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# The soil microbial carbon pump for carbon sequestration

Longkai Qiao, Junfei Wang, Shuangshuang Wei, Yilong Ren, Eric Lichtfouse,
Jie Han

► To cite this version:

Longkai Qiao, Junfei Wang, Shuangshuang Wei, Yilong Ren, Eric Lichtfouse, et al.. The soil microbial carbon pump for carbon sequestration. Environmental Chemistry Letters, 2025, 23, pp.1145-1151. 10.1007/s10311-025-01861-4 . hal-05145106

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# The soil microbial carbon pump for carbon sequestration

Longkai Qiao<fnref n="1" />,<fnref n="2" /> · Junfei Wang<fnref n="2" /> · Shuangshuang Wei<fnref n="3" /> Ⓓ ID · Yilong Ren<fnref n="3" /> Ⓓ ID · Eric Lichtfouse<fnref n="3" /> Ⓓ ID · Jie Han<fnref n="1" />,<fnref n="2" /> Ⓓ ID

Will humans survive the climate crisis? The burning of fossil fuels and other carbon dioxide-emitting industrial and agricultural activities have sharply increased the levels of atmospheric carbon dioxide (CO₂) from about 280 ppmv in 1850 to 430 ppmv in April 2025 [1–3]. This has induced a +1.49 °C increase of the global surface temperature versus the 1850–1900 pre-industrial average temperature, with the ten most recent years being the warmest years on record [4, 5]. This change is remarkably represented using data from the United States National Aeronautics Space Administration (US NASA, Fig. 1). In April 2025, the threshold of a maximum 1.5 °C increase of the 2015 Paris Agreement to limit greenhouse emissions has thus nearly been reached [6], which means that we have just entered an era where catastrophic events will highly intensify [7]. In fact, +1.5 °C is already too high and is likely to raise sea-level by several meters, thus causing substantial damage to coastal populations [8]. This calls for techniques such as radiative forcing geoengineering [9] that could rapidly decrease atmospheric CO₂ levels on the global scale. As a consequence, the number of academic reports on carbon capture and sequestration since 2015 has more than doubled compared to from 1992 to 2014 [10]. Here we discuss the global soil carbon pool, microbial carbon capture, the microbial carbon pump, contributions from plants, fungi and bacteria, and the use of synthetic microbial communities.

## Soil is a major global carbon pool

More than three-quarters of terrestrial organic carbon is stored in soils over 60% of the global land area [11]. Soils contain globally 2,500 Gt of carbon, comprising about 1,550 Gt of soil organic carbon (SOC) and 950 Gt of soil inorganic carbon (SIC). The soil carbon pool is 3.3 times the size of the atmospheric pool (760 Gt) and 4.5 times the size of the biotic pool (560 Gt) [12]. Soil organic carbon, included into soil organic matter (SOM), is the major global carbon pool [11]. Soil organic matter is a complex mixture originating from the residues and metabolic products of plants and soil organisms [13–15]. Plant residues in soil mainly consist of aboveground litterfall, root exudates, and fine root litter [16]. These plant residues undergo microbial decomposition, thereby contributing to the overall soil carbon pool. Carbon fixed by plant roots is estimated to be 2–13 times higher than that from their aboveground plant biomass [17]. Overall, soils represent a major global carbon pool that can increase or decrease atmospheric CO₂ levels depending on soil management practices; and the amount of soil carbon is controlled by various factors, in particular the microbial activity.

## Microbial carbon capture

Microorganisms play a critical role in soil carbon sequestration processes [18–21]. Indeed, shifts in the composition of key soil microbial communities directly influence carbon balance and total carbon stocks in soil [22]. Primary producers, such as plants, convert CO₂ and water into organic matter through photosynthesis [23]. Besides plants, autotrophic microbes are also primary producers, capable of assimilating CO₂ through various pathways. These pathways include the Calvin cycle, reductive tricarboxylic acid cycle, 3-hydroxypropionate cycle, 3-hydroxypropionate/4-hydroxybutyrate cycle, and dicarboxylate/4-hydroxybutyrate cycle, which are the primary assimilation pathways for photoautotrophic and chemolithoautotrophic microbes [24]. Nonetheless, the

<footnote>☒ Eric Lichtfouse
eric.lichtfouse@icloud.com</footnote>

<footnote>☒ Jie Han
jiehan@xjtu.edu.cn</footnote>

<footnote n="1">¹ Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi’an Jiaotong University, Xi’an Jiaotong University, Xi’an 710049, China</footnote>

