Microbial CH4 and N2O Consumption in Acidic Wetlands

Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH4), and nitrous oxide (N2O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH4 is consumed in sub soil by aerobic methanotrophs at anoxic–oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH4 in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH4 consumption have not been systematically evaluated. N2O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N2O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N2O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N2O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH4 and N2O in acidic wetlands

Actinobacterial Nitrate Reducers and Proteobacterial Denitrifiers Are Abundant in N2O-Metabolizing Palsa Peat

Palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N2O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland. In situ N2O fluxes were spatially variable, ranging from 0.01 to -0.02 μmol of N2O m-2 h-1. Fertilization with nitrate stimulated in situ N2O emissions and N2O production in anoxic microcosms without apparent delay. N2O was subsequently consumed in microcosms. Maximal reaction velocities (vmax) of nitrate-dependent denitrification approx-imated 3 and 1 nmol of N2O per h per gram (dry weight [gDW]) in soil from 0 to 20 cm and below 20 cm of depth, respectively. vmax values of nitrite-dependent denitrification were 2- to 5-fold higher than the vmax nitrate-dependent denitrification, and vmax of N2O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N2O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) of narG, nirK and nirS, and nosZ were retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected spe- cies, as well as Actino-, Alpha-, and Betaproteobacteria. Copy numbers of nirS always outnumbered those of nirK by 2 orders of magnitude. Copy numbers of nirS tended to be higher, while copy numbers of narG and nosZ tended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N2O are associated with denitrification, (ii) actinobacterial nitrate reducers and nirS-type and nosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent reservoirs of diverse acid-tolerant denitrifiers associated with N2O fluxes. Copyright 2012, American Society for Microbiology

Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra

Cryoturbated peat circles (pH 4) in the Eastern European Tundra harbor up to 2 mM pore water nitrate and emit the greenhouse gas N2O like heavily fertilized agricultural soils in temperate regions. The main process yielding N2O under oxygen limited conditions is denitrification, which is the sequential reduction of nitrate/nitrite to N2O and/or N2. N2O reduction to N2 is impaired by pH < 6 in classical model denitrifiers and many environments. Key microbes of peat circles are important but largely unknown catalysts for C- and N-cycling associated N2O fluxes. Thus, we hypothesized that the peat circle community includes hitherto unknown taxa and is essentially unable to efficiently perform complete denitrification, i.e., reduce N2O, due to a low in situ pH. 16S rRNA analysis indicated a diverse active community primarily composed of the bacterial class-level taxa Alphaproteobacteria, Acidimicrobiia, Acidobacteria, Verrucomicrobiae, and Bacteroidia, as well as archaeal Nitrososphaeria. Euryarchaeota were not detected. 13C2- and 12C2-acetate supplemented anoxic microcosms with endogenous nitrate and acetylene at an in situ near pH of 4 were used to assess acetate dependent carbon flow, denitrification and N2O production. Initial nitrate and acetate were consumed within 6 and 11 days, respectively, and primarily converted to CO2 and N2, suggesting complete acetate fueled denitrification at acidic pH. Stable isotope probing coupled to 16S rRNA analysis via Illumina MiSeq amplicon sequencing identified acetate consuming key players of the family Burkholderiaceae during complete denitrification correlating with Rhodanobacter spp. The archaeal community consisted primarily of ammonia-oxidizing Archaea of Nitrososphaeraceae, and was stable during the incubation. The collective data indicate that peat circles (i) host acid-tolerant denitrifiers capable of complete denitrification at pH 4–5.5, (ii) other parameters like carbon availability rather than pH are possible reasons for high N2O emissions in situ, and (iii) Burkholderiaceae are responsive key acetate assimilators co-occurring with Rhodanobacter sp. during denitrification, suggesting both organisms being associated with acid-tolerant denitrification in peat circles. © Copyright © 2021 Hetz and Horn

Whole-genome sequences of two new caballeronia strains isolated from cryoturbated peat circles of the permafrost-affected eastern european tundra

Annotated genomes of Caballeronia strains SBC1 and SBC2 from acidic permafrost suggest a new species with a facultative lifestyle via oxygen and nitrate respiration. Thus, a contribution to nitrogen cycling in cold and low-pH environments is anticipated. © 2020 Hetz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license

