Georges Halim Atallah
email: georges.halimatallah@inrs.fr@u-pem.fr

Emmanuel Belut

Sullivan Lechêne

Benoît Trouette

Stéphane Vincent

Simulation of a confined turbulent round jet at moderate Reynolds number

Keywords: Confined round jet, Moderate Reynolds number, comparison between DNS and experiments, LES

The objective of this study is to numerically simulate the turbulent flow of a confined round jet at moderate Reynolds number, which is representative, in a first step, of an available experiment characterizing a problem of pollutant transport in a confined medium.

Introduction

In numerous scientific research areas, particularly in chemistry, operators are very often required to handle materials that could be volatile and could probably be inhaled. Depending on the materials being studied, the gases generated can be toxic and therefore present a real danger to the operator's health in case of inhalation. Laboratory fume cupboards are devices that are supposed to ensure the protection of the operator. Their ability to contain pollutant gases is vulnerable to turbulent phenomena and aeraulic perturbations, which are themselves induced by drafts or moving objects. When a laboratory fume cupboard is disturbed, the pollutant gas, instead of being confined inside the device, leaks because of the induced turbulent flow. In order to simulate the pollutant transport process when the device is submitted to disturbances, we first propose to design a small-scale experimental model involving the same physical phenomena. This is an experiment describing the transport of pollutant injected into a confined enclosure through a round turbulent jet that allows to collect experimental data of time average velocity, kinetic energy and mean age air profile [START_REF] Belut | A new experimental dataset to validate cfd models of airborne nanoparticles agglomeration[END_REF][START_REF] Guichard | Simulation of airborne nanoparticles transport, deposition and aggregation: Experimental validation of a cfd-qmom approach[END_REF] so that numerical simulations can be validated against experimental measurements and statistics. In the present work, we only focus on flow characteristics and more particularly on the turbulent aspect of the carrier flow motion.

Model and numerical methods

All developments are investigated with the home made code Fugu, developped in the TCM team of MSME lab. We performed numerical simulation of an airflow assumed to be incompressible and isothermal using a finite volume method on an irregular and staggered Cartesian grid governed by the following set of equations:

∇ • u = 0, (1a)
ρ ∂u ∂t + ∇ • (u ⊗ u) = -∇p + ∇ • (µ + µ sgs ) ∇u + (∇u) T , ( 1b
)
where u is the velocity vector, p is the pressure, ρ = 1.2250 kg • m -3 is the density and µ = 1.7894 • 10 -5 Pa • s is the dynamic viscosity of the fluid. When a turbulence model is considered, a turbulent viscosity µ sgs is incorporated through an eddy viscosity model in the motion equations. In the present work, gravity effects are neglected. Boundary conditions for u are no-slip condition for all walls and zero gradient at the outlet for the normal component. Imposing a velocity profile such as the one of the experience requires taking into account a number of factors that are difficult to simulate. In practice, the injector nozzle is never really designed with perfect geometry and therefore has imperfections. They can then cause instabilities that directly affect the potential core area (nearfield) of the jet. Thus, a simple flat velocity profile such that u inlet = µRe/ρD is imposed at the inlet and only intermediate and far fields region of the jet are investigated and compared to experiments in the present work. A centered scheme is used to discretize the advection term and viscous terms whereas time integration is carried out with a second order Gear scheme. Pressure is obtained by using a time-splitting approach for handling pressure-velocity coupling. A scalar projection method is considered here [START_REF] Goda | A multistep technique with implicit difference schemes for calculating two-or three-dimensional cavity flows[END_REF]. These schemes are combined with the preconditioned MILU-BICGSTAB II solver to build a solution of equations (1a-1b).

A mesh convergence study was first performed with direct numerical simulation (DNS) to assess if the obtained numerical solutions reproduce the behavior of experimental data. The mesh convergence study was performed with mesh sizes of {n x , n y , n z } = {128, 64, 64}, {192, 96, 96} and {256, 128, 128}. For each case, the mesh is refined with 400, 900 and 1600 cells respectively along the jet inlet cross section. It was observed that a simple regular mesh size generates too much dissipation for the same number of cells, which inhibits the ability to capture a degeneration to turbulence. This is why we chose to use a refined irregular mesh in the jet inlet cross section to capture the effects of turbulence. The time step is defined as ∆t = CFL × h min with CFL = 0.5 and h min is the length of the smallest cell. The flow was also simulated with Large Eddy Simulation (LES) models on the coarsest mesh size. The idea is to measure the capability of LES to provide a suitable solution on a too coarse mesh for tackling with DNS.

Large Eddy Simulation (LES) turbulence modeling

Our LES simulations were performed with a variety of classical LES models [START_REF] Sagaut | Large Eddy Simulation for Incompressible Flows: An Introduction[END_REF]. The first is an eddy viscosity model based on the mixed scale approach, which is a combination of the Smagorinsky and the Turbulent Kinetic Energy (TKE) models. The subgrid-scale viscosity is classically evaluated by the following formula:

ν sgs = C m ∆ 1+α 2S ij S ij α/2 q 2 c (1-α)/2 , (2)
with

C m = C 2α s C 1-α TKE , ∆ = (∆x∆y∆z) 1/3
, S ij is the resolved strain rate tensor, q c is the subgrid-scale kinetic energy. In our implementation, α ∈ [0, 1] is a weighting coefficient (α = 0 gives the TKE model, α = 1 gives the Smagorinsky model). In our approach, α is taken equal to 0.5 for the mixed scale model. C s and C TKE are the constant of the Smagorinsky and TKE models and are taken equal to 0.18 and 0.2 respectively. In the motion equations, µ sgs = ρν sgs is then added to the molecular dynamic viscosity as shown in equation (1b).

The other one is the Wall Adaptating Local Eddy-viscosity (WALE) model [START_REF] Sagaut | Large Eddy Simulation for Incompressible Flows: An Introduction[END_REF]. Its known advantage is that it allows to reproduce a good asymptotic behaviour near solid walls for wall bounded flows. The subgrid-scale viscosity is define as:

ν sgs = C w ∆ 2 S d ij S d ij 3/2 S ij S ij 5/2 + S d ij S d ij 5/4 , (3)
with C w = 0.75 and

S d ij = S ik S kj + Ω ik Ω kj -1 3 S mn S mn -Ω mn Ω mn δ ij . Ω ij
is the resolved rotation tensor and δ ij is the Kronecker delta.

