An Aerobic Anoxygenic Phototrophic Bacterium Fixes CO<sub>2</sub>via the Calvin-Benson-Bassham Cycle

Tang, Kai; Liu, Yang; Zeng, Yonghui; Feng, Fan; Jin, Ke; Yuan, Bo

doi:10.1101/2021.04.29.441244

Cited by 3 publications

(6 citation statements)

References 78 publications

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“…S4). This is consistent with the emerging picture of Rhodospirillales AAPs that have Rubisco and the whole Calvin cycle for carbon fixation ( 54 ). There also are taxa without photosynthetic traits that contain a catalytically active Form I Rubisco, as in the case of Acidiphilium iwatense ( Fig.…”

Section: Resultssupporting

confidence: 89%

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The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

Degli Esposti,

Guerrero,

Rogel

et al. 2023

Microbiol Spectr

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We present here a comprehensive phylogenomic analysis of Acetobacteraceae , a vast group of alphaproteobacteria that has been widely studied for their economic importance. Our results indicate that the ancestor of Acetobacteraceae most likely was photosynthetic and evolved via a progressive transition from versatile photoferrotrophy to the incomplete oxidation of organic substrates defining acetous physiology. Vestigial signs of photosynthetic carotenoid metabolism are present in non-photosynthetic acetous taxa that have lost cytochrome oxidase, while their sister taxa retain such traits. The dominant terminal oxidase of acetous bacteria, the bo 3 ubiquinol oxidase, is derived from duplication and diversification of operons present in Acidocella taxa that have lost photosynthesis. We analyzed the bioenergetic traits that can compensate for the electron transfer function of photosynthetic reaction centers or constitute alternative pathways for the oxidoreduction of c -type cytochromes, such as iron oxidation. The latter pathway bypasses the deranged cytochrome bc 1 complex that is characteristically present in acidophilic taxa due to the loss of conserved ligands in both the Rieske iron-sulfur protein and cytochrome b subunit. The deranged or non-functional bc 1 complex may be retained for its structural role in stabilizing Complex I. The combination of our phylogenetic analysis with in-depth functional evaluations indicates that the order Acetobacterales needs to be emended to include three families: Acetobacteraceae sensu stricto , Roseomonadaceae fam. nov., and Acidocellaceae fam. nov. IMPORTANCE Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae , for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter . Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.

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Section: Resultssupporting

confidence: 89%

“…5A ). Indeed, aerobic photosynthesis helps a variety of bacteria to survive in deserts and other extreme, oligotrophic environments ( 54 , 61 ). Ultimately, the distribution pattern and the number of pyrroloquinoline (PQQ)-dependent Q reductases emerged as one of the most widespread traits compensating for the loss of RCs ( Fig.…”

Section: Resultsmentioning

confidence: 99%

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

Degli Esposti,

Guerrero,

Rogel

et al. 2023

Microbiol Spectr

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“…Also, the use of RNA quantification instead of DNA may better evidence abundance patterns between phototrophs and chemoautotrophs. Furthermore, our results show that AAnPBs represented ∼8% of total prokaryotes in Counozouls and ∼15% of total prokaryotes in Männikjärve, suggesting they may play a significant role in the C cycle of peatlands as some strains possessing CBB cycle genes can actively fix atmospheric CO 2 (Graham et al, 2018; Tang et al, 2021). Altogether these results show that further work is urgently needed to better quantify the contribution of microorganisms to peatland CO 2 uptake as current estimates based on sole oxygenic phototrophs (Hamard et al, 2021a) may be strongly underestimated.…”

Section: Resultsmentioning

confidence: 84%

“…Potential CO 2 fixation through the CBB cycle also recently emerged in aerobic anoxygenic phototrophic bacteria (AAnPBs). Recent studies found AAnPB strains possessing (and expressing) genes of the CBB cycle (Graham et al, 2018; Tang et al, 2021). Even though CFMs are now well recognized for their role in autotrophic CO 2 fixation in soils, their absolute quantification remains elusive (Liao et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Development of a ddPCR approach for the absolute quantification of soil microorganisms involved in atmospheric CO₂fixation

Le Geay,

Mayers,

Küttim

et al. 2024

Preprint

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Carbon fixing microorganisms (CFMs) play a crucial role in soil carbon (C) cycling contributing to carbon uptake and sequestration through various metabolic pathways. Despite their significance, quantification of the absolute abundance of CFMs in soils remains elusive. This study employed a digital droplet PCR (ddPCR) approach to quantify the abundance of key and emerging CFM pathways in fen and bog across different depths (0-15 cm). Targeting total prokaryotes (16S rRNA gene), oxygenic phototrophs (23S rRNA gene), aerobic anoxygenic phototrophic bacteria (AAnPB, pufM gene), and chemoautotrophs (cbbL gene), we optimized ddPCR conditions to achieve absolute quantification of these genes. Overall, our results revealed that oxygenic phototrophs were the most abundant CFMs, constituting 12% of total prokaryotic abundance, followed by chemoautotrophs (10%) and AAnPBs (9%). Fen exhibited higher gene concentrations than bog. Depth variations were also observed, differing between fen and bog for all genes. Our findings highlight the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimations that relied solely on oxygenic phototrophs for microbial CO2 fixation assessments. Incorporating absolute gene quantification is crucial for a comprehensive understanding of microbial contributions to soil processes, shedding light on the intricate mechanisms of soil functioning in peatlands.

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Section: Introductionmentioning

confidence: 99%

Development of a digital droplet PCR approach for the quantification of soil micro‐organisms involved in atmospheric CO₂ fixation

Le Geay,

Mayers,

Küttim

et al. 2024

Environmental Microbiology

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Carbon‐fixing micro‐organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro‐organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

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An Aerobic Anoxygenic Phototrophic Bacterium Fixes CO₂via the Calvin-Benson-Bassham Cycle

Cited by 3 publications

References 78 publications

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

Development of a ddPCR approach for the absolute quantification of soil microorganisms involved in atmospheric CO₂fixation

Development of a digital droplet PCR approach for the quantification of soil micro‐organisms involved in atmospheric CO₂ fixation

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An Aerobic Anoxygenic Phototrophic Bacterium Fixes CO2via the Calvin-Benson-Bassham Cycle

Cited by 3 publications

References 78 publications

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

Development of a ddPCR approach for the absolute quantification of soil microorganisms involved in atmospheric CO2fixation

Development of a digital droplet PCR approach for the quantification of soil micro‐organisms involved in atmospheric CO2 fixation

Contact Info

Product

Resources

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An Aerobic Anoxygenic Phototrophic Bacterium Fixes CO₂via the Calvin-Benson-Bassham Cycle

Development of a ddPCR approach for the absolute quantification of soil microorganisms involved in atmospheric CO₂fixation

Development of a digital droplet PCR approach for the quantification of soil micro‐organisms involved in atmospheric CO₂ fixation