¹³C‐chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern

Abstract

Chloromethane (CH 3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH 3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH 3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH 3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH 3 Cl combined with metagenomics.Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH 3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH 3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH 3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH 3 Cl degradation in the investigated tree ferns.

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

“…In 1976, the genus Methylobacterium was established with Methylobacterium organophilum as the only species within it (Patt et al, 1976); since then, the number of known Methylobacterium species has risen to 63 (Hedlund et al, 2021;Maeng et al, 2021) 1 . Various attempts have been made to examine PPFMs from a taxonomic perspective (Green and Bousfield, 1982;Hood et al, 1987;Tsuji et al, 1990;Tani et al, 2015;Kröber et al, 2021b). Green and Ardley (2018) recently divided the Methylobacterium species into three clades 1 https://lpsn.dsmz.de/genus/methylobacterium (A, B, and C) based on phenotypic characteristics, multilocus sequence analysis (MLSA), and 16S rRNA gene sequence analysis.…”

Triple-element stable isotope analysis of chloromethane emitted and degraded by royal fern and club moss

“…Methyl-H4F is oxidized to methylene-H4F and subsequently to formate and CO2 [25,26]. In addition to the Cmu pathway other yet uncharacterized metabolic pathways were identified in bacteria in the phyllosphere of fern trees such as Friedmanniella [14] or in bacteria from aquatic habitats such as Leisingera methylohalidivorans MB2 [26].…”

“…In this context, large emissions have been reported for tropical plants [6][7][8][9] but also for halophytic plants [10] and fern species [11] occurring in temperate climate regions. Apart from producing and emitting CH3Cl, plants are also known to consume CH3Cl [12][13][14] which complicates a more precise quantification of sources and sinks because the net flux is influenced by both [15]. Thus, large gaps in the budget of CH3Cl persist because the magnitude of emissions from vegetation includes large uncertainties [16] and the sink strength by plants is largely unknown.…”

A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics

“…The microorganisms active in terrestrial sink of CH 3 Cl are poorly characterized compared to other atmospheric trace gases such as methane or nitrous oxide. Among methylotrophs, a few are capable of utilizing CH 3 Cl as their primary growth substrate [ 15 – 17 ]. CH 3 Cl-degrading bacteria were isolated from diverse natural environments [ 11 , 13 , 18 ], including representatives from Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, and Firmicutes [ 15 , 19 ].…”

“…Genes cmuA and cmuB encoding methyltransferases essential for CH 3 Cl dehalogenation have been detected in various environments, including forest soils [ 16 , 20 , 23 – 25 ]. However, the absence of cmu genes in active CH 3 Cl degraders in metagenomics and labelling studies suggests this pathway is not the only CH 3 Cl degradation pathway [ 15 , 17 , 19 ] and limits CH 3 Cl-degrading bacteria detection by overlooking cmu -independent microbial sink in soils.…”