Metabolic pathways of CO2 fixing microorganisms determined C-fixation rates in grassland soils along the precipitation gradient

Huang, Qian; Huang, Yanqun; Wang, Baorong; Dippold, Michaela A.; Li, Haohao; Li, Na; Jia, Penghui; Zhang, Haixing; An, Shaoshan; Kuzyakov, Yakov

doi:10.1016/j.soilbio.2022.108764

Cited by 36 publications

(19 citation statements)

References 69 publications

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“…For example, the increase in abundance of genes involved in the Calvin cycle, the reductive tricarboxylic acid cycle, starch catabolism, cellulose and hemicellulose catabolism, and pectin catabolism that related to Y-strategy are favored microbial C formation ( Figure 4 and Supplementary Data S1 ). The Calvin cycle and reductive tricarboxylic acid cycle were the common C fixation pathways in farmland ecosystems ( Huang et al, 2022 ). The higher abundance of the cbbL gene that is responsible for the Calvin cycle in low-salinity soil indicated a greater ability to fix CO 2 than in high-salinity soil.…”

Section: Discussionmentioning

confidence: 99%

“…Similar results in a previous study reported that salt stress inhibited the expression of activities of the Calvin cycle enzymes ( Yu et al, 2011 ). Several genes, including nifJ, aclB, porA/B/C/D, ppc, and korA/B/D , that encode the reductive tricarboxylic acid cycle participate in the CO 2 fixation metabolic pathway, which is favored to maximize the microbial growth yield owing to the low energy consumption of the reductive tricarboxylic acid cycle ( Huang et al, 2022 ). In addition, starch, cellulose, hemicellulose, and pectin are easily taken up and metabolized by microorganisms ( Chen et al, 2014 ), which thereby promotes their biomass growth.…”

Section: Discussionmentioning

confidence: 99%

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Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Chen

et al. 2023

Front. Microbiol.

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Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Chen

et al. 2023

Front. Microbiol.

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“…In terrestrial ecosystems, CFMs are estimated to sequester ca. 4.9 Pg of carbon annually (Huang et al, 2022), making their carbon fixation function crucial for greenhouse gas regulation, soil carbon uptake and global carbon cycling (Liao et al, 2023;Mahmoudi & Wilhelm, 2023). Among the eight major carbon fixation pathways identified in nature, the Calvin cycle is the primary pathway for microbial assimilation of CO 2 (Berg, 2011).…”

Section: Introductionmentioning

confidence: 99%

Effect of soil flooding and drying on the metabolic pathways of CO₂ fixing microorganisms along an elevation gradient in the Three Gorges Reservoir drawdown area

Zhang,

Chen

et al. 2024

Soil Use and Management

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The construction of dams and subsequent water level fluctuations significantly alters the environmental conditions of reservoir ecosystems, affecting the metabolic pathways of CO2 fixing microorganisms (CFMs) and carbon storage in drawdown areas. We investigated the response of soil bacterial communities and carbon fixation pathways to periodic flooding and drying at different elevations by collecting surface soil samples (0–10 cm) in the drawdown area of the Three Gorges Reservoir. The results show that periodic flooding and drying increased the complexity of bacterial co‐occurrence networks. We identified the reductive citrate cycle (rTCA cycle), dicarboxylate‐hydroxybutyrate cycle (DC/4‐HB cycle), 3‐Hydroxypropionate cycle (3‐HP cycle) and reductive pentose phosphate cycle (Calvin cycle) as the main carbon fixation pathways. Notably, as the inundation duration increased, the abundance of the Calvin cycle and its key gene (cbbL) gradually decreased. We also found that soil moisture, pH and the different organic carbon components affected the composition of bacterial communities and the abundance of carbon fixation pathways. These findings elucidate evolutionary trends bacterial communities and the impacts of water level fluctuations on microbial‐mediated carbon cycling processes because of dam construction.

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“…After being amplified with a fluorescent probe or labeling dye, it is possible to discriminate between positive and negative droplets (see Hindson et al, 2011). Several studies have compared qPCR and ddPCR and found that ddPCR had better precision, repeatability, sensitivity and stability than qPCR (Zhao et al, 2016;Taylor et al, 2017;Xue et al, 2018;Wang et al, 2022). Nowadays, ddPCR is increasingly used in environmental studies (see Hou et al, 2023 for a complete review), even though several challenges are faced and require appropriate optimization of ddPCR parameters (see Kokkoris et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Carbon fixing microorganisms (CFMs) are key drivers of the carbon (C) cycle as they assimilate atmospheric CO 2 and contribute to the soil organic C sequestration (Yuan et al, 2012; Ge et al, 2013; Liu et al, 2018). CFMs fix CO 2 through six major metabolic pathways, namely, the reductive pentose phosphate cycle (also known as Calvin-Benson-Bassham, CBB cycle), the reductive citrate cycle (rTCA cycle), the 3-hydroxypropionate bi-cycle (3-HP cycle), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle), the dicarboxylate-hydroxybutyrate cycle (DC/4-HB cycle) and the reductive acetyl-CoA pathway (also known as Wood-Ljungdahl pathway) (Liu et al, 2018; Huang et al, 2022). The CBB cycle is the predominant pathway utilized by microorganisms in soils (Bay et al, 2021).…”

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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Metabolic pathways of CO2 fixing microorganisms determined C-fixation rates in grassland soils along the precipitation gradient

Cited by 36 publications

References 69 publications

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Effect of soil flooding and drying on the metabolic pathways of CO₂ fixing microorganisms along an elevation gradient in the Three Gorges Reservoir drawdown area

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

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Metabolic pathways of CO2 fixing microorganisms determined C-fixation rates in grassland soils along the precipitation gradient

Cited by 36 publications

References 69 publications

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Effect of soil flooding and drying on the metabolic pathways of CO2 fixing microorganisms along an elevation gradient in the Three Gorges Reservoir drawdown area

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

Contact Info

Product

Resources

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Effect of soil flooding and drying on the metabolic pathways of CO₂ fixing microorganisms along an elevation gradient in the Three Gorges Reservoir drawdown area

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