Fate of trace organic compounds in hyporheic zone sediments of contrasting organic carbon content and impact on the microbiome

The organic carbon in streambed sediments drives multiple biogeochemical reactions, including the attenuation of organic micropollutants. An attenuation assay using sediment microcosms differing in the initial total organic carbon (TOC) revealed higher microbiome and sorption associated removal efficiencies of trace organic compounds (TrOCs) in the high-TOC compared to the low-TOC sediments. Overall, the combined microbial and sorption associated removal efficiencies of the micropollutants were generally higher than by sorption alone for all compounds tested except propranolol whose removal efficiency was similar via both mechanisms. Quantitative real-time PCR and time-resolved 16S rRNA gene amplicon sequencing revealed that higher bacterial abundance and diversity in the high-TOC sediments correlated with higher microbial removal efficiencies of most TrOCs. The bacterial community in the high-TOC sediment samples remained relatively stable against the stressor effects of TrOC amendment compared to the low-TOC sediment community that was characterized by a decline in the relative abundance of most phyla except Proteobacteria. Bacterial genera that were significantly more abundant in amended relative to unamended sediment samples and thus associated with biodegradation of the TrOCs included Xanthobacter, Hyphomicrobium, Novosphingobium, Reyranella and Terrimonas. The collective results indicated that the TOC content influences the microbial community dynamics and associated biotransformation of TrOCs as well as the sorption potential of the hyporheic zone sediments

Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers

Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of ≥97% had a narG or nosZ similarity of ≥67% or ≥80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent. Copyright © 2009, American Society for Microbiology. All Rights Reserved

Association of Novel and Highly Diverse Acid-Tolerant Denitrifiers with N2O Fluxes of an Acidic Fen

Wetlands are sources of denitriflcation-derived nitrous oxide (N 2O). Thus, the denitrifler community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitriflers approximated 10 11 cells · gDW-1 (where DW is dry weight) and 108 cells • gDW-1, respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (vma-) values for denitriflcation in anoxic microcosms ranged from 1 to 24 and - 19 to - 105 nmol N2O h-1 • gDW-1, with maximal values occurring in the upper soil layers. Denitriflcation was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitriflcation. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomie units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifler diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifler community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifler communities capable of complete denitriflcation and consumption of atmospheric N2O at in situ pH. Copyright © 2010, American Society for Microbiology. All Rights Reserved

Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen

Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen

Microbial nitrogen cycling in permafrost soils: implications for atmospheric chemistry

[no abstract

Nitrite induced transcription of p450nor during denitrification by Fusarium oxysporum correlates with the production of N2O with a high 15N site preference

The greenhouse gas nitrous oxide (N2O) is produced in soil as a consequence of complex co-occurring processes conducted by diverse microbial species, including fungi. The fungal p450nor gene encodes a nitric oxide reductase associated with fungal denitrification. We thus hypothesized that p450nor gene expression is a marker for ongoing fungal denitrification. Specific PCR primers and quantitative PCR (qPCR) assays were developed targeting p450nor genes and transcripts. The novel PCR primers successfully amplified p450nor from pure cultures, and were used in an mRNA targeted qPCR to quantify p450nor gene transcription (i.e., gene expression) during denitrification activity in cultures of the fungal model denitrifier Fusarium oxysporum. Gene expression was induced by high (5 mM) and low (0.25 mM) nitrite concentrations. Nitrite stimulated N2O production rates by F. oxysporum, which correlated well with an up to 70-fold increase in p450nor gene expression during the first 12–24 h of anoxic incubation. The relative p450nor gene peak expression and peak N2O production rates declined 20- and 2-fold on average, respectively, towards the later phase of incubation (48–120 h). The 15N site preference of N2O (SP(N2O)) was high for F. oxysporum and independent of reaction progress, confirming the fungal origin of N2O produced. In conclusion, the developed fungal p450nor gene expression assay together with the analysis of SP(N2O) values provide a basis to improve current tools for the identification of fungal denitrification and/or N2O production in natural systems like soils