Results and discussion

Direct Numerical Simulation When possible, DNS is the simplest model for turbulence and also the more accurate to investigate on a numerical point of view. Its main drawback is the requirement of solving all the time and space scales of the flow, which is generally impossible as soon as the Reynolds number is high. In our experiment of turbulent round jet, the Reynolds number is moderate, so it is reasonable to try to simulate the problem with DNS. If we succeed, a reference simulation will be available, which could be degenerated in terms of mesh or time step in order to try to simulate faster the same problem with LES models.

After thirty seconds of physical time corresponding to an established jet motion, average fields are then calculated over thirty seconds of physical time, ensuting a converged behavior of these average fields. As shown in Fig. 2, outside the jet area (z ≤ 0.3 m), we can observe a little influence of the mesh size. In these zones, the flow is mainly laminar and all grids capture the correct motion. Inside the jet (z > 0.3 m), numerical solutions on all meshes globally reproduces the average velocity intensities. However, refining the grids allows to converge simulation results to those of the experiments, which is a nice feature of the Fugu code. Note that the fact that the maximum velocities are not at the same height z is explained by the fact that the imposed velocity profile is spatially constant in the injector, which is not the case in the experiment [START_REF] Belut | A new experimental dataset to validate cfd models of airborne nanoparticles agglomeration[END_REF].

The DNS gives results in fairly good agreement with those of the experiments, but the computation cost is far too high on the finer mesh, even with the MPI parallel implementation that we considered (512 processors). An important point is to be able to carry out this kind of simulation with mesh sizes of the order of the coarsest grid presented here (128 × 64 × 64 cells). Therefore, in the next section, LES simulations with models presented in Sect. 2.3 were performed on the coarsest mesh. Large Eddy Simulation In order to reach such results as in DNS on fine mesh at a lower cost, simulations were performed on the coarsest mesh using LES models with the same numerical setup as in DNS. A first observation is that the three Smagorinsky, TKE and mixed scale models maintain the jet in a laminar state and inhibit the transition to turbulence. However, the WALE model provides a better behaviour than the others despite the fact that the laminar-turbulent transition occurs farther than it occurs in DNS. This leads to an overestimation of velocity intensities as shown in Fig. 3.

Concluding remarks

The dynamics of a cylindrical jet at moderate Reynolds number of 1500 has been simulated with DNS and LES turbulence approaches. The results of the DNS compare favorably to those provided by the experiments. LES conducted on the coarsest DNS grid are not able to recover the correct experimental jet dynamics. The main reason that we have identified, by changing all physical and numerical parameters of the simulations, is that the results are very sensitive to inlet jet profile of mean velocity (for the DNS) and also to the fluctuating (or subgrid component) of the velocity, that is not considered in the present work. Future improvements of our LES simulations will be to impose synthetic turbulent unsteady inlet jet conditions [START_REF] Klein | A digital filter based generation of inflow data for spatially developing direct numerical or large eddy simulations[END_REF] in order to feed simulations with realistic subgrid scale fluctuations of the velocity.

Fig. 1 .

 1 Fig. 1. Geometric description of the confined air injection in a cavity with cylindridal inlet and outlet.

2 .

 2 Measured and computed (a) mean velocity profiles and (b) mean turbulent kinetic energy at the central plane y = 0 m and x = 0.3, 0.5 and 0.7 m. Comparison between DNS simulations (without explicit LES model) and experiments [2].

Fig. 3 .

 3 Fig. 3. Comparison between computed mean velocity at the central plane y = 0 m and x = 0.3, 0.5 and 0.7 m with LES WALE model and DNS on 256 × 128 × 128 mesh size.

Acknowledgements

The authors are grateful for access to the computational facilities of the French CINES (National computing center for higher education) and CCRT (National computing center of CEA) under project number A0032B06115.


Jesús Rodrigo-Comino
email: rodrigo-comino@uma.es977491asw0010.

Manuel López-Vicente

Vinod Kumar

Andrés Rodríguez-Seijo

Orsolya Valkó

Claudia Rojas

Hamid Reza Pourghasemi

Luca Salvati

Noura Bakr

Emmanuelle Vaudour

Eric C Brevik

Maja Radziemska

Manuel Pulido

Simone Di Prima

Marta Dondini

Wim De Vries

Erika S Santos

Maria De

Lourdes Mendonça-Santos

Yang Yu

Panos Panagos

Rodrigo-Comino

Re Pourghasemi

Soil Science Challenges in a New Era: A Transdisciplinary Overview of Relevant Topics

Keywords: Soil research, degradation, biogeochemical cycles, rehabilitation, soil and human health, soil modeling

Transdisciplinary approaches that provide holistic views are essential to properly understand soil processes and the importance of soil to society and will be crucial in the future to integrate distinct disciplines into soil studies. A myriad of challenges faces soil science at the beginning of the 2020s. The main aim of this overview is to assess past achievements and current challenges regarding soil threats such as erosion and soil contamination related to different United Nations sustainable development goals (SDGs) including (1) sustainable food production, (2) ensure healthy lives and reduce environmental risks (SDG3), (3) ensure water availability (SDG6), and (4) enhanced soil carbon sequestration because of climate change (SDG13). Twenty experts from different disciplines related to soil sciences offer perspectives on important research directions. Special attention must be paid to some concerns such as (1) effective soil conservation strategies; (2) new computational technologies, models, and in situ measurements that will bring new insights to in-soil process at spatiotemporal scales, their relationships, dynamics, and thresholds; (3) impacts of human activities, wildfires, and climate change on soil microorganisms and thereby on biogeochemical cycles and water relationships; (4) microplastics as a new potential pollutant; (5) the development of green technologies for soil rehabilitation; and (6) the reduction of greenhouse gas emissions by simultaneous soil carbon sequestration and reduction in nitrous oxide emission. Manuscripts on topics such as these are particularly welcomed in Air, Soil and Water Research.

