Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

Abstract

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 d 13 C 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.

Oxic water column methanogenesis as a major component of aquatic CH4 fluxes

“…3b). Consistent with this conclusion, observations of enriched surface d 13 C-CH 4 in numerous lakes 8,10,18,29,32 have been hypothesized to indicate dominance of acetoclastic methanogenesis in oxic freshwater pelagic zones 18 , and both known acetoclastic genera (Methanosaeta and Methanosarcina) have recently been detected in oxic freshwater 19,26 and terrestrial 27,28 environments. Furthermore, acetoclastic dominance was enhanced with the addition of nutrients and increased algal production (Fig.…”

“…In vitro experiments point to CH 4 production in both microanoxic habitats in metazoan guts and on particles 14,[17][18][19][20][21][22][23] , and in particle-free oxic water 15,16,18,19,[23][24][25] , via multiple biochemical pathways. The presence 19,22,[26][27][28] and activity 19,22,27 of hydrogenotrophic and acetoclastic methanogenic archaea have been confirmed at the molecular level in diverse oxic environments. At the same time, marine studies suggest that the microbial decomposition of methylated compounds such as methanethiol 15 and methylphosphonate 16,[23][24][25] could be an important source of CH 4 in surface waters of the open ocean.…”

“…Several methanogenic pathways exist, but as acetoclastic methanogenesis is less isotopically discriminatory than CO 2 reduction or methylotrophy 19,27,28 , apparent fractionation factors (a app; see Methods for calculation details) can be used to qualitatively distinguish whether CH 4 is produced via methanogenesis from acetate, or CO 2 reduction 30 . Our measured a app values were well within the range indicating dominance of the acetoclastic pathway (Fig.…”

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammoxNitrospirain the environment

“…Total nucleic acids were extracted from the environmental samples (Table 2) by using (i) the Fast DNA SPIN Kit for soil (MP Biomedicals, Santa Ana, CA, USA), (ii) the PowerSoil DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA), or (iii) a phenol-chloroform based total nucleic acid extraction protocol described by Angel et al (2012). PCRs were performed with either the DreamTaq Green PCR mix as described above, or with the PerfeCTa SYBR green FastMix PCR premix containing 1.5 mM of MgCl2 (Quanta Bioscience, Beverly, MA, USA) and 0.1 µM primers.…”

Stimulation of long-term ammonium nitrogen deposition on methanogenesis by Methanocellaceae in a coastal wetland

“…All biogenic methane is produced by methanogenic archaea (Angel et al, 2012). Nitrogen deposition can change microbial community structure and function to influence methane production (Sinsabaugh et al, 2015), so understanding the response of methanogenic archaea may be the key to clarify the effect of different types of nitrogen enrichment on methane emission.…”