Unexpected role of canonical aerobic methanotrophs in upland agricultural soils
Introduction
Increasing food supply to meet the global human population growth often results in the conversion of native to arable lands and intensification of agriculture. The change in land-use alters the soil physico-chemical parameters and nutrient turnover, in turn, induces a compositional shift in the soil methanotrophic community and abundance which severely impairs the methane sink function (Levine et al., 2011; Ho et al., 2015a; Tate et al., 2007, 2015; Malghani et al., 2016; Meyer et al., 2017). As methane is a potent greenhouse gas, accounting for up to 17% of global warming (IPCC, 2013), it is crucial to understand the sources and sinks of atmospheric methane in the ecosystem. Whether well-aerated, non-wetland (i.e., upland) agricultural soils are a weak sink or source of atmospheric methane (Ho et al., 2015a) after land-use conversion depends more strongly on changes in the methanotrophic population than on shifts among the methane-producing archaea (Meyer et al., 2017). (Circum-)atmospheric methane oxidation, defined here as oxidation of methane at <40 ppmv (Singh et al., 2016) (atmospheric methane at ∼1.8 ppmv), is thought to be catalyzed by the as-yet-uncultured high-affinity methanotrophs. These methanotrophs belong to a specialized group of methane-oxidizers that are taxonomically distinct from the low-affinity, canonical ones with cultured representatives (Holmes et al., 1999; Horz et al., 2002; Knief et al., 2003; Maxfield et al., 2008; Kolb, 2009; Levine et al., 2011). In contrast, genes regulating methane oxidation in a canonical methanotroph was only induced at > 600 ppmv methane (Baani and Liesack, 2008). These methanotrophs act as a methane bio-filter at oxic-anoxic interfaces in methane-emitting environments (Ho et al., 2013). The high-affinity methanotrophs have resisted cultivation to date, and are defined based on their pmoA gene (structural gene for methane oxidation) sequences and PLFA profiles (Bull et al., 2000; Knief et al., 2003; Bodelier et al., 2009). Consequently, these biomarkers are used to detect the high-affinity methanotrophs in the environment.
High-affinity methanotrophs belong to Gammaproteobacteria (e.g., clades upland soil cluster γ: USC γ) and Alphaproteobacteria (e.g., clades USCα) (Knief et al., 2003; Horz et al., 2005; Kolb et al., 2005; Shrestha et al., 2012). Although there are no isolated representatives of high-affinity methanotrophs, the genomic potential of a candidate bacterium belonging to the USCα has recently been characterized using a targeted cell-sorting approach coupled to metagenomic analysis (Pratscher et al., 2018). Phylogenetic analyses of the 16S rRNA, as well as the pmoA gene placed this microorganism close to known cultured methanotrophs of the genus Methylocapsa. Additionally, a cultured alphaproteobacterial methanotroph (Methylocystis) has been proven to oxidize methane at atmospheric or low (<600 ppm) methane concentrations (Baani and Liesack, 2008). Methylocystis, along with Methylosinus are the only known canonical methanotrophs harbouring an isozyme of the conventional pMMO (pMMO2), enabling methane oxidation at low concentrations (Yimga et al., 2003; Baani and Liesack, 2008). Despite the ability of these methanotrophs to oxidize methane at (circum-)atmospheric levels and the detection of other canonical methanotrophs in upland soils showing atmospheric methane consumption, it was long thought that the as-yet-uncultured high-affinity methane-oxidizers exclusively form the metabolically active population in native soils, as revealed by substrate labelling studies (Holmes et al., 1999; Knief et al., 2003; Kolb et al., 2005; Malghani et al., 2016; Pratscher et al., 2011, 2018). Hence, the role of the canonical methanotrophs as a methane sink in upland soils remains unclear.
In contrast to the canonical methanotrophs, the putative high-affinity methanotrophs are vulnerable to disturbances, requiring close to a century to recover in population and activity following abandonment of agriculture (Maxfield et al., 2008; Levine et al., 2011). Consequently, high-affinity methanotrophs are thought to be indigenous to native soils (i.e., relatively un-disturbed environments; forests, meadows, and grasslands) which were typically used as model ecosystems to investigate these microorganisms (Knief et al., 2003; see review Kolb, 2009). In a recent study, however, we showed that upland agricultural soils readily consume atmospheric methane, and the potential for methane oxidation was transiently, but significantly stimulated after the addition of bio-based residues (Ho et al., 2015a, 2017a); the elevated methane uptake was comparable to levels exhibited in native soils. The high-affinity methanotrophs were not detected in these soils despite atmospheric methane uptake and potential methane oxidation at circum-atmospheric levels (10–40 ppm) (Ho et al., 2015a). Therefore, we hypothesized that the agricultural soils harbor novel clades of high-affinity methanotrophs and/or we overlooked the potential role of canonical methanotrophs acting as a methane sink. This study aimed to determine the methane sink function in upland agricultural soils, and to resolve the active members contributing to (circum-)atmospheric methane oxidation in agriculture-impacted soils.