Introduction

Past, current, and, presumably, future scientific literature has and will include studies related to soils. Soils are a vital life sphere that can generate indispensable resources and goods to supply natural and human ecosystems. [START_REF]International Soil Classification System for Naming Soils and Creating Legends for Soil Maps[END_REF][START_REF]Soil Survey Staff. Keys to Soil Taxonomy[END_REF] The numerous biogeochemical cycles and different interactions among spheres 2 Air, Soil and Water Research (atmosphere, geosphere, biosphere, anthroposphere, hydrosphere) all converge into the pedosphere. Moreover, climate change, intensification of agricultural activities, urbanization, military conflicts, mining and other industrial activities and associated infrastructures for transport, such as roads and railroads among others, have affected soils over many centuries. However, these have become more and more intense during the last two decades, threatening the few spots that still have natural relatively unaltered soils. [START_REF] Mariet | Using bioindicators to assess the environmental risk of past mining activities in the Vosges Mountains (France)[END_REF][START_REF] Cao | Detachment of road surface soil by flowing water[END_REF][START_REF] Salvati | Land sensitivity to desertification across Italy: past, present, and future[END_REF] Therefore, it is inevitable that more literature will be published in the coming years and more fieldwork will be conducted (Figure 1), with more advanced modeling and data analysis techniques expected to be applied to soil issues. It is necessary to increasingly experience relevant debates about soil concepts that are widely applied in novel investigations by pioneering scientists. For example, scientific and technological work is advancing on soil quality and soil quality indicators, [START_REF] Acton | A conceptual framework for soil quality assessment and monitoring (chapter 2)[END_REF][START_REF] Karlen | Soil quality: a concept, definition, and framework for evaluation (a guest editorial)[END_REF] soil resilience from a sustainable perspective, [START_REF] Ludwig | Measuring soil sustainability via soil resilience[END_REF] soil degradation, [START_REF] Cerdà | Preface: soil erosion and degradation in Mediterranean type ecosystems[END_REF] soil and human health and security, [START_REF] Oliver | Soil and human health: a review[END_REF] soil rehabilitation, [START_REF]Agassi Soil Erosion, Conservation, and Rehabilitation[END_REF] or land degradation neutrality. [START_REF] Akhtar-Schuster | Unpacking the concept of land degradation neutrality and addressing its operation through the Rio Conventions[END_REF] Immersed in a globalized and capitalistic economic system, developing research in soil science should consider the costs of soil conservation and the value of benefits provided by soil services (eg, water filtration, carbon sequestration, supplying food, fuel, and shelter). Besides, the application of specific control measures should be a premise to put value in these studies for stakeholders, policymakers, and for all of society.

Soil sciences have acquired a very special relevance in recent decades. The United Nations (UN), both directly in different reports, and through the sustainable development goals (SDGs), has set the highest level of transdisciplinarity for soil sciences. There are several emerging societal research challenges, as described in the UN SDGs (https://sustainabledevelopment.un.org/?menu=130) that are linked to soil quality aspects such as (1) SDG 2: End hunger, achieve food security and improved nutrition, and promote sustainable agriculture;

(2) SDG 3: Ensure healthy lives and promote well-being for all at all ages (non-communicable diseases, mental health and environmental risks); (3) SDG 6: Ensure availability and sustainable management of water and sanitation for all; (4) SDG 13: Take urgent action to combat climate change and its impacts and (5) SDG 15: Protect, restore, and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss. These SDGs are connected to specific soil science challenges, including (1) sustainable food production, referring to proper nutrient management, avoiding or reducing soil threats, such as soil erosion, soil acidification, soil compaction, and soil biodiversity impacts, and reducing environmental impacts on air and water quality (SDG2 and SDG15); (2) solving soil pollution problems, related to metals/metalloids, pesticides and other organic components, microplastics, and emerging pollutants (SDG3); (3) enhancing the water storage and filtering/buffer capacity of soils (SDG6); and (4) enhanced soil carbon sequestration and reducing soil nitrous oxide emissions because of climate change (SDG13). Note that these challenges are also interrelated. For example, soil carbon sequestration enhances soil water and nutrient retention and organic pollutant decay.

This article aims to give a succinct overview of soil science challenges related to the above-mentioned societal perspectives and discuss possible steps forward. In this article, several examples of relevant soil threats and soil functions that pose challenges for soil research are presented, but it also opens the debate to colleagues for new challenges and topics to be addressed. To achieve this goal, 20 experts from the editorial team of Air, Soil and Water Research (SAGE; https://journals.sagepub.com/home/ asw), with backgrounds in multiple disciplines such as geography, soil science, geology, agronomy, biology, environmental sciences, engineering, ecology, cartography and remote sensing, present overviews of a selection of current and relevant topics related to soil. Five major topics were addressed: soil and human health, soil biodiversity and threats, soil and water systems, soil digital mapping, and soil organic carbon sequestration.

Soil Bioremediation and Human Health

Soils have an impact on human health, both directly and indirectly. Soils supply nutrients essential to overall organisms and human life that are passed up the food chain from the soil through the plant to the consumer and they supply medications from inorganic and organic compounds, and organisms. However, contamination of soil may be a cause for human disease in cases of high exposure to metals/metalloids, organic chemicals, soil pathogens, and radionuclides. Several recent articles have summarized the ways that soils influence human health. [START_REF] Kemper | Pay dirt! human health depends on soil health[END_REF][START_REF] Li | Urban soil and human health: a review[END_REF][START_REF] Baumgardner | Soil-related bacterial and fungal infections[END_REF][START_REF] Von Lindern | Estimating children's soil/dust ingestion rates through retrospective analyses of blood lead biomonitoring from the Bunker Hill superfund site in Idaho[END_REF] Despite the progress that has been made in unraveling the linkage between soil contamination and human health, there are still many areas that need additional investigation, such as enhanced understanding of how chemical mixtures in the environment influence human health, and the linkage between soil ecology and human health via crop production and nutrition, as discussed in articles such as Brevik et al [START_REF] Brevik | Soil and human health: current status and future needs[END_REF] and Oliver and Gregory. [START_REF] Oliver | Soil, food security and human health: a review[END_REF] One of the promising ways to address the potential negative effects of soil pollution on human health can be through bioremediation, with/without considering other technologies.

