Kyle Mason-Jones

Dr. Kyle Mason-Jones

Junior Researcher
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



I foresee that a deep understanding of soil microbial communities will allow us to predict and even steer their activity to benefit crops and the environment


Microorganisms are responsible for decomposing plant material in soil, which makes them central players in greenhouse gas production, soil carbon storage, and recycling of plant nutrients. My research targets the ecological mechanisms of these processes. In particular, I aim to understand how viruses (bacteriophages) shape bacterial communities and redirect the flow of carbon and plant nutrients between plants, soil and atmosphere. This focus fits within the broader goal of understanding soil microbial lifestyles and their interactions with agricultural practice. I study these ecological mechanisms in realistic soil systems using a variety of chemical, stable isotope and molecular tools.

Research groups



  • 2010–2014
    The Green House, Cape Town, South Africa, Environmental sustainability consultant
  • 2015–2018
    University of Goettingen, Department of Agricultural Soil Science, PhD candidate
  • 2018–2021
    Netherlands Institute of Ecology, Department of Terrestrial Ecology, Post-doctoral researcher
  • 2021–Present
    Netherlands Institute of Ecology, Department of Terrestrial Ecology, Junior group leader

Ancillary activities


Key publications

  • The ISME Journal

    Microbial storage and its implications for soil ecology

    Mason-Jones, K., Robinson, S.L., Veen, G.F., Manzoni, S., van der Putten, W.H.
  • Environmental Science & Technology

    T4-like phages reveal the potential role of viruses in soil organic matter mineralization

    Wei, X., Ge, T., Wu, C., Wang, S., Mason-Jones, K., Li, Y., Zhu, Z., Hu, Y., Liang, C., Shen, J., Wu, J., Kuzyakov, Y.
  • Frontiers in Ecology and Evolution

    Intracellular storage reduces stoichiometric imbalances in soil microbial biomass – A theoretical exploration

    Manzoni, S., Ding, Y., Warren, C., Banfield, C.C., Dippold, M.A., Mason-Jones, K.
  • Soil Biology and Biochemistry

    Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

    Kuzyakov, Y., Mason-Jones, K.
  • Soil Biology and Biochemistry

    Contrasting effects of organic and mineral nitrogen challenge the N-Mining Hypothesis for soil organic matter priming.

    Mason-Jones, K., Schmücker, N., Kuzyakov, Y.

Peer-reviewed publications

  • Nature Communications

    Microbial functional changes mark irreversible course of Tibetan grassland degradation

    Andreas Breidenbach, Per-Marten Schleuss, Shibin Liu, Dominik Schneider, Michaela A. Dippold, Tilman de la Haye, Georg Miehe, Felix Heitkamp, Elke Seeber, Kyle Mason-Jones, Xingliang Xu, Yang Huanming, Jianchu Xu, Tsechoe Dorij, Matthias Gube, Helge Norf, Jutta Meier, Georg Guggenberger, Yakov Kuzyakov, Sandra Spielvogel
    The Tibetan Plateau’s Kobresia pastures store 2.5% of the world’s soil organic carbon (SOC). Climate change and overgrazing render their topsoils vulnerable to degradation, with SOC stocks declining by 42% and nitrogen (N) by 33% at severely degraded sites. We resolved these losses into erosion accounting for two-thirds, and decreased carbon (C) input and increased SOC mineralization accounting for the other third, and confirmed these results by comparison with a meta-analysis of 594 observations. The microbial community responded to the degradation through altered taxonomic composition and enzymatic activities. Hydrolytic enzyme activities were reduced, while degradation of the remaining recalcitrant soil organic matter by oxidative enzymes was accelerated, demonstrating a severe shift in microbial functioning. This may irreversibly alter the world´s largest alpine pastoral ecosystem by diminishing its C sink function and nutrient cycling dynamics, negatively impacting local food security, regional water quality and climate.
  • Frontiers in Plant Science

    Biogels in Soils: Plant Mucilage as a Biofilm Matrix That Shapes the Rhizosphere Microbial Habitat

