Horticultural crops frequently use organic materials in growing media (GM) formulation to physically support plant growth while ensuring appropriate solid/air/water balance and nutrient supplies for healthy roots [1
]. The range of growing media constituents and stand-alone substrates includes peat, coir pith, wood fibers, bark, composted materials (e.g., green waste, bark). Among these organic materials, peat has been widely used in growing media during the last decades due to its reliable properties such as low bulk density, high biochemical stability, high porosity, and high air and water-holding capacity, making this substrate particularly suitable for growing a large number of vegetables and ornamentals [1
]. However, the availability of this natural resource is nowadays under pressure due to increasing demand for GM, increasing regulation policies about the preservation of peatland as carbon sinks, and transportation costs [2
]. Researchers and the GM industry are working to use peat more wisely and sparingly [7
] by partially or totally substituting it with other renewable or sustainable organic materials (e.g., coir, bark, wood fibers, green composts) [4
]. Another step toward sustainable soilless systems involves the use of organic fertilizers as a substitute to synthetic fertilizers [9
]. Dealing with nutrient excess or deficiency is extremely challenging and has been so far an obstacle to organic fertilization in horticulture [9
Microbes are central to manage nutrient status [11
] especially when organic fertilizers are added to GM [9
]. To be available for plants, organic fertilizers need first to be mineralized by heterotrophic microbes into simple organic compounds (e.g., sugars, amino acid) and inorganic forms (e.g., NH4+
]. Nitrogen (N) is first released as ammonium (i.e., NH4+
-N or ammonia NH3
-N whether pH above 8); then, it is converted to nitrite (i.e., NO2−
-N) by N-ammonium-oxidizing bacteria (AOB) or archaea (AOA) [13
] and then converted in nitrate (i.e., NO3−
-N) by nitrite-oxidizing bacteria (NOB) through nitrification [14
]. Microbial functions of GM types received little attention in the past [2
] and mainly concerned weed and pathogen controls [16
], biological stability, nutrient immobilization [2
], nitrification stimulated by urea or ammonium-based fertilization [11
], and more recently, regarding nutrient availability [18
] and the potential mitigation of greenhouse gas emission by adding biochars [19
]. The instability of GM related to carbon (C) cycle was studied through the loss of organic matter [20
], dioxygen and carbon dioxide evolution [21
], or dehydrogenase activity [26
] as indicators of global microbial activity. Concerning the nutrient availability of GM, attention was given to N immobilization [27
] and to a lesser extent phosphorus (P) [29
] due to microbial consumption.
To survive and reproduce in the environment, microbes degrade complex organic molecules as electron and energy sources for ATP production, which is needed for cellular reactions and new synthesis using carbon and nutrients from mineralization [30
]. Microbes mediate their resource allocation toward targeted substrates through C-, N-, P-, or S-acquiring enzyme production in order to meet their stoichiometric needs [31
] by adopting various strategies to detect and efficiently use these substrates [33
]. The constrained and stable elemental composition of microbes makes fertilizer’s quality an important factor that is supposed to drive biochemical cycles and thus nutrient availability [32
]. Usually, the organic fertilization of soil stimulates microbial growth and enhances enzyme activities [35
]. Increasing N availability can promote C- or P-acquiring enzyme production, but higher P availability does not necessarily increase N-acquiring enzymes [32
]. Recent works already showed differences in the ability of different growing media (e.g., green waste compost, coir, and peats) used alone to ensure microbial N mineralization (i.e., ammonification) and nitrification [36
]. Moreover, adding organic fertilizer (vegetable and animal-based materials) to GM was found to increase the number of amoA
copies, indicating an increase of nitrifier abundance [34
], but subsequent nitrification rate was not determined.
Managing nutrient availability in GM constituents with organic fertilizers is a question of microbial ecology (i.e., plant–microbes–fertilizer interactions) and thus is difficult to predict compared to mineral fertilization. Past studies dealing with the biological properties of GM lack comprehensive insight on microbial ecology, and the relationships between microbes and organic fertilizer in soilless cropping systems received only recent attention [34
]. In such organic fertilized systems, plant nutrition will depend on the resulted amount and form of available nutrients from fertilizer mineralization and nitrification mediated by microbes. As a matter of fact, available C is often the most limiting factor for microbial growth in soil, and in some cases, N and P can also be limiting [37
]. The availability of C to microbes was also suggested as the main driver of microbial decomposition rates and thus N immobilization in GM [38
]. Indeed, the addition of glucose to GM was found to increase microbial activity [39
], but the immobilization of N or P can also rapidly occur in GM [27
]. Thus, as microbes in GM seem to have multiple limitations, it is essential to assess microbial activities involved in mineralization processes driving nutrient availability in growing media depending on fertilizer type through an overview of C, N, P, and S cycles.
The aim of this paper was to assess microbial functions in three contrasted materials frequently used as stand-alone growing media (peat, coir, and bark) combined with three different organic fertilizers (horn meal and two different plant-based) that would lead to distinct nutrient availability dynamics. We suspected that GM type with strongly unbalanced stoichiometry ratios would affect the microbial functional response to fertilization. More specifically, we hypothesized that higher C:N, C:P, and C:S (i.e., low N, P, and S content) ratios of a GM type (Table 1) would increase microbial activities through enzyme production to get access to nutrients. In addition, we expected that high fertilizer elemental ratios and recalcitrance (Table 1 and Table S1
) would slow down microbial activities and organic matter mineralization rates (N, P, and S releases), limiting thereby nitrification process.
Our study provides evidence that GM chemical and biological properties drive N mineralization and nitrification after organic fertilization and consequently the amount of nutrients and their forms potentially available for plant uptake. Ammonification is not a limited process in our GM types, but nitrification is limited in peat because of the acidic pH. The microbial communities of each GM responded differently to organic fertilization expressed by both different enzymatic strategies and nutrient release patterns. Although we expected a strong relationship between enzyme activity and the related nutrient availability, our results suggested that enzyme activities in GM might not be strictly stimulated or repressed by nutrient availability but can also result from a constitutive production or a decoupled regulation. An iconography of correlations allowed us to highlight the particularity of each GM compared to the others. Peat was specifically related to ammonium accumulation due to weak nitrification and high acid phosphatase activity, which was probably inherited from peat bog and a strong C:P ratio. On the other hand, bark presented weak enzyme activities, but a strong nitrification capacity; however, this was limited by the ammonium content. Coir had an intermediate profile regarding mineralization processes but also showed a repressive arylsulfatase activity due to high sulfate content and a decrease in pH. Mixing different GM types seems a promising way to optimize microbial functions and thus N-P-S availabilities. This hypothesis needs to be tested, as the physicochemical properties will change in mixes, affecting microbial communities and functions.
Furthermore, fertilizer chemistry modulated mineralization rates and influenced enzyme strategy at some points. Iconography highlighted especially the high release of anions and high EC induced by F2 addition. F1 seemed to provide more suitable conditions for N release as ammonium in peat, as nitrate in bark, and both in coir. Overall, N being the most limiting element in GM, its status has to be managed carefully. Indeed, mining for N can induce a risk of salt toxicity for roots due to an excessive release of other nutrients. Further studies on microbial functions related to N and C cycles (and their interactions) with a wider range of N- and C-related enzymes (e.g., proteases) as well as microbial catabolism (i.e., actual activity) would provide additional clues for better understanding nutrient mineralization in GM.