van Bleijswijk Judith

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van Bleijswijk
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Judith
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  • Preprint
    Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea : a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids
    ( 2006-07-03) Coolen, Marco J. L. ; Abbas, Ben ; van Bleijswijk, Judith ; Hopmans, Ellen C. ; Kuypers, Marcel M. M. ; Wakeham, Stuart G. ; Sinninghe Damste, Jaap S.
    Within the upper 400 m at western, central, and eastern stations in the world’s largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alfa-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether (GDGT) of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 μM including layers where previously anammox bacteria were described (Kuypers et al., 2003). Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared to the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 μM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared to the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.
  • Preprint
    Archaeal nitrification in the ocean
    ( 2006-01-30) Wuchter, Cornelia ; Abbas, Ben ; Coolen, Marco J. L. ; Herfort, Lydie ; van Bleijswijk, Judith ; Timmers, Peer ; Strous, Marc ; Teira, Eva ; Herndl, Gerhard J. ; Middelburg, Jack J. ; Schouten, Stefan ; Sinninghe Damste, Jaap S.
    Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that they may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and show that it oxidizes ammonium to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with the decline in ammonium concentrations and with the abundance of Crenarcheota. Remarkably, the archaeal amoA abundance was 1-2 orders of magnitude higher than those of bacterial nitrifiers which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also one to three orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.
  • Article
    Planktonic marine fungi: A review
    (American Geophysical Union, 2024-03-03) Peng, Xuefeng ; Amend, Anthony S. ; Baltar, Federico ; Blanco-Bercial, Leocadio ; Breyer, Eva ; Burgaud, Gaetan ; Cunliffe, Michael ; Edgcomb, Virginia P. ; Grossart, Hans-Peter ; Mara, Paraskevi ; Masigol, Hossein ; Pang, Ka-Lai ; Retter, Alice ; Roberts, Cordelia ; van Bleijswijk, Judith ; Walker, Allison K. ; Whitner, Syrena
    Fungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of marine fungi has evolved over the past century. Currently, “marine fungi” are defined as any fungi recovered repeatedly from marine habitats that are able to grow and/or sporulate in marine environments, form symbiotic relationships with other marine organisms, adapt and evolve at the genetic level, or are active metabolically in marine environments. While there are a number of recent reviews synthesizing our knowledge derived from over a century of research on marine fungi, this review article focuses on the state of knowledge on planktonic marine fungi from the coastal and open ocean, defined as fungi that are in suspension or attached to particles, substrates or in association with hosts in the pelagic zone of the ocean, and their roles in remineralization of organic matter and major biogeochemical cycles. This review differs from previous ones by focusing on biogeochemical impacts of planktonic marine fungi and methodological considerations for investigating their diversity and ecological functions. Importantly, we point out gaps in our knowledge and the potential methodological biases that might have contributed to these gaps. Finally, we highlight recommendations that will facilitate future studies of marine fungi. This article first provides a brief overview of the diversity of planktonic marine fungi, followed by a discussion of the biogeochemical impacts of planktonic marine fungi, and a wide range of methods that can be used to study marine fungi.