Quantification of bacterial RubisCO genes in soils by cbbL targeted real-time PCR

Selesi, Draženka; Pattis, Isabelle; Schmid, Michael; Kandeler, Ellen; Hartmann, Anton

doi:10.1016/j.mimet.2007.03.002

Cited by 82 publications

(56 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This verrucomicrobial RuBisCO type has not been detected before by molecular approaches. This can be explained by the mismatches we observed when comparing the Methylacidiphilum-type cbbL sequence with all the available RuBisCO primers sets (1,11,26,29). The 13 C label percentage in the biomasses of both the batch and the chemostat experiments was in complete accordance with the 13 C label percentage of CO 2 in the cultures and confirms that biomass carbon was derived exclusively from CO 2 .…”

Section: Discussionmentioning

confidence: 59%

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

et al. 2011

View full text Add to dashboard Cite

Genome data of the extreme acidophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum strain SolV indicated the ability of autotrophic growth. This was further validated by transcriptome analysis, which showed that all genes required for a functional Calvin-Benson-Bassham (CBB) cycle were transcribed. Experiments with 13 Methanotrophs are a unique group of microorganisms within the methylotrophs that oxidize methane (CH 4 ) to carbon dioxide (CO 2 ). Until 2007, the phylogenetic distribution of the aerobic methanotrophs was limited to the ␣ and ␥ subclasses of the proteobacteria (16). In 2007, novel thermoacidophilic aerobic methanotrophs were discovered in geothermal areas in New Zealand, Russia, and Italy (9,18,23). These methanotrophs represented a distinct phylogenetic lineage within the Verrucomicrobia, for which the genus name Methylacidiphilum was proposed (22).Recently, methanotrophy was discovered in a member of the NC10 phylum. It was shown that "Candidatus Methylomirabilis oxyfera," enriched under strict anoxic conditions, produces its own oxygen from nitrite (12). This oxygen is then used for CH 4 oxidation in a biochemical pathway comparable to those of aerobic methanotrophs.During the aerobic oxidation of CH 4 and methanol by proteobacterial methanotrophs, formaldehyde is produced. This central metabolite can be further oxidized to CO 2 or directly assimilated via intermediates of the central metabolism. Based on the pathway used for formaldehyde assimilation, methanotrophs were divided into type I and type II. Type II methanotrophs use the serine pathway, in which formaldehyde and CO 2 are utilized in a one-to-one ratio to produce acetyl coenzyme A (acetyl-CoA) for biosynthesis (8), while type I methanotrophs use the ribulose monophosphate pathway for the assimilation of formaldehyde to form glyceraldehyde-3-phosphate as an intermediate of central metabolism (16). In the latter pathway, all cellular carbon is assimilated at the oxidation level of formaldehyde. Genome data of some proteobacterial methanotrophs (Methylococcus capsulatus Bath, Methylocella silvestris BL2 [7,31]) and nonproteobacterial aerobic methanotrophs (Methylacidiphilum infernorum V4, Methylacidiphilum fumariolicum SolV, and "Candidatus Methylomirabilis oxyfera" [12,17,22]) revealed the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key enzyme of the Calvin-Benson-Bassham (CBB) cycle. M. capsulatus Bath was found to contain RuBisCO in an active form (27), and genome analysis suggested that a variant of the CBB cycle may operate (19,31). Although hydrogen seems to support moderate growth with CO 2 on agar plates for M. capsulatus Bath and some other methanotrophs (3), autotrophic growth in liquid cultures has not been reported. Marker exchange mutagenesis deleting the genes encoding RuBisCO may give definite answers on the exact role of RuBisCO, but unfortunately, a good genetic system for manipulation of these bacteria is lacking.Analyses of the complete genome sequence of M. infernorum...

show abstract

Section: Discussionmentioning

confidence: 59%

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

et al. 2011

View full text Add to dashboard Cite

show abstract

“…However, in soils where organic carbon is not limiting, the role of obligate autotrophy vs mixotrophic and/or heterotrophic CO 2 assimilation is still unclear. Previous studies suggested a significant contribution of non-obligate autotrophic CO 2 assimilation to the overall soil carbon budget (Miltner et al, 2004;Š antrů čková et al, 2005;Selesi et al, 2005Selesi et al, , 2007, which might be as high as 3-5% of the net respiration (Miltner et al, 2005). Furthermore, addition of organic substrates to dark soil incubations stimulated CO 2 fixation and correlated with respiration (Miltner et al, 2005(Miltner et al, , Š antrů čková et al, 2005.…”

Section: Bacterial Groups Assimilating Volcanic Comentioning

confidence: 98%

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette

et al. 2014

View full text Add to dashboard Cite

Effects of extremely high carbon dioxide (CO 2 ) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO 2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (DpH B0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH 4 ) from hydrogen (H 2 ) and CO 2 consistent with elevated CH 4 and acetate levels in the mofette soil. 13 CO 2 mofette soil incubations showed high label incorporations with B512 ng 13 C g (dry weight (dw)) soil À 1 d À 1 into the bulk soil and up to 10.7 ng 13 C g (dw) soil À 1 d À 1 into almost all analyzed bacterial lipids. Incorporation of CO 2 -derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of 13 CO 2 . Subdivision 1 Acidobacteriaceae assimilated 13 CO 2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO 2 assimilation. We conclude that CO 2 -induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.

