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# Humus: dark side of life or intractable "aether"?

Jean-François Ponge

► To cite this version:

Jean-François Ponge. Humus: dark side of life or intractable "aether"?. Pedosphere, 2022, 32 (4), pp.660-664. 10.1016/S1002-0160(21)60013-9. hal-03651514

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Submitted on 25 Apr 2022

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Public Domain
Letter to the Editor

Humus: Dark side of life or intractable “aether”?

Dear Editor,

Johannes Lehmann and Markus Kleber, in a controver-
sial paper entitled “The contentious nature of soil organic
matter” (Lehmann and Kleber, 2015), suggested the aban-
donment of the term “humus” and other associated terms
such as “humic”, “humin”, “humified”, “humification”. The
first reason they cited was that these labels are only instru-
mental in outdated soil analytical methods, which are based
on alkaline extraction of soil organic matter (SOM). The se-
cond reason was that a wide array of soil analytical methods
suggests a continuum from macromolecules synthesized by
soil-dwelling organisms (plants, animals, and microbes) and
released from their living and dead parts to small organic
molecules excreted by organisms or issued from the enzy-
matic degradation of macromolecules. The third reason was
that too many “humus” chemists still rely only on extrac-
tion procedures, without due attention to the decomposer
community. These reasons prompted the authors to pro-
pose a model for the fate of organic debris, called the “soil
continuum model (SCM)”, which considers biopolymers of
various sizes, monomers, processes of aggregate formation
and destruction, transformation of residues to carbon dio-
xide, adsorption and desorption of organic matter to mineral
surfaces. I believe that their updated view of SOM, rejecting
the chemical sense appropriated to the word “humus”, is
received amiably since soil biology has currently become an
unavoidable component of “soil science”. However, a further
step should be taken towards clarifying our understanding
of the humus concept before rejecting it from the field of
science, as has been suggested by Ohno *et al.* (2019) in their
conclusion to an overview of the most recent developments
in SOM chemistry.

Piccolo (2002) described humic substances as “supramo-
lecular associations of self-assembling heterogeneous and
relatively small molecules deriving from the degradation
and decomposition of dead biological material”. This def-
inition is independent of previous ones and opens up new
avenues in SOM chemistry. The notion of “supramolecular
association”, already highlighted based on previous expe-
riments by Piccolo and Conte (2000), explains why humic
compounds extracted by classical analytical methods elude
chemical description. Even if unit components of humus
have been explored for a long time by soil chemists, no one

can describe a humus molecule with certainty. However,
the supramolecular concept (small molecules linked by van
der Waals forces and hydrogen bonds) allows explaining
that organic matter, not only in soils but also in sediments
and even in atmospheric aerosols (Kiss et al., 2003), may
upon degradation become self-reassembled in molecular
clouds dotted of original properties. Among them, the ability
to rapidly incorporate organic molecules (e.g., pesticides,
proteins, sugars) and to intimately associate with minerals
(e.g., clays, metal (oxyhydr)oxides) is remarkable (Livens,
1991; Senesi, 1992; Varadachari et al., 1994, Lichtfouse
et al., 1995; Zang et al., 2000). Molecular disorder operating
during humus formation is opposed to molecular ordering in
synthesis of proteins and other macromolecules by organ-
isms. Of interest is that the disordered regions of proteins
allow them to interact with their binding partners, like humus
does (Turoverov et al., 2010). The strong capacity of humic
substances to incorporate and sequester extraneous organic
molecules (Spaccini et al., 2002) points to the postulated
ability of humus to store recently added atmospheric carbon
and thus help mitigate climate change (Lal et al., 2007).

Gerke (2018) criticized the SCM model proposed by Lehmann and Kleber (2015), arguing that they did not take into consideration the polymerizing and further reacting ability of humic substances, restricting their model to decomposition processes and to the shift of plant and animal residues to biopolymers and then to monomers and finally to carbon dioxide. However, this criticism concerns only the processing chain displayed in the central part of the SCM model, overlooking that on both sides of their scheme, Lehmann and Kleber (2015) showed that the molecules derived from the degradation of organic debris and the organic debris itself contribute to the formation and destruction of aggregates and the adsorption and desorption processes involving mineral surfaces. The notion of “black carbon” (Goldberg, 1985) was also discussed in detail in Gerke’s review, claiming that humic aromatic structures are derived from fire-affected organic matter and thus should not be termed humus. Gerke explained why the methods used to quantify black carbon (molecular marker or UV methods) overestimated it and showed that black carbon and humic substances interacted strongly through covalent and non-covalent linkages.

Baveye and Wander (2019) also responded to Lehmann
and Kleber (2015). They showed that despite the turmoil
in the soil scientific community caused by Lehmann and Kleber's proposal to reject "humus", this term continues to be largely used by scientists, with an ever-increasing number of publications citing it routinely. They also showed that the "new" SCM model was not new and had been elaborated more than 80 years ago by Waksman (1936). This author defined humus as consisting "of certain constituents of the original plant material resistant to further decomposition, of substances undergoing decomposition, either by processes of hydrolysis or by oxidation and reduction, and of various compounds synthesized by microorganisms". Following Waksman's idea that a purely chemical assessment of humus was a dead end, Baveye and Wander (2019) pleaded for multidisciplinary research on humus, indicating that this notion was not a prerogative of chemists. From their point of view, microbiology and agronomy have their say, too. We also acknowledge and highly recommend involving zoology as well.