    Meisam Nazari, Samuel Bickel, Pascal Benard, Kyle Mason-Jones, Andrea Carminati, Michaela A. Dippold
    Mucilage is a gelatinous high-molecular-weight substance produced by almost all plants, serving numerous functions for plant and soil. To date, research has mainly focused on hydraulic and physical functions of mucilage in the rhizosphere. Studies on the relevance of mucilage as a microbial habitat are scarce. Extracellular polymeric substances (EPS) are similarly gelatinous high-molecular-weight substances produced by microorganisms. EPS support the establishment of microbial assemblages in soils, mainly through providing a moist environment, a protective barrier, and serving as carbon and nutrient sources. We propose that mucilage shares physical and chemical properties with EPS, functioning similarly as a biofilm matrix covering a large extent of the rhizosphere. Our analyses found no evidence of consistent differences in viscosity and surface tension between EPS and mucilage, these being important physical properties. With regard to chemical composition, polysaccharide, protein, neutral monosaccharide, and uronic acid composition also showed no consistent differences between these biogels. Our analyses and literature review suggest that all major functions known for EPS and required for biofilm formation are also provided by mucilage, offering a protected habitat optimized for nutrient mobilization. Mucilage enables high rhizo-microbial abundance and activity by functioning as carbon and nutrient source. We suggest that the role of mucilage as a biofilm matrix has been underestimated, and should be considered in conceptual models of the rhizosphere.
  • Plant and Soil

    Soil, climate, and variety impact on quantity and quality of maize root mucilage exudation

    Meisam Nazari, Nataliya Bilyera, Callum C. Banfield, Kyle Mason-Jones, Mohsen Zarebanadkouki, Rosepiah Munene, Michaela A. Dippold

    Aims: This study investigated the influence of climate and soil on the exudation rate and polysaccharide composition of aerial nodal root mucilage from drought-resistant and drought-susceptible maize varieties. Methods: Two maize varieties were grown in two different soils (sandy-clay loam Acrisol and loam Luvisol) under simulated climatic conditions of their agroecological zones of origin in Kenya and Germany. The exudation rate of mucilage from the aerial nodal roots was quantified as dry weight per root tip per day and the mucilage was characterized for its polysaccharide composition. Results: On average, the mucilage exudation rate was 35.8% higher under the Kenyan semi-arid tropical than under the German humid temperate climatic conditions. However, cultivation in the loam Luvisol soil from Germany led to 73.7% higher mucilage exudation rate than cultivation in the sandy-clay loam Acrisol soil from Kenya, plausibly due to its higher microbial biomass and nutrient availability. The drought-resistant Kenyan maize variety exuded 58.2% more mucilage than the drought-susceptible German variety. On average, mucilage polysaccharides were composed of 40.6% galactose, 26.2% fucose, 13.1% mannose, 11% arabinose, 3.5% glucose, 3.2% xylose, 1.3% glucuronic acid, and 1% an unknown uronic acid. Overall, significantly higher proportions of the uronic acids were found in the mucilage of the plants grown in the Kenyan sandy-clay loam soil and under the Kenyan semi-arid tropical climatic conditions. Conclusions: Maize is able to enhance its mucilage exudation rate under warm climatic conditions and in soils of high microbial activity to mitigate water stress and support the rhizosphere microbiome, respectively. Graphical abstract: [Figure not available: see fulltext.].
  • ISME Journal

    Microbial storage and its implications for soil ecology

    Kyle Mason-Jones, Serina L. Robinson, Ciska Veen, S. Manzoni, Wim H. van der Putten
    Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.
  • Environmental Science and Technology

    T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization

    Xiaomeng Wei, Tida Ge, Chuanfa Wu, Shuang-Yin Wang, Kyle Mason-Jones, Yong Li, Zhenke Zhu, Yajun Hu, Chao Liang, Jianlin Shen, Jinshui Wu, Yakov Kuzyakov