The negative effects of human activity on the Earth's surface have been the most severe in urban, industrial, and agricultural areas (Figure 2). [START_REF] Ferrara | Performance evaluation and cost assessment of a key indicator system to monitor desertification vulnerability[END_REF][START_REF] Ferrara | Towards a socioeconomic profile for areas vulnerable to soil compaction? A case study in a Mediterranean country[END_REF] Increased ecological awareness by society plays an increasingly significant role in expanding successful methods of remediating degraded areas. Contaminants, independently of the typology, with adverse effects on the natural environment and human health have an increasingly global character, though their effect is observed at a local level in many cases. It is very important to seek out innovative solutions regarding polluted areas, where activities connected with bioremediation, which are safer and interfere less with the natural environment than to other methods, have been gaining increasing significance. One of the main aims of introducing bioremediation treatments to degraded areas is to prevent the migration of contaminants into the food chain where they could pose a threat to human health. [START_REF] Zhang | Bioremediation of co-contaminated soil with heavy metals and pesticides: influence factors, mechanisms and evaluation methods[END_REF] There are many technologies for the bioremediation of contaminated areas.

Bioremediation is an interesting but not really new concept. Also, previous studies have shown that in some cases inorganic pollutant uptake from the soil by plants was much smaller than expected. [START_REF] Ighalo | Adsorption of pollutants by plant bark derived adsorbents: an empirical review[END_REF][START_REF] Agarwal | Phytoremediation of air pollutants: prospects and challenges (chapter 7)[END_REF] Uptake was too small to be of practical use in some cases, in order to reach pre-contamination levels over a reasonable amount of remediation time. [START_REF] Kayser | Evaluation and Enhancement of Phytoextraction of Heavy Metals From Contaminated Soils[END_REF] However, the situation has changed over the last 20 years considering new advances, but it is certainly worth taking a close look at the relevant literature to see that much work is still needed. [START_REF] Robinson | The phytomanagement of trace elements in soil[END_REF][START_REF] Mcgrath | Phytoextraction of metals and metalloids from contaminated soils[END_REF] In general, bioremediation has potential applications in, eg, degradation of organic contaminant, removing potentially toxic or hazardous elements from water and soil and the extraction/leaching of metals/metalloids from ores, as well as solid, liquid and gaseous wastes. [START_REF] Shah | Characterisation and bioremediation of wastewater: a review exploring bioremediation as a sustainable technique for pharmaceutical wastewater[END_REF] Among the different techniques of in situ, namely with plants, bioremediation is phytostabilization, which can be used in highly contaminated areas located in distinct climatic conditions and even in the presence of multi-elemental contamination (following the Environmental Protection Agency, and the report: Introduction to Phytoremediation EPA/600/R-99/107). This technology makes use of plants with/without various types of amendments, changing the properties of the soil to decrease the bioavailability of toxic elements. The function of plants, in this case, is connected with the absorption and accumulation of toxic elements in roots and/or precipitation or adsorption on the surface of the roots. [START_REF] Radziemska | The combined effect of phytostabilization and different amendments on remediation of soils from post-military areas[END_REF] Moreover, plants can also influence some changes in the chemical form of some trace elements and promote the precipitation and complexation of contaminants by altering soil properties, such as pH or oxidation-reduction potential, for instance by exudation of protons, hydroxyl ions, and/or organic acids. Phytostabilization is a technology of diminishing the impact of the contaminated areas on the surrounding ecosystem and reducing the introduction of potential contaminants into the food chain. Moreover, plant development can improve other characteristics of the degraded soils such as structure, fertility, microbiota activity, and diversity, and control leaching as well as wind and water erosion. [START_REF] Tordoff | Current approaches to the revegetation and reclamation of metalliferous mine wastes[END_REF][START_REF] Cunningham | Phytoremediation of contaminated soils[END_REF] Nonetheless, in some scenarios of soil contamination and/or climatic conditions, the development of the vegetation directly on contaminated soils can be very difficult and the growth very slowly so, the obtaining of positive effects on chemical and biological parameters of contaminated soils can be delayed.

It is important to perform long-term monitoring to avoid unfavorable and unexpected effects from bioremediation. The application of phytostabilization does not have to be the final method of managing the contaminated area, but merely an intermediate means of protection against the migration of contaminants until other methods act simultaneously in the rehabilitation are developed. Scientific literature from recent years contains many examples of studies and experiments achieved in this field. [START_REF] Teodoro | Seasonal fluctuations of Zn, Pb, As and Cd contents in the biomass of selected grass species growing on contaminated soils: implications for in situ phytostabilization[END_REF][START_REF] Orrego | Effect of single and combined Cu, NaCl and water stresses on three Atriplex species with phytostabilization potential[END_REF] These actions represent positive steps in protecting the surface of the Earth and human health; however, one question remains: Why those methods have not already been applied in an extensive way to remediate polluted soils? As mentioned above, bioremediation has been explored and tested in the past and was deemed not practical in some cases due to the inexistence of known tolerant plant species, low uptake rate, long time investment, and therefore prohibitive costs (at least in terms of metals/metalloid uptake using plants). However, the scientific community should not advocate abandoning the idea of bioremediation. Finally, emergencies such as the current COVID-19 pandemic may create new prioritization in research and exploring linkages between soils and human health considering the increasing literature recently published. [START_REF] Lal | Managing soils for recovering from the COVID-19 pandemic[END_REF][START_REF] Núñez-Delgado | SARS-CoV-2 in soils[END_REF][START_REF] Steffan | Soil pathogens that may potentially cause pandemics, including SARS coronaviruses [published online ahead of print September 8, 2020[END_REF]