Commonly, non-chemists use the term “humus” to designate any kind of organic matter which cannot be assigned by the naked eye to recognizable plant or animal debris, either in the form of dark-colored deposits of fine organic matter (in superficial humus layers, below the litter) or mixed with mineral matter deeper in the soil (Zanella et al., 2011). This highly transformed organic substrate is the target of well-managed composting processes (Sugahara and Inoko, 1981) and is used to amend the soil for agricultural or horticultural purposes under the name of “compost” (e.g., vermicompost). The application of humified matter to soil is known to improve water retention (Giusquiani et al., 1995), nutrient retention and exchange (Steiner et al., 2008), and heat capture (Pinamonti, 1998) and protect soil from erosion (Bazzoffi et al., 1998), among other ecosystem services. Humic substances have been recently shown to be biologically active from a nutritional or physiological point of view. They can be taken up by plants to be assimilated as extra carbon and nitrogen sources (Näsholm et al., 2009) and display nutrient-capture and growth-promoting hormone-like properties (Nardi et al., 2002), soil and roots being involved in a win-win feedback mediated by positive interactions (Nardi et al., 2017).

However, what is humus to a biologist? When observation moves from the naked eye to the microscopic level of organic and mineral-organic horizons, the biological nature of humus is revealed. Ponge (1984, 1985, 1988, 2016) showed that, by scrutinizing a small volume of pine litter at varying stages of decomposition, most plant (pine and moss) remains were processed by microbes and animals, turning to "black matter" composed of faecal pellets, in which minute plant, fungal, and bacterial remains were clearly visible under a light microscope. The most minute arthropods (e.g., springtails, mites) and annelids (e.g., earthworms and enchytraeids) comminute plant and fungal remains to such an

extent that they can only be identified using the maximum magnification of a light microscope. In contrast, larger litter-consuming arthropods (e.g., millipedes, woodlice, fly larvae) accumulate gross fragments, visible under a dissecting microscope, in their faeces. Similar observations were made in mineral-organic horizons, where the intimate association of organic matter with minerals can be unravelled. A large amount of debris, either of plant or microbial origin, can be easily identified in organic-mineral assemblages by transmitted electron microscopy (Foster, 1988; Saur and Ponge, 1988). Previously, Tisdall and Oades (1982) showed that in ultrathin sections, the so-called soil microaggregates are quiescent microbial colonies embedded in clay sheets. Bernier and Ponge (1994) showed that the links between the amorphous (non-recognizable using a light microscope) part of SOM and the silt- and clay-sized mineral particles are controlled by the dynamics of earthworm populations. Topoliantz and Ponge (2003) showed that in tropical slash-and-burn cultivated fields, charcoal pieces are ingested and ground into tiny particles in the muscular gizzard and mixed with mineral matter by earthworms. Such observations of biological contributions to humus formation are not new, being a long-standing aim of soil micromorphologists (Kubiëna, 1938; Zachariae, 1965; Zaiets and Poch, 2016; Colombini et al., 2020). Knowledge of the feeding and behavioral habits of soil organisms, together with plant anatomy, allows much more plant and microbial material to be observed and identified and much more structures (e.g., aggregates, coatings) to be assigned to the activity of animals and microbes, in particular when soil organisms can be observed and identified near traces of their activity (Ponge, 1990, 1991). Using total DNA as a tracer of biotic (mostly microbial) origin, Zaccone et al. (2018a) showed that most SOM located between aggregates (free or associated with minerals) originates from soil organisms, either as excreta or living or dead bodies.

For a biologist, humus comprises plant, fungal, and bacterial remains varying from micrometers to millimeters in size and “amorphous” matter where partly degraded plant and microbial cell pieces varying from nanometers to micrometers in size can be discerned by transmission electron microscopy (Foster, 1981). An increase in nanometer-sized electron-dense particles can be observed during plant cell wall degradation (Messner et al., 1985, Saur and Ponge, 1988). These particles could be considered, with caution, as “true” humic substances, the existence of which is still debated (Schmidt et al., 2011). In this regard, unfortunately, over the last 30 years, “modern” techniques of organic matter analysis, such as stable isotopes (Briones et al., 1999; Nguyen Tu et al., 2011), high-resolution molecular techniques (Lynch et al., 2004), and more recently metabolomics (Swenson et al., 2015), have taken precedence over soil imaging, while adapting the scale of observation to the studied process should
be a basic requirement of the search for causal relationships
in complex systems (Coleman *et al.*, 1992; Chapura, 2009).

