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Methylotetracoccus oryzae strain C50C1 is a novel type Ib gammaproteobacterial methanotroph adapted to freshwater environments

Ghashghavi, Mohammad (author), Belova, Svetlana E. (author), Bodelier, Paul L.E. (author), Dedysh, Svetlana N. (author), Kox, Martine A.R. (author), Speth, Daan R. (author), Frenzel, Peter (author), Jetten, M.S.M. (author), Lücker, Sebastian (author), Lüke, Claudia (author)

Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia...

journal article 2019

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Comparative genomics of Candidatus Methylomirabilis species and description of Ca. Methylomirabilis lanthanidiphila

Versantvoort, Wouter (author), Guerrero-Cruz, Simon (author), Speth, Daan R. (author), Frank, J. (author), Gambelli, Lavinia (author), Cremers, Geert (author), van Alen, Theo (author), Jetten, M.S.M. (author), Kartal, Boran (author), Op den Camp, Huub J.M. (author), Reimann, Joachim (author)

Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium 'Candidatus Methylomirabilis oxyfera,' a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of 'Ca. M. oxyfera' with cerium...

journal article 2018

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Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria

Ferousi, Christina (author), Lindhoud, S. (author), Baymann, Frauke (author), Kartal, Boran (author), Jetten, M.S.M. (author), Reimann, Joachim (author)

The most abundant transition metal in biological systems is iron. It is incorporated into protein cofactors and serves either catalytic, redox or regulatory purposes. Anaerobic ammonium oxidizing (anammox) bacteria rely heavily on iron-containing proteins – especially cytochromes – for their energy conservation, which occurs within a unique...

review 2017

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McrA primers for the detection and quantification of the anaerobic archaeal methanotroph ‘Candidatus Methanoperedens nitroreducens’

Vaksmaa, Annika (author), Jetten, M.S.M. (author), Ettwig, Katharina F. (author), Lüke, Claudia (author)

The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are...

journal article 2017

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Reverse Methanogenesis and Respiration in Methanotrophic Archaea

Timmers, Peer H.A. (author), Welte, Cornelia U. (author), Koehorst, Jasper J. (author), Plugge, Caroline M. (author), Jetten, M.S.M. (author), Stams, Alfons J M (author)

Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., "trace methane oxidation"). In turn, ANME can produce methane, but only...

review 2017

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Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

Speth, Daan R. (author), Lagkouvardos, Ilias (author), Wang, Yong (author), Qian, Pei Yuan (author), Dutilh, Bas E. (author), Jetten, M.S.M. (author)

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using...

journal article 2017

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Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment

Rasigraf, Olivia (author), Schmitt, Julia (author), Jetten, M.S.M. (author), Lüke, Claudia (author)

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was...

journal article 2017

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Enrichment of anaerobic nitrate-dependent methanotrophic ‘Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil

Vaksmaa, Annika (author), Guerrero-Cruz, Simon (author), van Alen, Theo A. (author), Cremers, Geert (author), Ettwig, Katharina F. (author), Lüke, Claudia (author), Jetten, M.S.M. (author)

Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and...

journal article 2017

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Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone

Lüke, Claudia (author), Speth, Daan R. (author), Kox, Martine A R (author), Villanueva, Laura (author), Jetten, M.S.M. (author)

Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and...

journal article 2016

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Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

Speth, Daan R. (author), In'T Zandt, Michiel H. (author), Guerrero-Cruz, Simon (author), Dutilh, Bas E. (author), Jetten, M.S.M. (author)

Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment...

journal article 2016

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Immunogold localization of key metabolic enzymes in the anammoxosome and on the tubule-like structures of Kuenenia stuttgartiensis

De Almeida, N.M. (author), Neumann, S. (author), Mesman, R.J. (author), Ferousi, C. (author), Keltjens, J.T. (author), Jetten, M.S.M. (author), Kartal, B. (author), Van Niftrik, L. (author)

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound “prokaryotic organelle” called the anammoxosome. The anammoxosome occupies most of the cell volume, has...

journal article 2015

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Draft Genome Sequence of Anammox Bacterium “Candidatus Scalindua brodae,” Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

Speth, D.R. (author), Russ, L. (author), Kartal, B. (author), Op den Camp, H.J.M. (author), Dutilh, B.E. (author), Jetten, M.S.M. (author)

