Chloromethane formation and degradation in the fern phyllosphere

Assembly processes of rhizosphere and phyllosphere bacterial communities in constructed wetlands created via transformation of rice paddies

Constructed wetlands are an efficient and cost-effective method of restoring degraded wetlands, in which the microorganisms present make a significant contribution to the ecosystem. In this study, we comprehensively investigated the patterns of diversity and assembly processes of 7 types of constructed wetlands at the rhizosphere and phyllosphere levels. The results showed that the rhizosphere communities of the constructed wetlands exhibited a more balanced structure than that of paddy fields, and 5 types of constructed wetland demonstrated higher potential diversity than that of paddy fields. However, the opposite trend was observed for the phyllosphere communities. Analysis of mean nearest taxon difference indicated that both deterministic and stochastic processes affected the establishment of the rhizosphere and phyllosphere communities, and stochastic processes may have had a larger effect. An iCAMP model showed that dispersal limitation was the most important factor (67% relative contribution) in the rhizosphere community, while drift was the most important (47% relative contribution) in the phyllosphere community. Mantel tests suggested that sucrase, average height, top height, total biomass, belowground biomass, maximum water-holding capacity, and capillary porosity were significantly correlated with processes in the rhizosphere community, whereas factors such as the deterministic process, average height, top height, and SOC were significantly correlated with deterministic processes in the phyllosphere community. Our results can assist in the evaluation of artificial restorations, and can provide understanding of the ecological processes of microbial communities, as well as new insights into the manipulation of microorganisms in polluted wetland ecosystems.

Methane Production by Facultative Anaerobic Wood-Rot Fungi via a New Halomethane-Dependent Pathway

The greenhouse gas methane (CH4) is of pivotal importance for Earth's climate system and as a human energy source. A significant fraction of this CH4 is produced by anaerobic Archaea. Here, we describe the first CH4 production by facultative anaerobic wood-rot fungi during growth on hydroxylated/carboxylated aromatic compounds, including lignin and lignite. The amount of CH4 produced by fungi is positively correlated with the amount of CH3Cl produced during the rapid growth period of the fungus. Biochemical, genetic, and stable isotopic tracer analyses reveal the existence of a novel halomethane-dependent fungal CH4 production pathway during the degradation of phenol and benzoic acid monomers and polymers and utilization of cyclic sugars. Even though this halomethane-dependent pathway may only play a side role in anaerobic fungal activity, it could represent a globally significant, previously overlooked source of biogenic CH4 in natural ecosystems. IMPORTANCE Here, we demonstrate that wood-rot fungi produce methane anaerobically without the involvement of methanogenic archaea via a new, halomethane-dependent pathway. These findings of an anaerobic fungal methane formation pathway open another avenue in methane research and will further assist with current efforts in the identification of the processes involved and their ecological implications.

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

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

Chloromethane (CH₃ Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH₃ Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH₃ Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH₃ 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 CH₃ Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH₃ Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH₃ Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH₃ 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 CH₃ Cl degradation in the investigated tree ferns.

Sources and sinks of chloromethane in a salt marsh ecosystem: constraints from concentration and stable isotope measurements of laboratory incubation experiments

Chloromethane (CH₃Cl) is the most abundant long-lived chlorinated organic compound in the atmosphere and contributes significantly to natural stratospheric ozone depletion. Salt marsh ecosystems including halophyte plants are a known source of atmospheric CH₃Cl but estimates of their total global source strength are highly uncertain and knowledge of the major production and consumption processes in the atmosphere-halophyte-soil system is yet incomplete. In this study we investigated the halophyte plant, Salicornia europaea, and soil samples from a coastal salt marsh site in Sardinia/Italy for their potential to emit and consume CH₃Cl and using flux measurements, stable isotope techniques and Arrhenius plots differentiated between biotic and abiotic processes. Our laboratory approach clearly shows that at least 6 different production and consumption processes are active in controlling atmospheric CH₃Cl fluxes of a salt marsh ecosystem. CH₃Cl release by dried plant and soil material was substantially higher than that from the fresh material at temperatures ranging from 20 to 70 °C. Results of Arrhenius plots helped to distinguish between biotic and abiotic formation processes in plants and soils. Biotic CH₃Cl consumption rates were highest at 30 °C for plants and 50 °C for soils, and microbial uptake was higher in soils with higher organic matter content. Stable isotope techniques helped to distinguish between formation and degradation processes and also provided a deeper insight into potential methyl moiety donor compounds, such as S-adenosyl-l-methionine, S-methylmethionine and pectin, that might be involved in the abiotic and biotic CH₃Cl production processes. Our results clearly indicate that cycling of CH₃Cl in salt marsh ecosystems is a result of several biotic and abiotic processes occurring simultaneously in the atmosphere-plant-soil system. Important precursor compounds for biotic and abiotic CH₃Cl formation might be methionine derivatives and pectin. All formation and degradation processes are temperature dependent and thus environmental changes might affect the strength of each source and sink within salt marsh ecosystems and thus considerably alter total fluxes of CH₃Cl from salt marsh ecosystems to the atmosphere.

Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment

Chloromethane (CH₃Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (ε_Cl) associated with the major abiotic and biotic CH₃Cl sinks in the environment, namely, CH₃Cl degradation by hydroxyl (^·OH) and chlorine (^·Cl) radicals in the troposphere and by reference bacteria Methylorubrum extorquens CM4 and Leisingera methylohalidivorans MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CH₃Cl with ^·OH and ^·Cl radicals, whereas a large chlorine isotope fractionation (ε_Cl) of -10.9 ± 0.7‰ (n = 3) and -9.4 ± 0.9 (n = 3) was found for CH₃Cl degradation by M. extorquens CM4 and L. methylohalidivorans MB2, respectively. The large difference in chlorine isotope fractionation observed between tropospheric and bacterial degradation of CH₃Cl provides an effective isotopic tool to characterize and distinguish between major abiotic and biotic processes contributing to the CH₃Cl sink in the environment. Our findings demonstrate the potential of emerging triple-element isotopic approaches including chlorine to carbon and hydrogen analysis for the assessment of global cycling of organochlorines.

Isotopic Characterization (2H, 13C, 37Cl, 81Br) of Abiotic Degradation of Methyl Bromide and Methyl Chloride in Water and Implications for Future Studies

Methyl bromide (CH₃Br) and methyl chloride (CH₃Cl) significantly contribute to stratospheric ozone depletion. The atmospheric budgets of both compounds are unbalanced with known degradation processes outweighing known emissions. Stable isotope analysis may be capable to identify and quantify emissions and to achieve a balanced budget. Degradation processes do, however, cause isotope fractionation in methyl halides after emission and hence knowledge about these processes is a crucial prerequisite for any isotopic mass balance approach. In the current study, triple-element isotope analysis (²H, ¹³C, ³⁷Cl/⁸¹Br) was applied to investigate the two main abiotic degradation processes of methyl halides (CH₃X) in fresh and seawater: hydrolysis and halide exchange. For CH₃Br, nucleophilic attack by both H₂O and Cl^- caused significant primary carbon and bromine isotope effects accompanied by a secondary inverse hydrogen isotope effect. For CH₃Cl only nucleophilic substitution by H₂O was observed at significant rates causing large primary carbon and chlorine isotope effects and a secondary inverse hydrogen isotope effect. Observed dual-element isotope ratios differed slightly from literature values for microbial degradation in water and hugely from radical reactions in the troposphere. This bodes well for successfully distinguishing and quantifying degradation processes in atmospheric methyl halides using triple-element isotope analysis.