygenase (amoA) of Thaumarchaeota have led to the classification of ‘shallow’ and ‘deep water’ clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate (GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amoA and GGGP synthase between ‘shallow’ and ‘deep water’ Thaumarchaeota. Intriguingly, amoA and GGGP synthase sequences of benthic Thaumarchaeota clustered with the ‘shallow water’ rather than with ‘deep water’ Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and ‘shallow water’ niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions

Sustainable Habitat Restoration: Fish, Farms, and Ecosystem Services

Biomass burning impacts biogeochemical cycling, vegetation dynamics and climate. However, interactions between fire, climate and vegetation are not well understood and therefore studies have attempted to reconstruct fire and vegetation history under different climatic conditions using sedimentary archives. Here we focus on levoglucosan, a thermal by-product of cellulose generated during biomass burning, and, therefore, a potential fire biomarker in the marine sedimentary archive. However, before levoglucosan can be applied as a biomass burning proxy in marine sediments, there is a need for studies on how levoglucosan is transported to the marine environment, how it is reflecting biomass burning on continents, as well as the fate of levoglucosan in the marine water column and during deposition in marine sediments. Here we present analyses of levoglucosan, using an improved Ultra High Pressure Liquid Chromatography-Electro Spray Ionization/High Resolution Mass Spectrometry (UHPLC-ESI/HRMS) method, in atmospheric particles, in particulate matter settling through the water column and in marine surface sediments on a longitudinal transect crossing the tropical North Atlantic Ocean at 12°N. Levoglucosan was detected in the atmosphere, although in low concentration, possibly due to the sampled particle size, the source area of the aerosols, or the short time interval of sampling by which large burning events may have been missed. In sinking particles in the tropical North Atlantic Ocean we find that levoglucosan deposition is influenced by a mineral ballast effect associated with marine biogenic particles, and that levoglucosan is not transported in association with mineral dust particles. Highest levoglucosan concentrations and seasonal differences in sinking particles were found close to continents and low concentrations and seasonal differences were found in the open ocean. Close to Africa, levoglucosan concentration is higher during winter, reflecting seasonal burning in northwestern Africa. However, close to South America levoglucosan concentrations appear to be affected by riverine transport from the Amazon River. In surface sediments close to South America, levoglucosan concentration is higher than in the middle of the Atlantic Ocean, implying that here the influence from the South American continent is important and perennial. Our study provides evidence that degradation of levoglucosan during settling in the marine water column is not substantial, but is substantial at the sediment–water interface. Nevertheless, levoglucosan was detected in all surface sediments throughout the tropical North Atlantic, indicating its presence in the marine sedimentary record, which reveals the potential for levoglucosan as a biomass burning proxy in marine sediments

Latitudinal differences in the amplitude of the OAE-2 carbon isotopic excursion: pCO2 and paleoproductivity [Discussion paper]

A complete, well-preserved record of the Cenomanian/Turonian (C/T) Oceanic Anoxic Event 2 (OAE-2) was recovered from Demerara Rise in the southern North Atlantic Ocean (ODP site 1260). Across this interval, we determined changes in the stable carbon isotopic composition of sulfur-bound phytane (δ13Cphytane, a biomarker for photosynthetic algae. The δ13Cphytane record shows a positive excursion at the onset of the OAE-2 interval, with an unusually large amplitude (~7 ‰) compared to existing C/T proto-North Atlantic δ13Cphytane records (3–6 ‰). Overall, the amplitude of the excursion of δ13Cphytane decreases with latitude. Using reconstructed sea surface temperature (SST) gradients for the proto-North Atlantic, we investigated environmental factors influencing the latitudinal δ13Cphytane gradient. The observed gradient is best explained by high productivity at DSDP Site 367 and Tarfaya basin before OAE-2, which changed in overall high productivity throughout the proto-North Atlantic during OAE-2. During OAE-2, productivity at site 1260 and 603B was thus more comparable to the mid-latitude sites. Using these constraints as well as the SST and δ13Cphytane-records from Site 1260, we subsequently reconstructed pCO2 levels across the OAE-2 interval. Accordingly, pCO2 decreased from ca. 1750 to 900 ppm during OAE-2, consistent with enhanced organic matter burial resulting in lowering pCO2. Whereas the onset of OAE-2 coincided with increased pCO2, in line with a volcanic trigger for this event, the observed cooling within OAE-2 probably resulted from CO2 sequestration in black shales outcompeting CO2 input into the atmosphere. Together these results show that the ice-free Cretaceous world was sensitive to changes in pCO2 related to perturbations of the global carbon cycle