Soil Biodiversity and Threats

Soils are one of the most diverse habitats on Earth. A single gram of soil can host billions of cells, distributed in tens of thousands of species of bacteria and on the order of thousands of different species of fungi. [START_REF] Paul | Soil Microbiology, Ecology and Biochemistry[END_REF] In addition, invertebrate species span from the order of hundreds to thousands of species per square meter in organic-rich soils. [START_REF] Cameron | Global gaps in soil biodiversity data[END_REF] Soils constitute the habitat for the organisms that inhabit them for a selected period or throughout their entire life cycle. For example, the majority of the terrestrial insect species spend at least some of their life stages in soil, and for most terrestrial plants, the soil is the most important substrate. This edaphic life can be classified according to body size, including microorganisms (μm scale), microfauna (<0.1 mm), mesofauna (0.1-2.0 mm), macrofauna (2-20 mm), and megafauna (>20 mm), [START_REF]ESDAC Global Soil Biodiversity Atlas-ESDAC-European Commission[END_REF] all of which are fundamental to support soil ecosystem functions. Microorganisms, including bacteria, archaea, and fungi, are the most important group driving biogeochemical processes. Still, their complex contribution to edaphic functions is yet to be fully understood and most of them are currently unculturable and not described. [START_REF] Fierer | Embracing the unknown: disentangling the complexities of the soil microbiome[END_REF][START_REF] Blagodatskaya | Active microorganisms in soil: critical review of estimation criteria and approaches[END_REF] Giller et al [START_REF] Giller | Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review[END_REF][START_REF] Giller | Heavy metals and soil microbes[END_REF] stated the necessity of deeper investigations into the interactions between belowground diversity and stability of ecosystem functions to develop a mechanistic understanding of anthropogenic effects on soil biota. To achieve a mechanistic understanding, standardization of protocols for sampling, extraction, and determination is essential to evaluate and compare biodiversity from the pedon to larger scales. [START_REF] Cameron | Global gaps in soil biodiversity data[END_REF][START_REF] Gardi | Soil biodiversity monitoring in Europe: ongoing activities and challenges[END_REF] There are several challenges to be solved in soil biodiversity monitoring programs related to taxonomic classification, biodiversity indices, and the selection of key species affected by the elevated number of activities and degrees of negative impact. This is also key to develop efficient restoration plans in areas with arid and semi-arid climates, hilly catchments, or poor soils such as the karst areas in the Loess Plateau (Figure 3A andB), highly affected by land degradation processes. [START_REF] Yu | Land preparation and vegetation type jointly determine soil conditions after long-term land stabilization measures in a typical hilly catchment, Loess Plateau of China[END_REF][START_REF] Pei | Time series of landsat imagery shows vegetation recovery in two fragile karst watersheds in Southwest China from 1988 to 2016[END_REF] Below an overview of 3 emerging threat factors to soil biodiversity are presented, namely potentially toxic elements and solutions for mitigating their negative effects using green technologies, wildfires, and microplastics.

Potentially toxic elements

Several anthropic activities are hotspots of environmental contamination, with soil often being the most affected natural resource. It is well known that the concentrations of potentially toxic elements (PTE) in the soil can vary significantly over spatial and temporal scales, even within the same studied area. Moreover, in many contaminated areas, the drivers of environmental degradation go beyond the PTE concentrations in total and available fractions (eg, loss of soil structure and fertility, acidification/alkalinization, and/or decrease of specific and functional diversity). Also, it is worth highlighting the different biogeochemical behaviors of metals, metalloids, and anions, which are oftentimes overlooked. The coexistence of several degradation factors (eg, loss of soil structure and fertility, acidification/alkalinization and/or decrease of specific and functional diversity) amplifies the complexity of the problem, complicating its rehabilitation. [START_REF] Da Silva | Jute bioblanket as a soil rehabilitation strategy in the Sorocaba, Brazil: soil chemistry and SWOT approaches[END_REF][START_REF] Villacís | Selection of forest species for the rehabilitation of disturbed soils in oil fields in the Ecuadorian Amazon[END_REF][START_REF] Santos | Engineered soils using amendments for in situ rehabilitation of mine lands (chapter 8)[END_REF] Major producers of PTE include human activities such as agriculture, industry, mining, tourism, and urbanization, [START_REF] Mckinney | Urbanization, biodiversity, and conservation: the impacts of urbanization on native species are poorly studied, but educating a highly urbanized human population about these impacts can greatly improve species conservation in all ecosystems[END_REF][START_REF] Huang | Spatial patterns and economic contributions of mining and tourism in biodiversity hotspots: a case study in China[END_REF] which directly affect soil health, fertility, quality, and the carbon cycle. [START_REF] Nielsen | Microorganisms as Indicators of Soil Health[END_REF][START_REF] Joergensen | Alive and kicking: why dormant soil microorganisms matter[END_REF] Nowadays, we do not have a clear understanding of the potential differences between potentially hazardous or toxic elements sources from the various anthropogenic activities that release them into the environment, such as industrial, domestic, and agronomic aspects. These activities include the use of pesticides, fertilizers, herbicides, industrial activities, wastewater, sludge, disposal of medical wastes, mining, and so forth, [START_REF] Godt | The toxicity of cadmium and resulting hazards for human health[END_REF][START_REF] Järup | Hazards of heavy metal contamination[END_REF][START_REF] Panagos | Potential sources of anthropogenic copper inputs to European agricultural soils[END_REF] and natural processes such as geogenic sources and weathering of rocks. [START_REF] Heidari | Appraisal of metallic pollution and ecological risks in agricultural soils of Alborz province, Iran, employing contamination indices and multivariate statistical analyses[END_REF][START_REF] Quinton | Enrichment of heavy metals in sediment resulting from soil erosion on agricultural fields[END_REF] Among the PTEs, metals and metalloids (eg, As and Sb) are toxic to most microorganisms and fauna when they occur in high concentrations, [START_REF] Giller | Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review[END_REF][START_REF] Chen | Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs[END_REF] some of them even in small concentrations, and represent a grave problem in soils not only in specific regions but throughout the world. [START_REF] Kumar | Pollution assessment of heavy metals in soils of India and ecological risk assessment: a state-of-the-art[END_REF] A usual approach to the risk assessment of contaminated soils is based on the comparison of the total concentrations of PTE to critical concentrations, which are often simply based on the background the established concentrations per country or regions [START_REF] Santos | Hazard assessment of soils and spoils from the Portuguese Iberian pyrite belt mining areas and their potential reclamation (chapter 3)[END_REF] which often do not take into account the local geochemical background. It is well known that the estimation of these pollutants and their concentration alone do not give an accurate pollution status in soils, water, and sediments. Only the elements included in the soil solution and associated with the exchange complex of inorganic and organic soil colloids are available to the organisms and biogeochemical cycles. To better estimate the pollution or contamination level from anthropic and natural processes, the application of contamination or pollution indices is necessary. The various indices, such as contamination factor (CF), enrichment factor (EF), pollution load index (PLI), geo-accumulation index (Igeo), potential contamination index (Cp), pollution index (PI), modified pollution index (MPI), potential ecological risk index (RI), and modified potential ecological risk index (MPI) can provide a meticulous assessment of contamination risk status for soils. However, more work must be done to standardize the input data and consider the spatiotemporal variability depending on each land-use system and soil characteristics. Besides the economic costs of remediation, the effectiveness of rehabilitation and conservation practices need additional investigation.