<footnote n="2">² School of Human Settlement and Civil Engineering, Xi’an Jiaotong University, Xi’an 710049, China</footnote>

<footnote n="3">³ State Key Laboratory of Multiphase Flow in Power Engineering, Xi’an Jiaotong University, Xi’an 710049, China</footnote>
<figure><img src="image_2.png" /><figcaption>**Fig. 1** Global surface temperatures in 1884 and 2022. Dark blue shows areas cooler than average. Dark red shows areas warmer than average. Short-term variations are smoothed out using a 5-year running average to make trends more visible in this map. Modified from NASA's Scientific Visualization Studio [4]</figcaption></figure>

capacity of soil autotrophic microbes to assimilate atmospheric CO₂ remains overall limited [25, 26]. Indeed, in a laboratory microcosm incubated with ¹⁴C-labeled CO₂ for 45 days, it was demonstrated that CO₂ fixed by autotrophic microorganisms in paddy soil represents only 0.37% to 1.18% of the soil organic carbon [27].

The role of heterotrophic microbes in fixing atmospheric carbon and their broader contributions to soil carbon cycling has received less attention [28]. As decomposers in the food web, heterotrophic microbes in soil obtain nutrients by breaking down animal, plant, and other organic residues. These nutrients are either respired back into the atmosphere as CO₂ and water, or used by microbes to synthesize new organic compounds and metabolic products [29, 30]. After death, microbial biomass is accumulated as microbial

necromass [31]. Due to its relative recalcitrance to decomposition, microbial necromass represents a significant component of stable organic matter in soil [32, 33]. Furthermore, microbial metabolites and necromass can form more stable soil organic matter through interactions with soil mineral particles via processes such as adsorption, occlusion, aggregation, redox reactions, and polymerization, ensuring long-term carbon sequestration [13, 34–36].

Two amino sugars, i.e., glucosamine and muramic acid, are commonly used to identify the microbial contribution to soil organic matter because these compounds are not biosynthesized by plants [37]. For instance, it has been estimated that microbial necromass accounts for more than 50% of soil organic carbon, using these markers of microbial necromass in temperate soils [38]. Similarly, data from two US
experimental farms show that organic carbon from microbial necromass comprises 40–70% of the total soil organic carbon [39]. A regional study of forest soils in eastern China also demonstrated that microbial necromass accounts, on average, 45.5% of the total soil organic carbon in tropical, subtropical, temperate, and boreal forests soil across the region [40]. These findings indicate that an abundant and active population of decomposers is a critical determinant of soil carbon sequestration capacity [31, 41, 42].

## The soil microbial carbon pump

The ‘microbial carbon pump’ has been conceptualized to elucidate the roles of microorganisms in carbon cycling processes in natural environments [35, 43–45]. This was initially developed to explain the microbial generation of recalcitrant dissolved organic matter and associated carbon storage in marine ecosystems [43]. The underlying mechanism involves microbial activities, e.g., heterotrophic processing, viral lysis, and exudation, which transform labile and semi-labile dissolved organic matter into recalcitrant forms that resist degradation and persist in oceans for thousands of years.

The microbial carbon pump in soil was proposed in 2017 [44], yet earlier molecular and imaging observations on humin, the chemically stabler fraction of soil organic matter, showed the occurrence of microbial resistant polymers [15, 33, 46, 47]. Researchers distinguish the microbial formation of soil organic matter in two pathways. First, ex vivo, extracellular modification, wherein microorganisms transform plant residues into plant-derived carbon that is not readily assimilated; and second, in vivo turnover of organic substrates via cell uptake, biosynthesis, growth, and death. Both pathways explain how microbial processing transforms labile and semi-labile organic matter into stable soil organic carbon. A refined conceptual model of the soil microbial carbon pump was recently proposed [45], which expands the existing model by incorporating autotrophic microbial pathways for carbon sequestration over long timescales (Fig. 2).