    Viruses are the most abundant biological entities in the world, but their ecological functions in soil are virtually unknown. We hypothesized that greater abundance of T4-like phages will increase bacterial death and thereby suppress soil organic carbon (SOC) mineralization. A range of phage and bacterial abundances were established in sterilized soil by reinoculation with 10-3 and 10-6 dilutions of suspensions of unsterilized soil. The total and viable 16S rRNA gene abundance (a universal marker for bacteria) was measured by qPCR to determine bacterial abundance, with propidium monoazide (PMA) preapplication to eliminate DNA from non-viable cells. Abundance of the g23 marker gene was used to quantify T4-like phages. A close negative correlation between g23 abundance and viable 16S rRNA gene abundance was observed. High abundance of g23 led to lower viable ratios for bacteria, which suggested that phages drove microbial necromass production. The CO2 efflux from soil increased with bacterial abundance but decreased with higher abundance of T4-like phages. Elimination of extracellular DNA by PMA strengthened the relationship between CO2 efflux and bacterial abundance, suggesting that SOC mineralization by bacteria is strongly reduced by the T4-like phages. A random forest model revealed that abundance of T4-like phages and the abundance ratio of T4-like phages to bacteria are better predictors of SOC mineralization (measured as CO2 efflux) than bacterial abundance. Our study provides experimental evidence of phages' role in organic matter turnover in soil: they can retard SOC decomposition but accelerate bacterial turnover.
  • Frontiers in Ecology and Evolution

    Intracellular Storage Reduces Stoichiometric Imbalances in Soil Microbial Biomass – A Theoretical Exploration

    S. Manzoni, Yang Ding, Charles Warren, Callum C. Banfield, Michaela A. Dippold, Kyle Mason-Jones
    Microbial intracellular storage is key to defining microbial resource use strategies and could contribute to carbon (C) and nutrient cycling. However, little attention has been devoted to the role of intracellular storage in soil processes, in particular from a theoretical perspective. Here we fill this gap by integrating intracellular storage dynamics into a microbially explicit soil C and nutrient cycling model. Two ecologically relevant modes of storage are considered: reserve storage, in which elements are routed to a storage compartment in proportion to their uptake rate, and surplus storage, in which elements in excess of microbial stoichiometric requirements are stored and limiting elements are remobilized from storage to fuel growth and microbial maintenance. Our aim is to explore with this model how these different storage modes affect the retention of C and nutrients in active microbial biomass under idealized conditions mimicking a substrate pulse experiment. As a case study, we describe C and phosphorus (P) dynamics using literature data to estimate model parameters. Both storage modes enhance the retention of elements in microbial biomass, but the surplus storage mode is more effective to selectively store or remobilize C and nutrients according to microbial needs. Enhancement of microbial growth by both storage modes is largest when the substrate C:nutrient ratio is high (causing nutrient limitation after substrate addition) and the amount of added substrate is large. Moreover, storage increases biomass nutrient retention and growth more effectively when resources are supplied in a few large pulses compared to several smaller pulses (mimicking a nearly constant supply), which suggests storage to be particularly relevant in highly dynamic soil microhabitats. Overall, our results indicate that storage dynamics are most important under conditions of strong stoichiometric imbalance and may be of high ecological relevance in soil environments experiencing large variations in C and nutrient supply.
  • Frontiers in Plant Science

    Mucilage Polysaccharide Composition and Exudation in Maize From Contrasting Climatic Regions

    Meisam Nazari, Sophie Riebling, Callum C. Banfield, Asegidew Akale, Margherita Crosta, Kyle Mason-Jones, Michaela A. Dippold, Mutez Ali Ahmed
    Mucilage, a gelatinous substance comprising mostly polysaccharides, is exuded by maize nodal and underground root tips. Although mucilage provides several benefits for rhizosphere functions, studies on the variation in mucilage amounts and its polysaccharide composition between genotypes are still lacking. In this study, eight maize (Zea mays L.) genotypes from different globally distributed agroecological zones were grown under identical abiotic conditions in a randomized field experiment. Mucilage exudation amount, neutral sugars and uronic acids were quantified. Galactose (∼39–42%), fucose (∼22–30%), mannose (∼11–14%), and arabinose (∼8–11%) were the major neutral sugars in nodal root mucilage. Xylose (∼1–4%), and glucose (∼1–4%) occurred only in minor proportions. Glucuronic acid (∼3–5%) was the only uronic acid detected. The polysaccharide composition differed significantly between maize genotypes. Mucilage exudation was 135 and 125% higher in the Indian (900 M Gold) and Kenyan (DH 02) genotypes than in the central European genotypes, respectively. Mucilage exudation was positively associated with the vapor pressure deficit of the genotypes’ agroecological zone. The results indicate that selection for environments with high vapor pressure deficit may favor higher mucilage exudation, possibly because mucilage can delay the onset of hydraulic failure during periods of high vapor pressure deficit. Genotypes from semi-arid climates might offer sources of genetic material for beneficial mucilage traits.
  • Soil Biology & Biochemistry