Wildfires

Although wildfires are natural disturbances that can occur in any terrestrial ecosystem, the current increase in fire intensity and severity in the era of accelerated climate change endangers the resilience of these habitats. Every year, approximately 4% of the global land surface burns. [START_REF] Doerr | Global trends in wildfire and its impacts: perceptions versus realities in a changing world[END_REF] Some examples of wildfires and the resulting degraded soils are shown in Figure 3, including examples from Iran (Figure 3C), Hungary (Figure 3D), and Chile (Figure 3E and3F). The two major parameters that determine the ignition of fire are the availability of flammable fuel and the proper climatic conditions that allow ignition. As both are highly affected by global climatic and land-use changes, modern fire regimes are changing, and in many regions, the frequency, extent, and severity of fires are expected to increase in the future. [START_REF] Pausas | The global fire-productivity relationship[END_REF] The effects of fires on soil properties depend primarily on pre-fire edaphic conditions, the type of ecosystem affected, the severity and intensity of the fire, and post-fire meteorological conditions. [START_REF] Neary | Fire effects on belowground sustainability: a review and synthesis[END_REF] The negative effect of fires on soil properties is well recognized, and the greater sensitivity of soil biological properties to disturbances (compared with abiotic conditions) has also been established. [START_REF] Alcañiz | Effects of prescribed fires on soil properties: a review[END_REF][START_REF] Hart | Post-fire vegetative dynamics as drivers of microbial community structure and function in forest soils[END_REF] Although soil biological processes are recognized as main drivers of ecosystem recovery following fires, the consequences of wildfires on soil biota are less understood than the effects on soil physicochemical properties. [START_REF] Yeager | Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire[END_REF] To cope with this globally relevant issue, and minimize the negative impact of fire on soil, major advances in science, management, and policy regarding soil biodiversity and ecosystem services are needed. Given the current scenario, finding feasible solutions, particularly those based on nature, is especially important to cope with the global fire crisis. In this sense, restoration approaches should focus on improvements of belowground conditions, a key component to sustaining aboveground recovery and succession following soil disturbances. [START_REF] Fierer | Embracing the unknown: disentangling the complexities of the soil microbiome[END_REF][START_REF] Harris | Soil microbial communities and restoration ecology: facilitators or followers?[END_REF] The major challenges and future needs for understanding and mitigating fire effects on soil biodiversity are as follows. (1) For effective conservation of soil systems and the ecosystem services they provide, it is necessary to understand the effect of fire regimes on soil and identify potential threats. Possibilities in the application of prescribed burning to maintain ecosystems also need to be explored. [START_REF] Valkó | Review: prospects and limitations of prescribed burning as a management tool in European grasslands[END_REF] (2) As most biodiversity research focuses on aboveground diversity, the understanding of most ecological processes and biodiversity patterns is biased, as belowground biodiversity research is largely underrepresented in the literature, [START_REF] Cameron | Global gaps in soil biodiversity data[END_REF] and belowground macroorganism diversity is underrepresented as compared with microorganism diversity. [START_REF] Oliver | Soil, food security and human health: a review[END_REF] In the future, more research should target the exploration of belowground soil biodiversity and the response of soil biota to global changes in climate, land use, and fire regimes, which could support the development of policies targeting the protection of soil biodiversity. (3) A stronger link should be established between aboveground and belowground biodiversity and ecosystem functioning [START_REF] Pérez-Cabello | Micro-scale post-fire surface cover changes monitored using high spatial resolution photography in a semiarid environment: a useful tool in the study of post-fire soil erosion processes[END_REF][START_REF] Delgado-Baquerizo | Multiple elements of soil biodiversity drive ecosystem functions across biomes[END_REF] to tackle the effects of global drivers, such as fire regimes, climate, and land use on the stability of ecosystems. (4) Post-fire rehabilitation measures need to be developed to support the recovery of fire-affected soil systems. [START_REF] Bajocco | Land degradation versus fire: a spiral process?[END_REF]

Microplastics: an increasingly important environmental issue that requires our attention concerning soils

The development of the plastic polymers that are widely used today took place between 1930 and 1950. Their massive introduction to the market at the end of the 1980s was an industrial and commercial revolution. These new versatile materials, with their higher durability, electrical resistance, plasticity, and especially their low cost of production, made them crucial and sometimes almost irreplaceable in our daily lives (Figure 2E and 2 F). More than 359 million tons of plastics are produced globally per year, and up to 40% of those plastics are packaging and single-use plastics with a short lifespan (approximately 50% of plastics have a service life between 10 minutes and 30 days). These represent serious environmental issues, as waste management technology has not increased at the same rate as plastic production and use [START_REF] Geyer | Production, use, and fate of all plastics ever made[END_REF][START_REF] Horton | Microplastics in freshwater and terrestrial environments: evaluating the current understanding to identify the knowledge gaps and future research priorities[END_REF] and changes in consumption habits are still in the first stages. The impact of microplastics on soil biodiversity is thus an increasingly important environmental issue that requires our attention in soil science.

