Paul L E Bodelier

Koninklijke Nederlandse Akademie van Wetenschappen | KNAW · Netherlands Institute of Ecology (NIOO)

Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methy...

Seasonal floodplains in the Amazon basin are important sources of methane (CH 4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH 4 cycling dynamics. To investig...

Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fie...

Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N 2) fixation and as a promising strategy to mitigate methane (CH 4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH 4 cycling in rice soils. Here, we focused...

Biodiversity‐ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmosph...

Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in me...

Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogen community composition and their...

Karst ecosystems are widely distributed around the world, accounting for 15–20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types...

So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gase...

We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by...

Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functi...

The holobiont concept places emphasis on the strict relationship between a host and its associated microbiome, with several studies supporting a strong effect of the quality of the microbiome on the host fitness. The generalities of the holobiont have been questioned for several invertebrates, including zooplankton. Here we assess the role of host...

Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2–), which can be further oxidized to nitrate (NO3–). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and pr...

Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane‐oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption...

The GHG (CO2, CH4, N2O) emission potential along a chronosequence of former agricultural soils abandoned for 9 to 32 years were compared to an actively managed (on-going) agricultural soil (reference). The soils were incubated in mesocosms with and without manure amendment, and microbial functional groups involved in nitrous oxide emission were qua...

Organic amendments (OAs) produced via composting, anaerobic digestion, or lactic acid fermentation, can be used to replenish soil carbon. Not all OAs production technologies preserve C and nutrients in the same way. In this study, we compared the influence of these technologies (i.e., treatments) on C and nutrient preservation and OAs chemical comp...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation...

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. He...

Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing C...

Aquatic ecosystems such as shallow lakes and wetlands are important emitters of the greenhouse gas methane (CH4). Increased phosphorus (P) loading is expected to increase CH4 production in these ecosystems. This increased CH4 production can potentially be mitigated by increased CH4 oxidation, but how P availability affects methane-oxidizing bacteri...

Here we use a top-down and bottom-up approach in landscape ecology to analyze the active microbes processing methane fluxes (FCH4) in seasonally flooded-forest (FOR) and -traditional farming systems (TFS) in Amazonian floodplains flooded with black, white, and clear water. Our results revealed higher CH4 emissions from water-atmosphere interface in...

We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of...

Fungi play an important role in carbon and nutrient cycling. It is, however, unclear if diversity of fungi is essential to fulfill this role. With this meta-analysis, we aim to understand the relationship between fungal diversity and decomposition of plant materials (leaf litter and wood) in terrestrial and aquatic environments. The selection crite...

Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidatio...

• Shallow aquatic systems exchange large amounts of carbon dioxide (CO2) and methane (CH4) with the atmosphere. The production and consumption of both gases is determined by the interplay between abiotic (such as oxygen availability) and biotic (such as community structure and trophic interactions) factors. • Fish communities play a key role in dri...

Ammonium-induced stimulatory, inhibitory, and/or neutral effects on soil methane oxidation have been attributable to the ammonium concentration and mineral forms, confounded by other edaphic properties (e.g., pH, salinity), as well as the site-specific composition of the methanotrophic community. We hypothesize that this inconsistency may stem from...

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovatio...

Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising of methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial...

The increasing frequency of extreme weather events, such as floods, requires management strategies that promote resilience of grassland productivity. Mixtures of plant species may better resist and recover from flooding than monocultures, as they could combine species with stress‐coping and resource acquisition traits. This has not yet been tested...

It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their “host”. However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA)...

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in differen...

Intensively managed grasslands are large sources of the potent greenhouse gas nitrous oxide (N2O) and important regulators of methane (CH4) consumption and production. The predicted increase in flooding frequency and severity due to climate change could increase N2O emissions and shift grasslands from a net CH4 sink to a source. Therefore, effectiv...

Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially-driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmosph...

Analysis of microbial functional genes from high-throughput amplicon sequencing data is crucial to study ecology and biodiversity. To conduct such analysis, we need a robust pipeline that offers analysing of sequencing data of any functional gene in an automated manner with flexibility (e.g., different reference database support) and reproducibilit...

To improve sustainability in agricultural systems, winter cover crops are increasingly replacing fallow to stimulate soil functions that reduce nutrient losses and greenhouse gas production, reduce pests for the next cash crops, increase soil organic matter pools and reduce erosion. Several of these functions are highly dependent on soil microbes d...

The dynamics of methane concentrations in the atmosphere in recent decades has demonstrated many anomalies which are poorly understood. The only biological way of degrading this potent greenhouse gas is by microbial oxidation. Aerobic methanotrophic bacteria (MB) play an important role in many ecosystems worldwide degrading methane before it can es...

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 and ty...

Straw application is a common agricultural fertilisation practice, providing an additional carbon and nutrient source for soil microorganisms. We investigated the influence of rice straw application on root exudate consuming microorganisms in the rhizosphere of Zea mays based on ¹³CO2 pulse labelling and phospholipid fatty acid stable isotope probi...

Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments...

Aerobic oxidation of methane at (circum-)atmospheric concentrations (< 40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have...

Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestratio...

The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community compo...

EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater...

Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium add...

Proxy-indicators in lake sediments provide the only approach by which the dynamics of in-lake methane cycling can be examined on multi-decadal to centennial time scales. This information is necessary to constrain how lacustrine methane production, oxidation and emissions are expected to respond to global change drivers. Several of the available pro...

The increase of extreme drought and precipitation events due to climate change will alter microbial processes. Perturbation experiments demonstrated that microbes are sensitive to environmental alterations. However, only little is known on the legacy effects in microbial systems. Here, we designed a laboratory microcosm experiment using aerobic met...

Volatile organic compounds play an important role in microbial interactions. However, little is known about how volatile-mediated interactions modulate biogeochemical processes. In this study, we show the effect of volatile-mediated interaction on growth and functioning of aerobic methane-oxidizing bacteria, grown in co-culture with five different...

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on m...

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a...

Methane-derived carbon, incorporated by methane-oxidizing bacteria, has been identified as a significant source of carbon in food webs of many lakes. By measuring the stable carbon isotopic composition (δ¹³C values) of particulate organic matter, Chironomidae and Daphnia spp. and their resting eggs (ephippia), we show that methane-derived carbon pr...

With the projected rise in the global human population, agriculture intensification and land-use conversion to arable fields is anticipated to meet the food and bio-energy demand to sustain a growing population. Moving towards a circular economy, agricultural intensification results in the increased re-investment of bio-based residues in agricultur...

The balance of microbial nitrogen (N) transformation processes in sub-arctic terrestrial ecosystems is most likely affected by global change, with potential feedbacks to greenhouse gas emissions and eutrophication. Soil temperature and N availability – their global increases being two of the most pressing global change features - will be prime driv...

Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intracta...

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic c...

Network analysis of 16s rRNA gene sequences derived from the “heavy” fraction of a 13C-CH4 labeled community in a grassland soil (Daebeler et al., 2014). The correlating OTUs with >1% relative abundance are given in the figure, and the corresponding taxonomic affiliation are listed in the Supplementary Information (Table S3).