We present the draft genome of anammox bacterium “Candidatus Scalindua brodae,” which at 282 contigs is a major improvement over the highly fragmented genome assembly of related species “Ca. Scalindua profunda” (1,580 contigs) which was previously published.

journal article 2015

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Lysozyme and Penicillin Inhibit the Growth of Anaerobic Ammonium-Oxidizing Planctomycetes

Hu, Z. (author), Van Alen, T. (author), Jetten, M.S.M. (author), Kartal, B. (author)

Anaerobic ammonium-oxidizing (anammox) planctomycetes oxidize ammonium in the absence of molecular oxygen with nitrite as the electron acceptor. Although planctomycetes are generally assumed to lack peptidoglycan in their cell walls, recent genome data imply that the anammox bacteria have the genes necessary to synthesize peptidoglycan-like cell...

journal article 2013

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Nitrogen Removal by a Nitritation-Anammox Bioreactor at Low Temperature

Hu, Z. (author), Lotti, T. (author), De Kreuk, B.M. (author), Kleerebezem, R. (author), Van Loosdrecht, M. (author), Kruit, J. (author), Jetten, M.S.M. (author), Kartala, B. (author)

Currently, nitritation-anammox (anaerobic ammonium oxidation) bioreactors are designed to treat wastewaters with high ammonium concentrations at mesophilic temperatures (25 to 40°C). The implementation of this technology at ambient temperatures for nitrogen removal from municipal wastewater following carbon removal may lead to more-sustainable...

journal article 2013

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How to make a living from anaerobic ammonium oxidation

Kartal, B. (author), De Almeida, N.M. (author), Maalcke, W.J. (author), Op den Camp, H.J.M. (author), Jetten, M.S.M. (author), Keltjens, J.T. (author)

Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It...

journal article 2013

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Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

Gori, F. (author), Tringe, S.G. (author), Folino, G. (author), Van Hijum, S.A.F.T. (author), Op den Camp, H.J.M. (author), Jetten, M.S.M. (author), Marchiori, E. (author)

Background Sequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this paper we investigate how well different technologies represent information related to a considered organism of interest in a...

journal article 2013

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Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway

Kampschreur, M.J. (author), Kleerebezem, R. (author), Picioreanu, C. (author), Bakken, L. (author), Bergaust, L. (author), De Vries, S. (author), Jetten, M.S.M. (author), Van Loosdrecht, M.C.M. (author)

journal article 2012

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Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway

Kampschreur, M.J. (author), Kleerebezem, R. (author), Picioreanu, C. (author), Bakken, L. (author), Bergaust, L. (author), De Vries, S. (author), Jetten, M.S.M. (author), Van Loosdrecht, M.C.M. (author)

A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response...

journal article 2012

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The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

Van de Vossenberg, J. (author), Woebken, D. (author), Maalcke, W.J. (author), Wessels, H.J.C.T. (author), Dutllh, B.E. (author), Kartal, B. (author), Janssen-Megens, E.M. (author), Roeselers, G. (author), Yan, J. (author), Speth, D. (author), Gloerich, J. (author), Geerts, W. (author), Van der Blezen, E. (author), Pluk, W. (author), Francoijs, K.J. (author), Russ, L. (author), Lam, P. (author), Malfatti, S.A. (author), Green Tringe, S. (author), Haaijer, S.C.M. (author), Op den Camp, H.J.M. (author), Stunnenberg, H.G. (author), Amann, R. (author), Kuypers, M.M.M. (author), Jetten, M.S.M. (author)

Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species...

journal article 2012

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Effects of Nitrogen Dioxide and Anoxia on Global Gene and Protein Expression in Long-Term Continuous Cultures of Nitrosomonas eutropha C91

Kartal, B. (author), Wessels, H.J. C. T. (author), Van der Biezen, E. (author), Francoijs, K.J. (author), Jetten, M.S.M. (author), Klotz, M.G. (author), Stein, L.Y. (author)

Nitrosomonas eutropha is an ammonia-oxidizing betaproteobacterium found in environments with high ammonium levels, such as wastewater treatment plants. The effects of NO2 on gene and protein expression under oxic and anoxic conditions were determined by maintaining N. eutropha strain C91 in a chemostat fed with ammonium under oxic, oxic-plus-NO2...

journal article 2012