Section snippets
Site description and mesocosm incubation
The mesocosm experiment was performed using sandy loam and clay soils, respectively collected from agricultural fields in Vredepeel (51˚32′32“N, 05˚50′54“E) and Lelystad (52˚31′20“N, 05˚34′57“E) belonging to the Wageningen University and Research, the Netherlands in August 2015. Detailed soil sampling procedure, subsequent processing (air-dried at room temperature and sieved to 2 mm), and soil physico-chemical properties were described before (Ho et al., 2015a, 2017a). These soils contained
Response of the methane uptake rate to bio-based residue amendments
Methane uptake rate was significantly stimulated after bio-based residue amendment when compared to the un-amended incubation (P < 0.05), and the increased activity was sustained up to 50 days in the compost-amended soils (Fig. 1). The stimulatory effect of the residues on the soil methane uptake rate diminished over time. Potential methane oxidation was further confirmed by analysis of the 13C/12C isotope ratio of CO2, showing significant accumulation of 13CCH4-derived CO2 (13CCO2) over time
Stimulation of methane uptake in upland agricultural soils
The agricultural soils showed potential for high-affinity methane oxidation as was evident from detectable methane uptake in both the residue- and un-amended soils when incubated under circum-atmospheric methane concentrations (6–40 ppm). The methane oxidation rate was significantly stimulated after residue amendment, but the stimulatory effect was transient (up to 50 days; Fig. 1). This finding was consistent with our previous work (Ho et al., 2015a) despite soils and residues of the previous
Declarations of interest
None.
Acknowledgements
We are grateful to Iris Chardon for excellent technical assistance. We extend our gratitude to Mattias de Hollander for assistance during the sequence analysis. AH is financially supported by the BE-Basic grant F03.001 (SURE/SUPPORT), and from funds by the Deutsche Forschungsgemeinschaft (DFG grant HO 6234/1-1) and the Leibniz Universität Hannover (Germany). This publication is publication no. 6657 of the Netherlands Institute of Ecology.
References (55)
- et al.
Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis
Soil Biology and Biochemistry
(1993) Soil microbial community structure in relation to vegetation management on former agricultural land
Soil Biology and Biochemistry
(2002)- et al.
Resilience of (seed bank) aerobic methanotrophics and methanotrophic activity to desiccation and heat stress
Soil Biology and Biochemistry
(2016) - et al.
Effect of salt stress on aerobic methane oxidation and associated methanotrophs; a microcosm study of a natural community from a non-saline environment
Soil Biology and Biochemistry
(2018) - et al.
Activity and community structure of methane-oxidizing bacteria in a wet meadow soil
FEMS Microbiology Ecology
(2002) - et al.
Soil methanotroph abundance and community composition are not influenced by substrate availability in laboratory incubations
Soil Biology and Biochemistry
(2016) - et al.
Methane uptake in soils from Pinus radiata plantations, a reverting shrubland and adjacent pastures: effects of land-use change, and soil texture, water and mineral nitrogen
Soil Biology and Biochemistry
(2007) Soil methane oxidation and land-use change – from process to mitigation
Soil Biology and Biochemistry
(2015)- et al.
Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2
Proceeding of the National Academy of Sciences USA
(2008) - et al.
A rapid method of total lipid extraction and purification
Canadian Journal of Biochemistry and Physiology
(1959)
A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria
The ISME Journal
Microbial minorities modulate methane consumption through niche partitioning
The ISME Journal
Linking microbial community structure and functioning: stable isotope (13C) labelling in combination with PLFA analysis
Detection and classification of atmospheric methane oxidizing bacteria in soil
Science
Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils
Nature Communications
The diversity of Archaea and Bacteria in association with the roots of Zea mays L
Microbial Ecology
Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps
Frontiers in Microbiology
Long-term effects of organic amendments on soil fertility: a review
Agronomy for Sustainable Development
Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN
Frontiers in Microbiology
UCHIME improves sensitivity and speed of chimera detection
Bioinformatics
PAST: paleontological statistics software package for education and data analysis
Palaeontologia Electronica
Field-scale tracking of active methane-oxidizing communities in a landfill-cover soil reveals spatial and seasonal variability
Environmental Microbiology
A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes
Frontiers in Microbiology
Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies
Environmental Microbiology Reports
Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application
Global Change Biology
Manure-associated stimulation of soil-borne methanogenic activity in agricultural soils
Biology and Fertility of Soils
Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition
Global Change Biology Bioenergy
Cited by (37)
Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils
2024, Soil Biology and BiochemistryThe use of small emitter flow rate in drip irrigation favored methane uptake in arid potato fields
2024, Agricultural Water ManagementMethanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave
2023, Science of the Total Environment