Once in the environment, plastics undergo degradation when exposed to physical, chemical, or biological factors (eg, UV radiation, mechanical abrasion, temperature, moisture, redox conditions). Degradation results in small particles of plastic of irregular shape and size (usually < 5 mm) called "microplastics" (MP), which are the main form of plastic debris found in the environment. These MP can easily be dispersed, enter food webs and damage organisms, and potentially affect several ecosystem functions. While the impact of MP in aquatic ecosystems is widely known with the first studies occurring in the 1970s, knowledge of the effects of MP on soil systems is still recent (less than 10 years). [START_REF] Horton | Microplastics in freshwater and terrestrial environments: evaluating the current understanding to identify the knowledge gaps and future research priorities[END_REF][START_REF] Rillig | Microplastic effects on plants[END_REF][START_REF] Rodríguez-Seijo | Small plastic wastes in soils: what is our real perception of the problem?[END_REF] Studies that have been conducted have investigated the impacts of MP on soil physicochemical properties (bulk density, soil structure, etc) or soil fauna (eg, earthworms, collembolan). [START_REF] De Souza Machado | Impacts of microplastics on the soil biophysical environment[END_REF][START_REF] De Souza Machado | Microplastics as an emerging threat to terrestrial ecosystems[END_REF][START_REF] Rodríguez-Seijo | Oxidative stress, energy metabolism and molecular responses of earthworms (Eisenia fetida) exposed to low-density polyethylene microplastics[END_REF] Adverse impacts on terrestrial plants and soil microbial activities have recently been reviewed, but the knowledge is limited, especially concerning soil (micro-)organisms and the interactions between MP and soil properties. [START_REF] Guo | Source, migration and toxicology of microplastics in soil[END_REF] In general, long-term contamination by plastic film residues has been correlated with the inhibition of soil microbial activity and fertility due to changes in the activity of enzymes involved in C, N, and P biogeochemical cycles. However, the study of the interaction of MP with the soil microbial community has received little attention to this time. 80- 82 It has also been pointed out that plastics could act as carriers of inorganic and organic contaminants in the water-soil interface, releasing these contaminants into the environment and affecting soil (micro-)organisms, with adverse consequences for the food web. [START_REF] Rodríguez-Seijo | Low-density polyethylene microplastics as a source and carriers of agrochemicals to soil and earthworms[END_REF][START_REF] Liu | Effect of weathering on environmental behavior of microplastics: properties, sorption and potential risks[END_REF] As a result of increased environmental awareness, biodegradable, oxo-biodegradable, and compostable plastics have been proposed as environmentally friendly alternatives to conventional plastics. [START_REF] Haider | Plastics of the future? The impact of biodegradable polymers on the environment and on society[END_REF][START_REF] Napper | Environmental deterioration of biodegradable, oxobiodegradable, compostable, and conventional plastic carrier bags in the sea, soil, and open-air over a 3-year period[END_REF] However, the ecotoxicological implications of these materials are not well studied or they have sometimes been reported to have unanticipated problems such as low environmental degradation under realistic conditions. [START_REF] Napper | Environmental deterioration of biodegradable, oxobiodegradable, compostable, and conventional plastic carrier bags in the sea, soil, and open-air over a 3-year period[END_REF] Thus, there are some knowledge gaps on the occurrence and environmental impact of MP in terrestrial ecosystems that need urgent attention to inform changes in the policies that address and regulate the use and disposal of plastic: (1) the identification of potential sources of MP contamination (eg, agricultural irrigation using wastewater, tire abrasion, or microfibers released after washing), (2) mobility and degradation of MP in the soil under field conditions, (3) ingestion of plastic fibers by soil organisms, (4) understanding the impact of global warming and soil characteristics on the biodegradation rate of plastic polymers, and (5) developing adequate techniques for the extraction and identification of these materials in soils, as current techniques have several issues.

Finally, during the COVID-19 pandemic use of disposable face masks (produced from polymers) is one of the most relevant precautionary measures. The most recent publications claim that the increase in production/consumption of this product is adding a large amount of plastic and plastic particle waste to the environment, reaching waterways [START_REF] Silva | Rethinking and optimising plastic waste management under COVID-19 pandemic: policy solutions based on redesign and reduction of single-use plastics and personal protective equipment[END_REF] (freshwater and marine environments) and the surrounding soils. [START_REF] Aragaw | Surgical face masks as a potential source for microplastic pollution in the COVID-19 scenario[END_REF][START_REF] Fadare | Covid-19 face masks: a potential source of microplastic fibers in the environment[END_REF] This will be another key challenge related to microplastics and soil pollution for the scientific community in this new era. [START_REF] Silva | Increased plastic pollution due to COVID-19 pandemic: challenges and recommendations[END_REF]

Integrated rehabilitation of degraded areas using green technologies

Several degraded soils are non-productive and incapable of generating the ecosystem functions and economic profitability necessary for their recovery. [START_REF] Santos | Rehabilitation of mining areas through integrated biotechnological approach: technosols derived from organic/inorganic wastes and autochthonous plant development[END_REF] Although governmental and other public/private entities recognize the importance of rehabilitating these areas, the conventional techniques usually applied are limited at the environmental level, because they only act on a few parameters of the medium (eg, increase of pH or organic matter), giving a partial solution. [START_REF] Khan | An overview and analysis of site remediation technologies[END_REF] Therefore, more research is necessary for this area. Besides the environmental effectiveness, economic evaluation, especially in the initial implementation, is important in selecting a rehabilitation strategy. [START_REF] Meuser | Soil Remediation and Rehabilitation: Treatment of Contaminated and Disturbed Land (Environmental pollution)[END_REF][START_REF] Lombi | Remediation of polluted soils[END_REF] For successful rehabilitation of a system as a whole, the design and application of strategies adapted to the characteristics of each area that integrate the different components of the ecosystem and their interrelations, coexistence of all degradation factors, the new land use, and the cost and technical efficiency need to be tested. Moreover, it is important to develop and apply sustainable and green technologies, which are increasingly favored (eg, phytodegradation, phytovolatilization, phytoextraction, etc). A combination of green technologies, that may or may not be incorporated into a designed Technosol with phytostabilization, has been demonstrated to be cost-effective in the integrated remediation of contaminated areas at the laboratory, micro-, and mesocosm scales under controlled conditions. [START_REF] Santos | Potential environmental impact of technosols composed of gossan and sulfide-rich wastes from São Domingos mine: assay of simulated leaching[END_REF][START_REF] Lan | Phytostabilization of Cd and Pb in highly polluted farmland soils using ramie and amendments[END_REF][START_REF] Santos | Improvement of chemical and biological properties of gossan mine wastes following application of amendments and growth of Cistus ladanifer L[END_REF] This is due to the simultaneous action on several biogeochemical processes; some of them are complimentary and involved in the environmental rehabilitation process.

