Biology subjects

Op den Camp, H. J. M.

Publications and source records attributed to Op den Camp, H. J. M..

5 recordsLinked to original sources

bioRxiv2022

Methanotrophs are vigorous H2S oxidizers using a sulfide:quinone oxidoreductase and a ba3-type terminal oxidase

Hydrogen sulfide (H2S) is produced in a wide range of anoxic environments where sulfate (SO42-) reduction is coupled to decomposition of organic matter. In the same environments, methane (CH4) is the end product of an anaerobic food chain and both H2S and CH4 diffuse upwards into oxic zones where aerobic microorganisms can utilize these gases. Methane-oxidizing bacteria are known to oxidize a major part of the produced CH4 in these ecosystems, mitigating the emissions of this potent greenhouse gas to the atmosphere. However, how methanotrophy is affected by toxic H2S is largely unexplored. Here, we show that a single microorganism can oxidize CH4 and H2S simultaneously. By oxidizing H2S, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV can alleviate the inhibitory effects on CH4 oxidation. In response to H2S, strain SolV upregulated a type III sulfide:quinone oxidoreductase (SQR) and a sulfide-insensitive ba3-type terminal oxidase to dissipate the reducing equivalents derived from H2S oxidation. Through extensive chemostat cultivation of M. fumariolicum SolV we demonstrate that it converts high loads of H2S to elemental sulfur (S0). Moreover, we show chemolithoautotrophy by tracing 13CO2 fixation into new biomass by using H2S as sole energy source. Molecular surveys revealed several putative SQR sequences in a range of proteobacterial methanotrophs from various environments, suggesting that H2S detoxification is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in new ways.

microbiology↗

bioRxiv2022

An alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs: Primer design for folD and ftfL and transformation of E. coli

Methylotrophs make a living by using one-carbon compounds as energy and carbon source. Methanol (CH3OH) is utilized by various methylotrophs and is oxidized by a methanol dehydrogenase. The calcium-dependent methanol dehydrogenase MxaFI converts methanol to formaldehyde (CH2O). In addition to MxaFI, the lanthanide-dependent methanol dehydrogenase XoxF is found in a wide range of bacteria. XoxF isolated from the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV possesses an unusually high affinity for both methanol and formaldehyde and converts methanol to formate (HCOOH) in vitro. However, genomic analyses and biochemical studies on related XoxF methanol dehydrogenases have questioned whether these enzymes are dedicated to the conversion of formaldehyde to formate in vivo. Instead, the genes encoding the bifunctional enzyme FolD and the enzyme FtfL, which we detected in all verrucomicrobial methanotrophs, were proposed to form a formaldehyde oxidation pathway utilizing tetrahydrofolate as C1-carrier. folD and ftfL are expressed in M. fumariolicum SolV and most closely related to homologues found in the phyla Verrucomicrobia and Proteobacteria, respectively. Here, we designed primers targeting Mf-folD and Mf-ftfL and amplified these genes through PCR. The amplified genes were ligated into pET30a(+) vectors which were subsequently used for the successful transformation of E. coli XL1-Blue cells. The vectors can be used for heterologous expression and subsequent His-tag purification to biochemically investigate whether FolD and FtfL could form an alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs.

microbiology↗

bioRxiv2022

Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs. HighlightsO_LIParacetamol was fully degraded by activated sludge from hospital wastewater. C_LIO_LILow paracetamol concentrations were removed by a diverse microbial community. C_LIO_LIPseudomonas sp. dominated cultures with high paracetamol concentration. C_LIO_LIUncharacterized amidases are probably involved in degrading paracetamol in WWTPs. C_LIO_LIDeaminases and dioxygenases might be degrading paracetamol transformation products. C_LI

microbiology↗

bioRxiv2020

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other countries, is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the active layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled at different locations along the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of [≥]70% and with [≤]10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction. HighlightsO_LIMicrobial distribution was mainly influenced by sampling location within the DWTP C_LIO_LIClade A comammox Nitrospira were the dominant nitrifiers in the primary sand filter C_LIO_LIClade B was most abundant in samples from wall biofilm and the secondary filter C_LIO_LIA novel Methylophilaceae-affiliated methanotroph dominated the primary sand filter C_LI

microbiology↗

bioRxiv2019

A novel mesocosm set-up reveals strong methane emission reduction in submerged peat moss Sphagnum cuspidatum by tightly associated methanotrophs.

Wetlands present the largest natural sources of methane (CH4) and their potential CH4 emissions greatly vary due to the activity of CH4-oxidizing bacteria associated with wetland plant species. In this study, the association of CH4-oxidizing bacteria with submerged Sphagnum peat mosses was studied, followed by the development of a novel mesocosm set-up. This set-up enabled the precise control of CH4 input and allowed for monitoring the dissolved CH4 in a Sphagnum moss layer while mimicking natural conditions. Two mesocosm set-ups were used in parallel: one containing a Sphagnum moss layer in peat water, and a control only containing peat water. Moss-associated CH4 oxidizers in the field could reduce net CH4 emission up to 93%, and in the mesocosm set-up up to 31%. Furthermore, CH4 oxidation was only associated with Sphagnum, and did not occur in peat water. Especially methanotrophs containing a soluble methane monooxygenase enzyme were significantly enriched during the 32 day mesocosm incubations. Together these findings showed the new mesocosm setup is very suited to study CH4 cycling in submerged Sphagnum moss community under controlled conditions. Furthermore, the tight associated between Sphagnum peat mosses and methanotrophs can significantly reduce CH4 emissions in submerged peatlands.

ecology↗