Showing papers by "W. Irene C. Rijpstra published in 2004"

Stable carbon isotopic Fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria

Abstract: Anaerobic ammonium oxidation (anammox) is the oxidation of ammonium with nitrite as the electron acceptor and dinitrogen gas as the product (for reviews, see references 7 and 8). The process is mediated by obligately anaerobic chemolithoautotrophic bacteria that form a monophyletic cluster inside the Planctomycetales, one of the major divisions of the Bacteria. So far, four species have been detected and enriched from the biomass of sewage treatment plants: Candidatus “Brocadia anammoxidans” (18), Candidatus “Kuenenia stuttgartiensis” (13), Candidatus “Scalindua wagneri,” and Candidatus “Scalindua brodae” (14). Candidatus “Scalindua sorokinii” was detected in the anoxic water column of the Black Sea (9), providing the first direct evidence for anammox bacteria in the natural environment. Anammox bacteria have a cell compartment known as the anammoxosome, which is the site of anammox catabolism. The lipid bilayer membrane surrounding this anammoxosome contains unusual lipids, so-called “ladderane” lipids, concatenated cyclobutane moieties that are either ether and/or ester linked to the glycerol backbone or occur as free alcohols (e.g., Fig. ​Fig.1,1, structures II to IV) (16). The other membranes of anammox bacteria contain lipids typical for planctomycetes in general: iso, normal, and mid-chain methyl hexadecanoic acids (e.g., Fig. ​Fig.1,1, structure I). FIG. 1. Structure of anammox lipids, i.e., branched fatty acids (I), ladderane fatty acids (II), ladderane glycol ether (III), ladderane glycerol ether (IV), and hop-17(21)-ene (V), present in the enrichment culture of Candidatus “Brocadia anammoxidans.” ... Anammox bacteria have been shown to be chemoautotrophic organisms (17), but it is still unclear which carbon fixation pathway they use. There are currently four known pathways for CO2 fixation in microorganisms (see, e.g., references 2 and 3). The Calvin cycle, with ribulose bisphosphate carboxylase as a key enzyme, is operative in many organisms. The 3-hydroxypropionate pathway has been observed in Chloroflexus aurantiacus and some archaea. The reverse citric acid cycle, with citrate lyase as a key enzyme, has been found in some sulfate-reducing bacteria and phototrophic bacteria. Finally, the acetyl coenzyme A (acetyl-CoA) pathway, with carbon monoxide dehydrogenase/acetyl-CoA synthase as the indicative enzyme, is detected in many anaerobic microorganisms. In addition to enzyme activities, stable carbon isotopic compositions of total cell material and individual lipids, carbohydrates, and amino acids are often used to infer these biosynthetic pathways in organisms, as the fractionation from the inorganic carbon source to the autotrophic biomass in 13C depends on the biosynthetic pathway used (1, 19, 20, 21). Here, we determined enzyme activities and studied the stable carbon isotopic fractionations of Candidatus “Brocadia anammoxidans” to investigate its carbon fixation pathway. Since this bacterium can be grown only in enrichment cultures, and bulk cell material is thus not solely derived from anammox bacteria, we also determined the isotopic compositions of the specific lipids of this bacterium. Furthermore, the isotopic compositions of ladderane lipids derived from Candidatus “Scalindua sorokinii” growing in the anoxic water column of the Black Sea (9) were determined in order to examine the 13C fractionation patterns of anammox bacteria under natural conditions.

Total organic carbon content and redox-sensitiv trace metal concentrations of selected late Cenoman claystones from DSDP Hole 93-603B, supplement to: Kuypers, Marcel MM; Lourens, Lucas Joost; Rijpstra, W Irene C; Pancost, Richard D; Nijenhuis, Ivar A; Sinninghe Damsté, Jaap S (2004): Orbital forcing of organic carbon burial in the proto-North Atlantic during oceanic anoxic event 2. Earth and Planetary Science Letters, 228(3-4), 465-482

Abstract: The Cenomanian/Turonian (C/T) intervals at DSDP Sites 105 and 603B from the northern part of the proto-North Atlantic show high amplitude, short-term cyclic variations in total organic carbon (TOC) content. The more pronounced changes in TOC are also reflected by changes in lithology from green claystones (TOC 1%). Although their depositional history was different, the individual TOC cycles at Sites 105 and 603B can be correlated using stable carbon isotope stratigraphy. Sedimentation rates obtained from the isotope stratigraphy and spectral analyses indicate that these cycles were predominately precession controlled. The coinciding variations in HI, OI, delta13Corg and the abundance of marine relative to terrestrial biomarkers, as well as the low abundance of lignin pyrolysis products generated from the kerogen of the black claystones, indicate that these cyclic variations reflect changes in the contribution of marine organic matter (OM). The cooccurrence of lamination, enrichment of redox-sensitive trace metals and presence of molecular fossils of pigments from green sulfur bacteria indicate that the northern proto-North Atlantic Ocean water column was periodically euxinic from the bottom to at least the base of the photic zone (<150 m) during the deposition of the black claystones. In contrast, the green claystones are bioturbated, are enriched in Mn, do not show enrichments in redox-sensitive trace metals and show biomarker distributions indicative of long oxygen exposure times, indicating more oxic water conditions. At the same time, there is evidence (e.g., abundance of biogenic silica and significant 13C-enrichment for OC of phytoplanktic origin) for enhanced primary productivity during the deposition of the black claystones. We propose that increased primary productivity periodically overwhelmed the oxic OM remineralisation potential of the bottom waters resulting in the deposition of OM-rich black claystones. Because the amount of oxygen used for OM remineralisation exceeded the amount supplied by diffusion and deep-water circulation, the northern proto-North Atlantic became euxinic during these periods. Both Sites 105 and 603B show trends of continually increasing TOC contents and HI values of the black claystones up section, which most likely resulted from both enhanced preservation due to increased anoxia and increased production of marine OM during oceanic anoxic event 2 (OAE2).