Biology subjects

Klomp, R.

Publications and source records attributed to Klomp, R..

3 recordsLinked to original sources

bioRxiv2026

ANME-2a drive methane oxidation in brackish coastal sediments via multiple pathways

Methane is a powerful greenhouse gas. Typically, a large fraction of the methane formed in coastal sediments is removed via anaerobic methane oxidation (AOM). Here, we demonstrate the potential for a range of AOM pathways in brackish coastal sediments by ANME-2a archaea. At our study site, geochemical profiles indicate that AOM is primarily restricted to a shallow, metal-oxide-rich sulfate-methane transition zone (SMTZ). ANME-2a were the sole methanotrophs detected, and metatranscriptomics showed the highest expression levels of the ANME-2a genes in the SMTZ. AOM activity was observed in sediment incubations with various electron acceptors, including sulfate, metal oxides, and the organic matter analogue graphene oxide. Highest potential rates were observed in sediments from below the SMTZ, pointing towards fast stimulation of the deeper methanotrophic community when alleviating the electron acceptor limitation. The variety of AOM pathways and persistence of methanotrophs below the SMTZ likely contribute to the resilience of the microbial methane filter in brackish coastal sediments.

microbiology↗

bioRxiv2026

Potential for metal-coupled methane oxidation by Candidatus Methanocomedenaceae in coastal sediments

Anaerobic methanotrophic (ANME) archaea are important players in the microbial methane cycle, mitigating methane emissions from anoxic environments. ANME are found ubiquitously in methane-rich sediments, where they can couple anaerobic methane oxidation (AOM) to different electron acceptors such as sulfate, metal oxides, and natural organic matter (NOM). However, we still lack understanding of the geochemical niches and preferred metabolic pathways of most ANME subclades. Here, we investigated the genomic potential and ecophysiology of ANME-2a with respect to metal-dependent AOM in brackish metal-rich coastal sediments. We assembled several high-quality ANME MAGs from subclades with high strain heterogeneity and analyzed the genomic potential for metal-AOM. Additionally, we monitored long-term enrichments with various electron acceptors from the same sediments. Ultimately, we recovered 8 novel genomes of ANME-2a that clustered with an uncharacterized genus with only 2 representatives in public databases for which we propose the name Candidatus Methanoborealis. The analysis of the MAGs showed two different clusters within this genus; one comprising of MAGs from the Baltic Sea that showed high potential for extracellular electron transfer (EET) required for metal-AOM, and another cluster form more diverse environments with less EET potential. The Baltic Sea Ca. Methanoborealis were the only canonical methanotrophs in the incubations during active methane oxidation and metal reduction. Our results contribute to the understanding of the phylogenomic and metabolic diversity in ANME subclades, which will help to further characterize novel ANME lineages from complex sediment samples.

microbiology↗

bioRxiv2025

Seasonal dynamics of nitrification in the water column of marine Lake Grevelingen

Coastal ecosystems serve as vital connectors between land and ocean, and their nitrogen cycle and ammonium removal can be affected by various factors. During our seasonal sampling campaign in 2021, the eutrophic marine Lake Grevelingen exhibited high ammonium concentrations and low nitrification rates in the water column, except for a brief period in late summer. Our study revealed ammonium accumulation in the anoxic middle and bottom water layers due to restricted transport caused by water column stratification. Only when ammonium reached the oxic part of the water column, was a short-lived peak in nitrification activity and nitrifier abundance observed at the end of August. Amplicon sequencing indicated very low abundances of Nitrosococcus and Nitrospira (<0.2%) in March, while Nitrosomonas and Nitrospina peaked at the end of August with relative abundances of 2.5% and 1.3%, respectively. Archaea and archaeal ammonium oxidizers were found in very low abundances. Anammox 16S rRNA genes were not detected. Together, these observations suggest a limited role for nitrification in ammonium removal in marine Lake Grevelingen.

microbiology↗