Archaeal diversity and community structure in a Swedish barley field: Specificity of the EK510R/(EURY498) 16S rDNA primer

Poplawski, Andrzej; Mårtensson, Lotta; Wartiainen, Ingvild; Rasmussen, Ulla

doi:10.1016/j.mimet.2006.12.018

Cited by 20 publications

(13 citation statements)

References 84 publications

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“…Certainly, this stems from our analysis of methanogenic pathways, where in the latter part of the incubations aceticlastic methanogenesis accounted for roughly twothirds of the newly formed CH 4 , but also generally speaking Methanosarcina had a higher relative abundance in the TRFLP profiles and their absolute abundance correlated better with CH 4 production rates. Similarly, Methanosarcina and Methanocella were also the methanogenic types that were found by Nicol et al (2003) in a pasture soil in Scotland and by Poplawski et al (2007) in a barley field in Sweden, thus reinforcing our notion that these types are universal upland soil methanogens. In cases where heavy grazing was involved, the authors have also found Methanosarcina as dominant methanogens, but along with it other types that could be directly associated to rumen microflora Radl et al, 2007).…”

Section: Discussionsupporting

confidence: 78%

“…However, these authors have attributed most of this activity to the effect that livestock had on the soil by enriching it with nutrients from urine and manure and by introducing rumen microflora to the soil. Last, Poplawski et al (2007) retrieved sequences of Methanosarcina and Methanocella in a Swedish barley field but did not attempt to measure potential methanogenic activity.…”

Section: Introductionmentioning

confidence: 99%

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

2011

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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.

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Section: Discussionsupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

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

2011

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“…Indication of methanogenic Euryarchaeota was also found in compacted interrow soil of a potato field when phospholipid etherlipid derived isoprenoids were analysed by Gattinger et al (2002). Some methanogenic Euryarchaeotal 16S rRNA gene sequences have been found from Swedish barley field agricultural sandy soil (Table 2, Poplawski et al 2007;Ruppel et al 2007).…”

Section: Euryarchaeota In Soilsmentioning

confidence: 90%

Archaea in dry soil environments

Timonen

Bomberg

2009

Phytochem Rev

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Archaea belong to the least well known major group of soil inhabiting microbes as the concept of the very existence of the archaea was introduced only in 1977 and the domain of Archaea established in 1990. The first reports of finding these organisms in soils were published even later. This paper will review the research carried out of the archaea in dry moderate soil environments. It will particularly consider the specific habitats where the archaea live in soils, as well as their associations with other organisms. There is thus far relatively little knowledge about the metabolism of the soil archaea, but the knowledge about their exact habitats and associations as well as their genetic potential point the way to discovering more about the different soil archaeal functions.

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“…Similarly, West and Schmidt (2002) were able to induce methanogenesis in well-drained alpine soils when incubated under an H 2 /CO 2 -enriched atmosphere. Teh et al (2005) also found methanogenesis occurring in tropical forest soils, Poplawski et al (2007) retrieved sequences of methanogens in a well-aerated Swedish barley field, and Lee et al (2012) observed growth of methanogens in aerated laboratory incubations. These findings suggest that methanogens not only become active under relatively moist or saturated conditions, but are also active in anaerobic microenvironments within otherwise oxic, upland soils (Angel et al 2012).…”

Section: Evidence For Anaerobic Metabolism In Upland Soilsmentioning

confidence: 94%

Are oxygen limitations under recognized regulators of organic carbon turnover in upland soils?

et al. 2016

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Understanding the processes controlling organic matter (OM) stocks in upland soils, and the ability to management them, is crucial for maintaining soil fertility and carbon (C) storage as well as projecting change with time. OM inputs are balanced by the mineralization (oxidation) rate, with the difference determining whether the system is aggrading, degrading or at equilibrium with reference to its C storage. In upland soils, it is well recognized that the rate and extent of OM mineralization is affected by climatic factors (particularly temperature and rainfall) in combination with OM chemistry, mineral-organic associations, and physical protection. Here we examine evidence for the existence of persistent anaerobic microsites in upland soils and their effect on microbially mediated OM mineralization rates. We corroborate long-standing assumptions that residence times of OM tend to be greater in soil domains with limited oxygen supply (aggregates or peds). Moreover, the particularly long residence times of reduced organic compounds (e.g., aliphatics) are consistent with thermodynamic constraints on their oxidation under anaerobic conditions. Incorporating (i) pore length and connectivity governing oxygen diffusion rates (and thus oxygen supply) with (ii) 'hot spots' of microbial OM decomposition (and thus oxygen consumption), and (iii) kinetic and thermodynamic constraints on OM metabolism under anaerobic conditions will thus improve conceptual and numerical models of C cycling in upland soils. We conclude that constraints on microbial metabolism induced by oxygen limitations act as a largely unrecognized and greatly underestimated control on overall rates of C oxidation in upland soils.

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Archaeal diversity and community structure in a Swedish barley field: Specificity of the EK510R/(EURY498) 16S rDNA primer

Cited by 20 publications

References 84 publications

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

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

Archaea in dry soil environments

Are oxygen limitations under recognized regulators of organic carbon turnover in upland soils?

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