Metagenomic and 13C tracing evidence for autotrophic atmospheric carbon absorption in a semiarid desert

Liu, Zhen; Sun, Yanfei; Zhang, Yuqing; Feng, Wei; Lai, Zongrui; Fa, Keyu; Qin, Shugao

doi:10.1016/j.soilbio.2018.07.012

Cited by 64 publications

(39 citation statements)

References 56 publications

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“…There are indications that dark soil microbial CO 2 fixation occurs in a large range of soils, including Mediterranean soils (Nel & Cramer, ), semiarid desert soils (Liu et al, ), arctic tundra soils (Šantrůčková et al, ), temperate peatland soils (Beulig et al, ; Nowak et al, ), paddy soils (Ge et al, ; Yuan et al, ), temperate meadow soils (Šantrůčková et al, ) as well as cropland soils (Miltner, Richnow, Kopinke, & Kästner, ). Thus, the process might occur ubiquitously in soils, and if quantitatively important, might affect the global C cycle.…”

Section: Introductionmentioning

confidence: 99%

Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Spohn

Müller

Höschen

et al. 2019

Global Change Biology

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Dark, that is, nonphototrophic, microbial CO2 fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO2 fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO2 fixation in temperate forest soils, to determine the relationship between the soil CO2 concentration and dark microbial CO2 fixation, and to estimate the relative contribution of different microbial groups to dark CO2 fixation. For this purpose, we conducted a 13C‐CO2 labeling experiment. We found that the rates of dark microbial CO2 fixation were positively correlated with the CO2 concentration in all soils. Dark microbial CO2 fixation amounted to up to 320 µg C kg−1 soil day−1 in the Ah horizon. The fixation rates were 2.8–8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%–3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO2 contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO2 was mostly fixed by gram‐positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO2 fixation rate in temperate forest soils increases in periods of high CO2 concentrations, that dark microbial CO2 fixation is mostly accomplished by gram‐positive bacteria, and that dark microbial CO2 fixation contributes to the formation of soil organic matter.

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Section: Introductionmentioning

confidence: 99%

Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Spohn

Müller

Höschen

et al. 2019

Global Change Biology

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“…Results show that the Calvin cycle is the most abundant pathway in paddy soils according to marker genes analysis (Fig. 1), while other studies show that the reductive citric cycle dominates in desert soils (Liu et al ., 2018), and the reverse tricarboxylic acid cycle dominates in free‐fiving microorganisms at deep‐sea hydrothermal vents (Campbell and Cary, 2004). These results indicate the niche preference of different autotrophic metabolisms.…”

Section: Discussionmentioning

confidence: 99%

“…Metagenomics involves the direct sequencing of DNA from the environment and thus allows the examination of multiple biochemical pathways and associated processes, bypassing PCR primers, and so it is not limited to studying individual pieces of the metabolic puzzle (Venter et al ., 2004; Mackelprang et al ., 2011). With the development of high‐throughput sequencing techniques and a dramatic drop of sequencing prices, diversity analysis based on metagenomes is now feasible, which can target all metabolic pathways in soil and does not rely on the specificity and coverage of the primers used (Liu et al ., 2018; Ma et al ., 2018). Moreover, metagenomics allows us to specifically analyse or explore functional groups, study gene function and even reconstruct whole microbial genome from complex environment samples (Tyson et al ., 2004; Hultman et al ., 2015; Lam et al ., 2015; Anantharaman et al ., 2016; Metcalf et al ., 2016).…”

Section: Introductionmentioning

confidence: 99%

Metagenomic and ¹⁴C tracing evidence for autotrophic microbial CO₂ fixation in paddy soils

Xiao

et al. 2020

Environmental Microbiology

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Summary Autotrophic carbon dioxide (CO2) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with 14C‐labelling to investigate all known autotrophic pathways and CO2 assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%–82%) coding the ribulose‐bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of 14C‐CO2 are assimilated into SOC (74.3–175.8 mg 14C kg−1) and microbial biomass (5.2–24.1 mg 14C kg−1) after 45 days incubation, where more than 70% of 14C‐SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

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“…The raw reads were screened to generate clean data by removing adaptor contamination, host sequences, and low-quality reads [ 16 ]. After assembling with SOAP denovo 2.21 ( http://soap.genomics.org.cn/soapdenovo.html ) [ 17 ], scaffolds were split into scaftigs by removing the Ns.…”

Section: Methodsmentioning

confidence: 99%

Prebiotics enhance the biotransformation and bioavailability of ginsenosides in rats by modulating gut microbiota

Zhang

Chen

Duan

et al. 2021

Journal of Ginseng Research

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Background Gut microbiota mainly function in the biotransformation of primary ginsenosides into bioactive metabolites. Herein, we investigated the effects of three prebiotic fibers by targeting gut microbiota on the metabolism of ginsenoside Rb1 in vivo . Methods Sprague Dawley rats were administered with ginsenoside Rb1 after a two-week prebiotic intervention of fructooligosaccharide, galactooligosaccharide, and fibersol-2, respectively. Pharmacokinetic analysis of ginsenoside Rb1 and its metabolites was performed, whilst the microbial composition and metabolic function of gut microbiota were examined by 16S rRNA gene amplicon and metagenomic shotgun sequencing. Results The results showed that peak plasma concentration and area under concentration time curve of ginsenoside Rb1 and its intermediate metabolites, ginsenoside Rd, F2, and compound K (CK), in the prebiotic intervention groups were increased at various degrees compared with those in the control group. Gut microbiota dramatically responded to the prebiotic treatment at both taxonomical and functional levels. The abundance of Prevotella , which possesses potential function to hydrolyze ginsenoside Rb1 into CK, was significantly elevated in the three prebiotic groups (P < 0.05). The gut metagenomic analysis also revealed the functional gene enrichment for terpenoid/polyketide metabolism, glycolysis, gluconeogenesis, propanoate metabolism, etc. Conclusion These findings imply that prebiotics may selectively promote the proliferation of certain bacterial stains with glycoside hydrolysis capacity, thereby, subsequently improving the biotransformation and bioavailability of primary ginsenosides in vivo .

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Metagenomic and 13C tracing evidence for autotrophic atmospheric carbon absorption in a semiarid desert

Cited by 64 publications

References 56 publications

Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Metagenomic and ¹⁴C tracing evidence for autotrophic microbial CO₂ fixation in paddy soils

Prebiotics enhance the biotransformation and bioavailability of ginsenosides in rats by modulating gut microbiota

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Metagenomic and 13C tracing evidence for autotrophic atmospheric carbon absorption in a semiarid desert

Cited by 64 publications

References 56 publications

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Metagenomic and 14C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Prebiotics enhance the biotransformation and bioavailability of ginsenosides in rats by modulating gut microbiota

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Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Dark microbial CO₂ fixation in temperate forest soils increases with CO₂ concentration

Metagenomic and ¹⁴C tracing evidence for autotrophic microbial CO₂ fixation in paddy soils