show abstract

“…Also numbers of RubisCO encoding genes are 2 orders of magnitude more abundant than in agricultural soils (Selesi et al, 2007) and twice as high as in organic rich paddy rice fields (Wu et al, 2015), suggesting microbial carbon derived from CO 2 assimilation as an important carbon source. Further evidence is given by the isotope data, as mofette SOM at 0-10 cm differs from a pure plant signal.…”

Section: Carbon Sources In Mofette Soilsmentioning

confidence: 99%

“…lating enzyme for obligate and facultative chemo-or photoautotrophic microorganisms that fix CO 2 using the CalvinBenson-Bassham (CBB) cycle has been shown to be highly abundant in agricultural, forest, and volcanic soils (Nanba et al, 2004;Tolli and King, 2005;Selesi et al, 2007). Direct uptake of CO 2 into microbial biomass (MB) and soil organic matter (SOM) by photoautotrophic and chemoautotrophic organisms has been measured in paddy rice and agricultural upland soils (Liu and Conrad, 2011;Wu et al, 2015Wu et al, , 2014 as well as under manipulating experimental conditions, such as H 2 amendment (Stein et al, 2005) or addition of reduced sulfur compounds (Hart et al, 2013).…”

Section: E Nowak Et Al: Autotrophic Fixation Of Geogenic Co 2 Bymentioning

confidence: 99%

Autotrophic fixation of geogenic CO<sub>2</sub> by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

et al. 2015

View full text Add to dashboard Cite

Abstract.To quantify the contribution of autotrophic microorganisms to organic matter (OM) formation in soils, we investigated natural CO 2 vents (mofettes) situated in a wetland in northwest Bohemia (Czech Republic). Mofette soils had higher soil organic matter (SOM) concentrations than reference soils due to restricted decomposition under high CO 2 levels. We used radiocarbon ( 14 C) and stable carbon (δ 13 C) isotope ratios to characterize SOM and its sources in two mofettes and compared it with respective reference soils, which were not influenced by geogenic CO 2 .The geogenic CO 2 emitted at these sites is free of radiocarbon and enriched in 13 C compared to atmospheric CO 2 . Together, these isotopic signals allow us to distinguish C fixed by plants from C fixed by autotrophic microorganisms using their differences in 13 C discrimination. We can then estimate that up to 27 % of soil organic matter in the 0-10 cm layer of these soils was derived from microbially assimilated CO 2 .Isotope values of bulk SOM were shifted towards more positive δ 13 C and more negative 14 C values in mofettes compared to reference soils, suggesting that geogenic CO 2 emitted from the soil atmosphere is incorporated into SOM. To distinguish whether geogenic CO 2 was fixed by plants or by CO 2 assimilating microorganisms, we first used the proportional differences in radiocarbon and δ 13 C values to indicate the magnitude of discrimination of the stable isotopes in living plants. Deviation from this relationship was taken to indicate the presence of microbial CO 2 fixation, as microbial discrimination should differ from that of plants. 13 CO 2 -labelling experiments confirmed high activity of CO 2 assimilating microbes in the top 10 cm, where δ 13 C values of SOM were shifted up to 2 ‰ towards more negative values. Uptake rates of microbial CO 2 fixation ranged up to 1.59 ± 0.16 µg g −1 dw d −1 . We inferred that the negative δ 13 C shift was caused by the activity of autotrophic microorganisms using the Calvin-Benson-Bassham (CBB) cycle, as indicated from quantification of cbbL/cbbM marker genes encoding for RubisCO by quantitative polymerase chain reaction (qPCR) and by acetogenic and methanogenic microorganisms, shown present in the mofettes by previous studies. Combined 14 C and δ 13 C isotope mass balances indicated that microbially derived carbon accounted for 8-27 % of bulk SOM in this soil layer.The findings imply that autotrophic microorganisms can recycle significant amounts of carbon in wetland soils and might contribute to observed radiocarbon reservoir effects influencing 14 C signatures in peat deposits.

show abstract

Quantification of bacterial RubisCO genes in soils by cbbL targeted real-time PCR

Cited by 82 publications

References 29 publications

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette

Autotrophic fixation of geogenic CO<sub>2</sub> by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

Contact Info

Product

Resources

About

Quantification of bacterial RubisCO genes in soils by cbbL targeted real-time PCR

Cited by 82 publications

References 29 publications

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette

Autotrophic fixation of geogenic CO&lt;sub&gt;2&lt;/sub&gt; by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

Contact Info

Product

Resources

About

Autotrophic fixation of geogenic CO<sub>2</sub> by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette