New <i>Methyloceanibacter</i> diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

Vekeman, Bram; Kerckhof, Frederiek‐Maarten; Cremers, Geert; Vos, Paul De; Vandamme, Peter; Boon, Nico; Camp, Huub J. M. Op den; Heylen, Kim

doi:10.1111/1462-2920.13485

Cited by 82 publications

(51 citation statements)

References 99 publications

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“…Methyloceanibacter can become methanotrophic by acquiring sMMO (Vekeman et al, 2016). The phylogenomic analysis and low ANI value to other members of this family (77.26%) suggest that P-RSF-NP-02 represents a novel species within the Methylophilaceae (Figure 7B) and the extremely high coverage of this MAG indicates a major role in methane removal in the DWTP Breehei.…”

Section: Methane and One-carbon Metabolismmentioning

confidence: 98%

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

Poghosyan

Koch

Frank

et al. 2020

Preprint

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Highlights 10• Microbial distribution was mainly influenced by sampling location within the DWTP.• Clade A comammox Nitrospira were the most abundant nitrifying guild in samples from the primary sand filter, while clade B dominated in samples from wall biofilm and the secondary filter.• A novel methanotrophic bacterium affiliated with the Methylophilaceae family comprised 15 the largest bacterial fraction in the primary sand filter. AbstractElevated 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 20 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 compositionbased binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an 25 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 30 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 35 water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction. Methane uptakeMethane-oxidizing capacity was determined for the P-RSF and WB samples collected in 2016. 115For the P-RSF, 2.5, 5, 10, and 20 g of sand material were mixed with 20 ml top water. After settling of the sand, overlaying water samples (20 ml) were transferred into 120 ml serum bottles with Deep aquifer Clay Shallow aquifer Sand and gravel NH 4 + CH 4 Fe H 2 S Mn Groundwater Air supply Air supply WB P-RSF S-RSF Storage and distribution Wall

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Section: Methane and One-carbon Metabolismmentioning

confidence: 98%

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

Poghosyan

Koch

Frank

et al. 2020

Preprint

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“…To date, only a few marine methanotrophs have been described (Hirayama et al 2013, Tavormina et al 2015, Vekeman et al 2016 and not much is known about their ecological capabilities.…”

Section: Response Of Marine Mob Communities To Decreasing Salinitymentioning

confidence: 99%

“…Most known methane oxidizing bacteria (MOB) have been isolated from non-saline environments (soils, sediments and lakes) (Hanson & Hanson 1996, Khmelenina et al 1999; however, there are some examples of MOB isolated from marine environments (Hirayama et al 2013, Tavormina et al 2015, Vekeman et al 2016 and other hypersaline environments (Trotsenko & Khmelenina 2002). MOB adapted to high salinity and/or pH values are geno-and phenotypically different from the inhabitants of freshwater environments with neutral pH values and have been de scribed as new species (Khmelenina et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Effect of salinity on microbial methane oxidation in freshwater and marine environments

Osudar¹,

Klings²,

Wagner³

et al. 2017

Aquat. Microb. Ecol.

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Salinity is an important environmental control of aerobic methane oxidation, which reduces the emission of the potent greenhouse gas methane into the atmosphere. The effect of salinity on methane oxidation is especially severe in river estuaries and adjacent coastal waters, which are important sources of methane emission and, at the same time, are usually characterized by pronounced salinity gradients. Using methane oxidation rates determined by a radiotracer technique as a measure of methanotrophic activity, we tested the effect of immediate and gradual salinity changes on pure cultures of methanotrophic bacteria, and natural freshwater (Elbe River) and natural marine (North Sea) methanotrophic populations. According to our results, Methylomonas sp. and Methylosinus trichosporium are resistant to an increase in salinity, whereas Methylovulum sp. and Methylobacter luteus are sensitive to such an increase. Natural methanotrophic populations from freshwater are more resistant to an increase in salinity than those from marine water are to a decrease in salinity. In contrast to an immediate change of salinity, gradual change (1.25 PSU d −1) can attenuate salinity stress. Experiments with the natural populations revealed different reactions to changes in salinity; thus, we assume that the initial composition of the methanotrophic population, i.e. the ratio of sensitive versus resistant strains, also governs the community response to salinity stress.

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“…The subsurface sediment had a larger community of likely anaerobes and facultative taxa, including Aeromonas and Bacteroides [70,71], as well as the endospore formers, Bacillus and Paenibacillus [72]. The hydrated samples were separated from the desiccated state by previously identified marine sediment bacteria [73][74][75][76], as well as the genera Mycobacterium, commonly known as a pathogen [77], Luteolibacter, previously identified in Arctic soil [78], and Methyloceanibacter, isolated from near a hydrothermal vent [79]. Among the archaeal sequences, the surface samples were characterized by an abundance of halobacteriaceae and haloferacaceae, both extreme halophiles [80,81].…”

Section: Discussionmentioning

confidence: 99%

The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

2020

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Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.

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New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

Cited by 82 publications

References 99 publications

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

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

Effect of salinity on microbial methane oxidation in freshwater and marine environments

The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

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