How to reconcile the view of the biologist with the
most recent developments in humus chemistry? The trans-
formation of organic matter in soil, as viewed by the biologist,
is mainly a physical process, including comminution (Mori
et al., 2009), leaching of decomposition products (Nykvist,
1963), compaction (Chauvel et al., 1999), physicochemical
protection (Balesdent et al., 2000; Giannetta et al., 2018),
mechanical displacement along the soil profile, and mixing
(or not) with mineral matter (Lavelle et al., 2016). The net
result of these transformations, occurring over a large range
of scales, is exemplified in the concept of humus form (Bal,
1970; Zanella et al., 2018b). This physical transformation of
organic matter is mainly affected by saprophagous animals
(Wolters, 2000) and, to a more limited extent, by microbial
(Tisdall and Oades, 1982) and abiotic processes (Denef
et al., 2001). To these physical transformations, visible to
the naked eye in the formation of humus horizons (Zanella
et al., 2018b), are superimposed microbial (Keeler et al.,
2009) and, to a lesser extent, faunal (Garvî'n et al., 2000)
enzymatic degradations, resulting in the formation of eas-
ily leached (Allison and Vitousek, 2004) or metabolized
small molecules (Tian et al., 2010). At the same time, every
soil-dwelling organism elaborates its own biomass (Powlson
et al., 1987), which is in turn processed along soil trophic net-
works (Lueders et al., 2006) or accumulates as more or less
degraded dead bodies (Kallenbach et al., 2015). All those are
humus. Most properties humus confers to the soil ecosystem
(Ponge, 2015) are linked to its high surface area for nutrient
exchange and water retention (Chiou et al., 1990) and its
strong affinity to mineral surfaces (Vermeer et al., 1998).
Some of the abovementioned biological processes contribute
to the degradation of organic matter (until respired as carbon
dioxide), whereas others stabilize it in various forms, e.g.,
deep carbon by roots (Kell, 2011) or earthworms (Shuster
et al., 2001), clay-humus assemblages by earthworms (Scul-
lion and Malik, 2000) or bacteria (Zaccone et al., 2018a).
However, humus-forming processes where biological acti-
vity does not play an active role should be mentioned, too.
This is the case for peat soils, where humification progresses
at a very low rate due to the inherent recalcitrance of organic
inputs and the anoxic environment (Zaccone et al., 2018b),
and for mor humus (also called "raw humus") accumulating
in nutrient-poor terrestrial environments in the absence of
notable faunal activity (Hempfling et al., 1987).

All models proposed by soil chemists cope with this
view as far as they do not give precedence to a pure chemical
formulation of humus which does not fit to SOM complexity
even at the smallest scale (Lehmann *et al.*, 2008). It has been
claimed that most properties given to the soil by organic
matter cannot be deduced from its molecular composition

(Schmidt *et al.*, 2011), and thus that a better knowledge of the
environment and of the organisms which contribute to SOM
dynamics is urgently needed if we want to dispose of reliable
models of carbon cycling and storage (Hedges *et al.*, 2000).
Models of SOM dynamics proposed by Komarov *et al.* (2017)
and Blankinship *et al.* (2018), including measurements of
microbial and animal effect traits, indicative of their activity,
are pivotal steps in this direction. We suggest speaking of
humus as the “dark side” of life and not as an abiotic SOM
component, as most authors suggest it to be (Gerke, 2018).
The recognition of the biological nature of humus would
allow better assessment of its origin, dynamics, and emergent
properties (Ponge, 2005), like a step has been taken in soil
science when the direct role of soil organisms in mineral
weathering has been universally acknowledged (Neilands,
1995; Jongmans *et al.*, 1997).

Our knowledge of the large array of soil organic and
mineral-organic components collectively called ‘humus’
could benefit from a close cooperation between chemists
and biologists. The concept of soil as a collection of em-
bedded aggregates, the basic unit being the microaggregate
(Totsche et al., 2018), is highly promising, because it allows
processes (e.g., stability, respiration, organic-mineral intera-
tions, nutrient exchange) to be studied at the scale at which
they occur in the soil ecosystem (Ponge, 2015). Another
promising aspect of strong cooperation between chemists
and biologists is the inclusion of biological processes in
modelling SOM formation (Chertov et al., 2017a, b; Blank-
inship et al., 2018). Some burning questions such as the
use of soil for mitigating climate warming by sequestering
more atmospheric carbon (Lal, 2010) could be resolved by
focusing our research effort on the interplay between biotic
and abiotic soil compartments, with humus at the interface
(Zanella et al., 2018a).

In conclusion, this short focus on humus and its various
significances (for the gardener, for the chemist, and for the
biologist) was intended to show that this complex matter
(in both literal and figurative senses) could benefit from a
better cooperation between all scientific disciplines devoted
to soil studies. Rather than abandoning the term “humus”,
as provocatively suggested by Lehmann and Kleber (2015),
I propose considering humus as a prominent agent of mea-
surable soil ecosystem services, including plant growth and
fixation of atmospheric carbon, requiring as much protection
as life, from which it might be considered as the “dark side”.

ACKNOWLEDGEMENT

The author greatly acknowledges the editorial board of
Pedosphere and three anonymous reviewers for their major
contribution to the improvement of the original manuscript.

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Jean-François PONGE*

Muséum National d'Histoire Naturelle, CNRS UMR 7179,
Brunoy 91800 (France)

<footnote>*Corresponding author. E-mail: ponge@mnhn.fr.</footnote>