Delherbe Nathalie A, Gomez Oscar, Plominsky Alvaro M, Oliver Aaron, Manzanera Maximino, Kalyuzhnaya Marina G
Department of Biology, San Diego State University, San Diego, CA 92129, United States.
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States.
ISME J. 2025 Jan 2;19(1). doi: 10.1093/ismejo/wraf026.
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.
旱地覆盖了地球表面的三分之一，是甲烷最大的陆地汇之一。了解干旱生物群落成员之间的结构 - 功能相互作用，可为应对人为和气候变化驱动的环境压力因素（缺水、热浪和大气温室气体增加）的恢复机制提供关键见解。本研究将原位测量与对美国南加州典型干旱生态系统安萨 - 博雷戈沙漠土壤中消耗甲烷的微生物群落进行的非培养和基于富集的调查相结合。大气甲烷消耗范围在2.26至12.73 μmol m² h⁻¹之间，在植被覆盖区域的白天达到峰值。宏基因组研究揭示了植被覆盖和无植被区域土壤微生物群落组成相似，甲基暖菌属是主要的甲烷氧化菌分支。共获得了84个宏基因组组装基因组，其中6个由甲烷氧化细菌代表（3个甲基暖菌属、2个甲基杆菌属和未培养的甲基球菌科）。宏基因组数据集中含铜甲烷单加氧酶的存在表明，在典型甲烷氧化菌和未培养的γ - 变形菌中甲烷氧化具有多种潜在可能性。获得了5种甲烷氧化细菌的纯培养物，包括4个甲基暖菌属。对甲基暖菌属分离株和宏基因组组装基因组的基因组分析表明，存在多个独立的甲烷单加氧酶亚基C旁系同源物，其功能可能超出甲烷氧化。此外，这些甲烷氧化菌具有通常与与植物共生相互作用相关的遗传特征，包括色氨酸合成和吲哚 - 3 - 乙酸产生。基于原位通量和土壤微生物群落组成，我们提出存在干旱土壤反向烟囱，这是一种由沙漠植被和消耗甲烷的微生物群落之间尚未明确的合作所代表的强大甲烷汇。