Latitudinal differences in the amplitude of the OAE-2 carbon isotopic excursion : pCO2 and paleo productivity

A complete, well-preserved record of the Cenomanian/Turonian (C/T) Oceanic Anoxic Event 2 (OAE-2) was recovered from Demerara Rise in the southern North Atlantic Ocean (ODP site 1260). Across this interval, we determined changes in the stable carbon isotopic composition of sulfur-bound phytane (δ13Cphytane), a biomarker for photosynthetic algae. The δ13Cphytane record shows a positive excursion at the onset of the OAE-2 interval, with an unusually large amplitude (~7‰) compared to existing C/T proto-North Atlantic δ13Cphytane records (3–6‰). Overall, the amplitude of the excursion of δ13Cphytane decreases with latitude. Using reconstructed sea surface temperature (SST) gradients for the proto-North Atlantic, we investigated environmental factors influencing the latitudinal δ13Cphytane gradient. The observed gradient is best explained by high productivity at DSDP Site 367 and Tarfaya basin before OAE-2, which changed in overall high productivity throughout the proto-North Atlantic during OAE-2. During OAE-2, productivity at site 1260 and 603B was thus more comparable to the mid-latitude sites. Using these constraints as well as the SST and δ13Cphytane-records from Site 1260, we subsequently reconstructed pCO2 levels across the OAE-2 interval. Accordingly, pCO2 decreased from ca. 1750 to 900 ppm during OAE-2, consistent with enhanced organic matter burial resulting in lowering pCO2. Whereas the onset of OAE-2 coincided with increased pCO2, in line with a volcanic trigger for this event, the observed cooling within OAE-2 probably resulted from CO2 sequestration in black shales outcompeting CO2 input into the atmosphere. Together these results show that the ice-free Cretaceous world was sensitive to changes in pCO2 related to perturbations of the global carbon cycle

Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment

The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP. Nevertheless, this strategy is not universal among piezophiles, highlighting the need to further understand the effects of HHP on microbial lipid membranes. Challenges in the study of lipid membrane adaptations by piezophiles also involve methodological developments, cross-adaptation studies, and insight into slow-growing piezophiles. Moreover, the effects of HHP on piezophiles are often difficult to disentangle from effects caused by low temperature that are often characteristic of the deep sea. Here, we review the knowledge of membrane lipid adaptation strategies of piezophiles, and put it into the perspective of marine systems, highlighting the future challenges of research studying the effects of HHP on the microbial lipid composition

Discerning adaptive value of seasonal variation in preen waxes:comparative and experimental approaches

Birds possess a preen (or uropygial) gland on their rump that secretes substances which are preened into the plumage, and which are probably essential for plumage maintenance. Secretions of the uropygial gland consist predominantly of wax-esters: fatty acids esterified to alcohols. These wax components vary in chain length and in degree and location of branching of the carbon skeletons, resulting in complex mixtures of many different wax esters in preen gland secretions. We have found that shorebirds show pronounced seasonal changes in the composition of their preen waxes. Between arrival on and departure from breeding grounds, their usual monoester wax at winter quarters changes dramatically to a more complex diester-based wax, which is maintained throughout the breeding season. The diesters have higher molecular weights and probably different physical properties than monoesters, and the secretion and use of diesters rather than monoesters may entail specific costs and benefits. We discuss how natural and sexual selection could explain the evolution of compositional shifts in preen waxes and outline possible approaches for future research