    Short-term temperature history affects mineralization of fresh litter and extant soil organic matter, irrespective of agricultural management

    Kyle Mason-Jones, Pim Vrehen, Kevin Koper, Jin Wang, Wim H. van der Putten, Ciska Veen
    The influence of temperature on mineralization of plant litter and pre-existing soil organic matter (SOM) involves not only the prevailing temperature, but also how it has changed through time. However, little is known about how temperature variability through time influences mineralization processes. Here, we investigated how short-term temperature history affects the mineralization of SOM and plant litter in soils from different agricultural management systems. We used soils from a long-term experiment with conventional and organic management treatments to set up microcosms. The microcosms were exposed to eight days of contrasting temperature regimes (different mean temperatures and constant versus fluctuating temperatures). Microcosms were then returned to a common temperature of 16 °C, 13C-labelled plant litter was added to half of them, and CO2 efflux was measured over the following week. We found that SOM and litter mineralization were both sensitive to the temperature history, with lower mean temperatures during preliminary treatment associated with higher mineralization during the subsequent common-temperature incubation. This effect persisted through the week after temperature differences were removed. Different patterns of temperature fluctuation and agricultural management did not significantly affect mineralization during common-temperature incubation. The history sensitivity of litter mineralization, despite litter being added after temperature differences had ended, indicates that the temperature history effects may be driven by short-term microbial acclimation. We conclude that organic matter and litter mineralization, which are key processes in the carbon cycle, are sensitive to short-term temperature history. This suggests that future investigations of soil CO2 efflux may need to take recent weather effects into account.
  • Biology and Fertility of Soils

    Form of nitrogen deposition affects soil organic matter priming by glucose and cellulose

    Peng Tian, Kyle Mason-Jones, Shengen Liu, Qingkui Wang, Tao Sun
    To examine the interplay of C and N availability, glucose (high microbial availability) and cellulose (low microbial availability)
    were added to soils collected from a temperate forest that had received simulated N deposition for 6 years (organic and/or
    inorganic N). The priming effect was higher for glucose addition than for cellulose. N deposition decreased the priming effect of
    easily available glucose but increased the priming effect of cellulose. This confirmed an interactive effect of fresh organic matter
    (FOM) availability and N deposition on priming. Furthermore, the interactive effect was affected by the form of N deposition,
    with interaction mainly observed with organic N deposition. Qualitatively different patterns of priming were observed for the two
    FOM types and were accompanied by contrasting abundance of fungi and bacteria in the community, as determined by phospholipid
    fatty acid (PLFA) analysis. Organic N deposition increased bacterial biomass but decreased the intensity of priming. In
    contrast, a competitive advantage of fungi with respect to organic N sources may drive priming by cellulose. The results
    highlighted the importance of the availability of FOM in regulating the priming effect and showed that interactions between
    the form of N deposition and the availability of the FOM should be considered when predicting soil C cycling in scenarios of
    increased N deposition. Organic N deposition had a greater impact on priming effects than inorganic N deposition, and the
    influence of microbial availability of FOM largely depended on organic N deposition.

Projects & collaborations


  • Small but deadly: The role of viruses in bacterial death and soil carbon storage

    Project 2021–2024
    Billions of microorganisms live and die in the soil beneath our feet, affecting soil carbon storage and its release to the atmosphere. This project investigates how viruses drive bacterial death and the fate of bacterial remains, to better understand how soil can contribute to maintaining a healthy climate.
    Bacteriophage plaques on petri dish
  • Vital soils for sustainable intensification of agriculture

    Project 2016–2021
    A key challenge for sustainable intensification of agriculture is to produce increasing amounts of food for a growing world population, with minimal loss of biodiversity and ecosystem services. In order to facilitate ecological intensification of agriculture, the underlying principles need to be understood and validated in farmers’ fields

Additional Projects

Small but deadly: The role of viruses in bacterial death and soil carbon storage


Billions of microorganisms live and die in the soil beneath our feet, affecting soil carbon storage and its release to the atmosphere. This project investigates how viruses drive bacterial death and the fate of bacterial remains, to better understand how soil can contribute to maintaining a healthy climate.