Kröber Eileen, Kanukollu Saranya, Wende Sonja, Bringel Françoise, Kolb Steffen
Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany.
Environ Microbiome. 2022 May 8;17(1):24. doi: 10.1186/s40793-022-00416-2.
Chloromethane (CHCl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CHCl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CHCl-degrading methylotrophs occurring in soils might be an important and overlooked sink.
The objective of our study was to link the biotic CHCl sink with the identity of active microorganisms and their biochemical pathways for CHCl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CHCl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CHCl g dry weight h, were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CHCl degradation compartments of forest ecosystems. The DNA of these [C]-CHCl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CHCl degradation, via the methyltransferase system encoded by the CHCl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CHCl sink in this deciduous forest soil operates by a cmu-independent metabolism.
氯甲烷（CHCl）是大气中含量最丰富的卤代有机化合物，对平流层臭氧层的破坏负有重大责任。自《蒙特利尔议定书》（1987年）实施以来，人为氯甲烷来源已变得微不足道，而植被和土壤等自然来源在全球预算中所占比例相应增加。土壤中存在的能降解氯甲烷的甲基营养菌可能是一个重要但被忽视的汇。
我们研究的目的是将生物氯甲烷汇与落叶林土壤中活跃微生物的身份及其氯甲烷降解的生化途径联系起来。在实验室微观世界中进行测试时，落叶、衰老叶片以及有机和矿质土壤层中均发生了生物氯甲烷消耗现象。在有机土壤和衰老叶片中测得的最高消耗率约为2 mmol CHCl·g干重·h，这表明表层土壤是森林生态系统中活跃的（微）生物氯甲烷降解区室。使用稳定同位素探测（SIP）标记了这些[C] - 氯甲烷降解微生物群落的DNA，并通过高通量宏基因组测序分析研究了相应的分类群及其代谢途径。与拜叶林克氏菌科密切相关的[C] - 标记宏基因组组装基因组可能代表了变形菌门α亚纲中的一个新的甲基营养菌家族，在全球森林土壤样本的宏基因组数据库中均有发现。在DNA - SIP宏基因组数据中未检测到通过氯甲烷利用基因（cmu）编码的甲基转移酶系统进行的需氧氯甲烷降解唯一已知途径的基因标记，这表明该落叶林土壤中的生物氯甲烷汇通过不依赖cmu的代谢方式运行。