数値地図データセットからの情報抽出および汎用地図ツールへの転用

We followed the abundance and distribution of ammonia-oxidizing Archaea (AOA) in the North Sea from April 2003 to February 2005 and from October 2007 to March 2008 by quantification of archaeal genes and core glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids in suspended particulate matter, to determine whether their abundance in the North Sea is seasonal. GDGT and gene abundance increased during winters and was low during the summer. Crenarchaeol-a GDGT specific to AOA-was a major fraction of the GDGTs and varied in concert with AOA gene abundance, indicating that AOA are the predominant source of crenarchaeol. The presence of crenarchaeol-based intact polar lipids (IPLs) confirmed that the GDGTs recovered were derived from living AOA, as IPLs are rapidly degraded upon cell senescence and thus their occurrence represents living biomass more robustly than their fossil (i.e., core GDGT) counterparts. Dark incubations of North Sea water sampled during the 2007-2008 seasonal cycle with C-13-labeled bicarbonate revealed incorporation of inorganic carbon into IPL-derived GDGTs, directly showing autotrophic production of Thaumarchaeota biomass during the winter. Inhibition of C-13 uptake by nitrification inhibitors confirmed that ammonia oxidation was the main source of energy for carbon fixation. Winter blooms of planktonic AOA in the North Sea were recurrent and predictable, occurring annually between November and February, emphasizing the potential importance of AOA in nitrogen cycling in the North Sea

Nitrification and growth of autotrophic nitrifying bacteria and Thaumarchaeota in the coastal North Sea

Nitrification and the associated growth of autotrophic nitrifiers, as well as the contributions of bacteria and Thaumarchaeota to total autotrophic C-fixation by nitrifiers were investigated in the Dutch coastal North Sea from October 2007 to March 2008. Rates of nitrification were determined by incubation of water samples with ¹⁵N-ammonium and growth of autotrophic nitrifiers was measured by incubation with ¹³C-DIC (dissolved inorganic carbon) in the presence and absence of nitrification inhibitors (nitrapyrin and chlorate) in combination with compound-specific stable isotope (¹³C) analysis of bacterial and Thaumarchaeotal lipid biomarkers. Net nitrification during the sampling period was evident from the concentration dynamics of ammonium, nitrite and nitrate. Measured nitrification rates were high (41–221 nmol N L^-1 h^-1). Ammonium assimilation was always substantially lower than nitrification – with nitrification on average contributing 89% (range 73–97%) to total ammonium consumption.¹³C-DIC fixation into bacterial and Thaumarchaeotal lipids was strongly reduced by the nitrification inhibitors (27–95 %). The inhibitor-sensitive ¹³C-PLFA (phospholipid-derived fatty acid) pool was dominated by the common PLFAs 16:0, 16:1?7c and 18:1?7c throughout the whole sampling period and occasionally also included the polyunsaturated fatty acids 18:2?6c and18:3?3. ¹³C-DIC fixation activity of the nitrifying bacteria was much higher than that of the nitrifying Thaumarchaeota throughout the whole sampling period, even during the peak in Thaumarchaeotal abundance and activity. This suggests that the contribution of autotrophic Thaumarchaeota to nitrification during winter in the coastal North Sea may have been smaller than expected from their gene abundance (16S rRNA and <i>amoA</i> (ammonia monooxygenase)). These results emphasize the importance of direct measurements of the actual activity of bacteria and Thaumarchaeota, rather than abundance measurements only, in order to elucidate their biogeochemical importance. The ratio between rates of nitrification versus DIC fixation by bacterial nitrifiers was higher or even much higher than typical values for autotrophic nitrifiers, indicating that little DIC was fixed relative to the amount of energy that was generated by nitrification