Summary: Agricultural ecosystems annually receive approximately 25% of the global nitrogen input, much of which is oxidized at least once by ammonia‐oxidizing prokaryotes to complete the nitrogen cycle. Recent discoveries have expanded the known ammonia‐oxidizing prokaryotes from the domain Bacteria to Archaea . However, in the complex soil environment it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea as implied by their exceptionally high abundance. Here we show that Bacteria rather than Archaea functionally dominate ammonia oxidation in an agricultural soil, despite the fact that archaeal versus bacterial amoA genes are numerically more dominant. In soil microcosms, in which ammonia oxidation was stimulated by ammonium and inhibited by acetylene, activity change was paralleled by abundance change of bacterial but not of archaeal amoA gene copy numbers. Molecular fingerprinting of amoA genes also coupled ammonia oxidation activity with bacterial but not archaeal amoA gene patterns. DNA‐stable isotope probing demonstrated CO ₂ assimilation by Bacteria rather than Archaea . Our results indicate that Archaea were not important for ammonia oxidation in the agricultural soil tested.

The prototypical representatives of the Euryarchaeota—the methanogens—are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ¹³C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.

Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ¹³C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H₂/CO₂ under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle.

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO ₂ fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO ₂ fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase ( accA / pccB ) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO ₂ using the 3-hydroxypropionate–4-hydroxybutyrate cycle, one of the two pathways recently identified for CO ₂ fixation in Crenarchaeota . Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase ( amoA ) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO ₂ assimilation and that their importance to the overall archaeal community might be larger than previously thought.

Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O₂, anaerobic processes such as CH₄ production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O₂. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH₄. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O₂ to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH₄ production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH₄, probably due to the peculiarities of the resident methanotrophic bacteria.

Summary: Uptake of molecular hydrogen (H ₂ ) by soil is a biological reaction responsible for ∼80% of the global loss of atmospheric H ₂ . Indirect evidence obtained over the last decades suggests that free soil hydrogenases with an unusually high affinity for H ₂ are carrying out the reaction. This assumption has recently been challenged by the isolation of Streptomyces sp. PCB7, displaying the high‐affinity H ₂ uptake activity previously attributed to free soil enzymes. While this finding suggests that actinobacteria could be responsible for atmospheric H ₂ soil uptake, the ecological importance of H ₂ ‐oxidizing streptomycetes remains to be investigated. Here, we show that high‐affinity H ₂ uptake activity is widespread among the streptomycetes. Among 14 streptomycetes strains isolated from temperate forest and agricultural soils, six exhibited a high‐affinity H ₂ uptake activity. The gene encoding the large subunit of a putative high‐affinity [NiFe]‐hydrogenase ( hydB ‐like gene sequence) was detected exclusively in the isolates exhibiting high‐affinity H ₂ uptake. Catalysed reporter deposition‐fluorescence in situ hybridization (CARD‐FISH) experiments targeting hydB ‐like gene transcripts and H ₂ uptake assays performed with strain PCB7 suggested that streptomycetes spores catalysed the H ₂ uptake activity. Expression of the activity in term of biomass revealed that 10 ⁶ –10 ⁷ H ₂ ‐oxidizing bacteria per gram of soil should be sufficient to explain in situ H ₂ uptake by soil. We propose that specialized H ₂ ‐oxidizing actinobacteria are responsible for the most important sink term in the atmospheric H ₂ budget.