## Distinct fungal and bacterial contributions

To understand the role of bacterial-fungal interactions in carbon sequestration, scientists have grown artificial bacterial-fungal communities [48]. They found that fungal and bacterial necromass contribute distinctively to the forms, stability, and accumulation of soil organic carbon, due to differences in their cellular structure and functional roles. For example, bacteria tend to decompose easily degradable litter, whereas fungi dominate the decomposition of more recalcitrant plant residues [49, 50]. Specifically, fungi acted as the dominant

<figure><img src="image_3.png" /><figcaption>**Fig. 2** The soil microbial carbon pump. Heterotrophic microbes transform plant residues via in vivo turnover and ex vivo modification, while autotrophic microbes directly assimilate atmospheric carbon dioxide (CO₂) into cellular biomass. Microbial biomass and metabolites generated through these processes are further stabilized via the mineral carbon pump, where soil minerals enhance soil organic carbon persistence through adsorption, occlusion, aggregation, redox reactions, and polymerization, forming organo-mineral complexes that are too large to be ingested by microbes and/or limiting the functioning of hydrolytic enzymes [35, 44]</figcaption></figure>

decomposers of plant residues through the expression of cellulases, xylanases, and ligninolytic enzymes, while bacteria functioned as exploiters, utilizing the degradation products of fungi via glycosidases [48].

Fungal necromass primarily consists of carbon-rich cell wall fragments, whereas bacterial cell walls are nitrogen-rich [51]. The recalcitrant nature of fungal cell walls implies that fungal necromass decomposes more slowly than bacterial necromass in soil. Consequently, fungi generate higher quantities of stable soil organic carbon compared to bacteria when an equivalent amount of nutrients is consumed. Fungal necromass typically constitutes the majority of microbial-derived residues in the topsoil, from 0 to 60 cm, and serves as a precursor to stable organic carbon in soil [52–55]. A
global meta-analysis, utilizing 1,716 observations of glu-
cosamine and muramic acid content in cropland, grassland,
and forest soils, mostly within the depth of 0–75 cm, dem-
onstrated that fungal necromass contributed more than 65%
of the total microbial necromass, while bacterial necromass
accounted for 32–36% of the total microbial necromass, in
the top and shallow soils [55]. Furthermore, fungal hyphae
act as binding agents, entangling soil mineral particles and
micro-aggregates in the topsoil to form larger aggregates,
thereby providing physical protection to soil organic carbon
[41, 56, 57].

By contrast, bacterial necromass is the primary contribu-
tor to soil organic carbon in the subsoil, from 60 to 100 cm
[53, 58]. The carbon-to-nitrogen ratio of fungal biomass,
C/N of 5–17, is typically higher than that of bacterial bio-
mass, of about 6.5 [59]. Nitrogen-rich bacterial necromass
undergoes faster turnover in soil, releasing more nutrients
than fungal necromass [54]. Moreover, the nitrogen-rich
organic carbon in bacterial necromass binds more readily
to mineral particles than fungal-derived carbon [60]. In the
topsoil, the low bulk density, high porosity, abundant plant
residues, and ample dioxygen promote higher microbial
activity, thus accelerating bacterial necromass turnover. In
the subsoil, however, factors including high bulk density,
limited porosity, reduced oxygen availability, restricted fresh
organic inputs, and the overall lower microbial activity, favor
the long-term stabilization of organic carbon derived from
bacterial necromass [53, 58].

Synthetic microbial communities

Synthetic microbial communities, named ‘SynComs’, are a
new tool in research at the intersection of synthetic biology
and environmental microbiology [61]. SynComs refer to the
artificial construction of multi-species microbial consortia
characterized by well-defined community compositions
and high manipulability. Initially developed for biomedical
applications, SynComs were first reported in 2011, where
they mimicked a simplified human gut bacterial community
in germ-free mice, to investigate how these communities
respond to dietary influences [62]. Subsequently, SynComs
were adopted in agricultural research to investigate the roles
of plant-associated microbial communities in promoting host
health and stress tolerance.

Investigations have gradually expanded from model
plants such as *Arabidopsis thaliana* [63, 64] to agricultural
crops such as maize [65, 66], and from rhizosphere microbi-
ota to phyllosphere microbiota [67–69]. SynComs have also
been employed to combat plant diseases, such as the root
rot disease in *Astragalus mongholicus* [70]. Furthermore, in
2019–2020, SynComs were used to study the degradation of
organic contaminants, e.g., atrazine, chloramphenicol, and

phthalate esters, in contaminated soils [71–73]. Despite
these advancements, investigations into soil microbial car-
bon sequestration, particularly the use of SynComs, remain
limited [48]. This lack of knowledge is accentuated by our
actual poor knowledge of the molecular structure, precise
sources and transformation pathways of humic substances
[46, 74, 75].

**Funding** This work was funded by the Shaanxi Provincial Department of Science and Technology “Scientist + Engineer” Team Building Project (2023KJT-198), the Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd. and Xi’an Jiaotong University (Grant No. 201912131-D9).

Declarations

**Conflict of interest** The authors declare that they have no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

**Competing interest** EL and JH are Chief Editors of Environmental Chemistry Letters.

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