Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Abstract

Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

Keywords: Methylocaldum; and methane cycle; arid soil; desert microbiomes; methanotrophs; plants.

Figure 1

The methane flux (consumption) comparing vegetated and unvegetated patches in the Anza Borrego Desert State Park. (A) the presence of vegetation and methanotrophs correlated positively with an increased consumption rate of methane. (B) Comparison of methane consumption between morning and afternoon. Significance with P value <0.0001 (^****) and 0.0229 (^*) obtained with unpaired parametric t-test. (C) Graphical summary of the chimney effect. The ribbons in (C) and (D) represent soil moisture (WATER) and organic content (ORG.MATTER). (D) Graphical summary of the proposed reverse chimney effect in arid ecosystems.

Figure 2

(A) Relative abundance of reads taxonomically assigned groups at a family level. Only abundant families are listed on the legend (>0.5% of assigned reads). (B) Relative abundance of reads taxonomically assigned to methanotrophic groups at family level. (C) Relative abundance of reads taxonomically assigned to methanotrophic genera. (D) Alpha diversity of all normalized taxonomically assignable metagenomic reads of samples with and without vegetation. Non-significant differences were found for Shannon (paired t-test P value = 0.184) and Simpson (paired t-test P value = 0.2354) indexes. Normalized data was randomly rarefied to 1 721 047 reads. (E) Beta diversity was visualized through a NMDS plot of the Bray–Curtis dissimilarity distances between all the taxonomically assignable metagenomic reads.

Figure 3

Maximum likelihood trees representing the phylogenetic relationship between CuMOs across bacteria and archaea retrieved from the metagenomes and publicly available genomes. The functional richness of the different subunits from the Anza-Borrego metagenomes is represented by green (vegetated) and yellow (unvegetated) lines at the tips of their corresponding leaves. The outside color-coded ring guides the function of CuMOs, which was assigned based on the taxon at the corresponding leaf. The phylogenetic trees do not show the branch length to facilitate the visualization of clade topology.

Figure 4

Comparison of the metabolic potential of isolates and relevant MAGs obtained from Anza-Borrego (2016 and 2023). The analysis indicates the presence of key genes involved in relevant pathways for this study.

Figure 5

(A) Maximum likelihood tree representing the phylogenetic relationship of Methylocaldum particulate methane monooxygenase, based on the amino acid sequences of the pmoC gene. Next to each branch, the projection has a color-coded representation of the predicted functions for the genes in the vicinity of each pmoC. Next to each clade, brackets indicate with a number the type of pmoC corresponding to each clade. Type 1 PmoC is part of the canonical pMMO, whereas Types 2 to 5 correspond to the different stand-alone PmoC. Predicted AlphaFold models were based on the prediction obtained from the CryoEM structure of Methylococcus capsulatus (bath) pMMO in a native lipid nanodisc at 2.16 Angstrom resolution (ID 7S4J). Predicted structures are color-coded according to the confidence percentage in the model accuracy. (B) Gene function prediction for genes in the vicinity of each of the five types of pmoC from Methylocaldum strains. The canonical pmoC from 0917 was recovered from a metatranscriptome.

Figure 6

Genomic potential for cobalamin (vitamin B₁₂) de novo synthesis and salvaging by Anza-Borrego isolates of Bradyrhizobium and Methylocaldum, respectively. The required genes for de novo cobalamin synthesis are present in the Bradyrhizobium genome. The absence of the initial required genes for de novo synthesis and the presence of two paralogs of the cobalamin outer membrane cobalamin receptor and transporter gene, btuB, indicates that Methylocaldum relies on a salvaging pathway of cobalamin.

Figure 7

Genomic potential for tryptophan and indole-3-acetic acid (IAA) synthesis in Anza-Borrego isolates of Bradyrhizobium and Methylocaldum. (A) Comparison of metabolic potential for the synthesis of IAA by Anza-Borrego isolates. (B) The major difference in their tryptophan synthesis pathway relies on the gene encoding the initial step enzymes; Bradyrhizobium has the fused version of the anthranilate synthase TrpEG, and Methylocaldum has its two components separately.