The use of different so-called green technologies (the "greenness" of which sometimes still has to be demonstrated, in terms of energetic balance) and heterogeneity of the environmental problem would be key. [START_REF] Garg | Green technologies for restoration of damaged ecosystem[END_REF] Combined methods may also accelerate the rehabilitation processes. Nowadays, some international business groups and governmental entities from several countries are considering and in some cases (little by little) implementing this new approach in their operational and closure activities. [START_REF] Arenas-Lago | Cistus monspeliensis L. as a potential species for rehabilitation of soils with multielemental contamination under Mediterranean conditions[END_REF]100 Sharing information from case studies where new and integrated approaches are used, including levels of environmental improvements and associated costs, is essential to improving our knowledge of these technologies.

Soil and Water Interactions

The nexus between soil, water, energy, and food has recently evolved as a resource-management concept to deal with this intimately interwoven set of resources, their complex interactions, and the growing and continuously changing internal and external sets of influencing factors including climate change, population growth, habits, and lifestyle alterations. At the heart of those complex interactions, soil health and water conservation have emerged as global challenges in a world where pressures from growing demands and shrinking supplies have reached a critical junction for several major global resources, particularly water, energy, and food. To address those challenges, the science community is increasingly challenged with finding more accurate methods of modeling water and nutrient/pollutant distributions in natural, agricultural, forestry, and urban soils to sustain healthy soils, preserve water resources, and secure sustainable food supply for the 7.8 billion inhabitants of this planet.

Soil water and hydrology

The quality of groundwater is highly dependent on soils' ability to infiltrate and filter stormwater and rainwater, thereby removing contaminants. Modeling this ability is dependent on our ability to characterize the complex and heterogeneous nature of soils and the filtration processes. Water recharge processes can be divided into slow uniform movements of water through smaller pores, and fast non-uniform water movement along larger and more active pathways referred to as preferential flow. 101 Preferential flow can contribute to the rapid transport of contaminants from the soil surface into receiving streams, bypassing the filtering capacity of the soil. 102 Developing appropriate approaches to study preferential water movement is a prerequisite to understanding groundwater recharge processes. Preferential flow and its consequences for (contaminant) transport have been studied for decades by soil physicists, soil chemists, and (hydro-)geologists. The fundamental understanding of how preferential flow works has been largely developed. There is, however, still no silver bullet to model preferential flow, storage processes, and related contaminant transport. 103 Several models were developed by the scientific community in the last few decades for interpreting and simulating soil water processes. They are fundamental to gain insight into (1) water and nutrients available for plant root systems from the perspective of sustainable agriculture in widely different environments; (2) understanding point or diffuse pollution of aquifers; (3) water conservation, losses and salinity issues in arid environments; (4) soil water erosion; and (5) management of soil structure in urban environments. [104][105][106] These models rely on soil hydraulic properties that are incorporated into two fundamental characteristics: (1) the soil water retention curve θ(h), describing the relationship between volumetric soil water content, θ (L3 L-3), and soil water pressure head, h (L); and (2) the hydraulic conductivity function, K(θ) or K(h), describing the relationship between θ or h and soil hydraulic conductivity, K (L T-1). 107 Many studies have focused on the development of methods for predicting or measuring soil hydraulic characteristics. The predictive methods allow estimation of soil hydraulic parameters through empirical relationships (pedo-transfer functions [PTFs]) from more widely available data (eg, texture, bulk density). However, the PTFs often rely on site-specific statistical regression equations; thus, they may lack generality. 108 The direct measurement techniques are generally difficult to apply over large areas and are mainly devoted to the field scale. They include either laboratory-or field-based procedures. The former ones allow accurate measurement of flow processes, but they can induce experimental artifacts, such as soil compaction and samples biased by an unrepresentative sampling of pores, that may limit their comparability with in situ measurements. 109 On the other hand, field techniques are based on time-consuming procedures and are more difficult to control, but they allow the estimation of more representative in situ soil hydraulic properties. Therefore, it is desirable to focus on simple field methods that can alleviate time-consuming constraints. 110,111 In conclusion, all methods have their pros and cons, and their selection mainly depends on the processes to be investigated and the temporal and spatial scales involved.

Runoff, soil losses, and sediment transport from the pedon to watershed scale

Soil erosion is a natural process driven by climate, topography, soil, and vegetation factors, which can be assessed using diverse methods depending on the spatiotemporal scale. 112,113 However, human activities (eg, deforestation, agriculture, changes in topography and landscape features) have been intensifying and even altering the natural dynamic and magnitude of soil particle detachment and redistribution, making these studies even more complex. 114 Since the first half of the 20th century, equations and indices have been developed as empirical approaches describing the complex hydrological response of soils to human activities and climate change. 115 Process-based model development enables us to integrate the knowledge of the natural and human-induced mechanisms and interactions among factors affecting runoff, using distinct approaches (eg, empirical, process-based and of mass or energy balance) and techniques (eg, GIS, remote sensing). 116 Some models allow the mapping of spatially distributed rates and patterns of runoff and soil redistribution. 117 Overland flow-mediated processes, such as soil and water pollution, flood prediction, landslide risk, and even crop yield can be also evaluated with these tools (Figure 4A andB). Also, models help assess the effectiveness/impact of soil and water conservation measures and agricultural, environmental, and climate policies. From the pedon to the hillslope scales, natural hazards and human-induced disasters such as landslides, floods, and landsubsidence can cause damages ranging from severe financial losses to the loss of life and irreparable damages to ecosystems (eg, fragile water bodies, peatlands). 120,121 Preparing susceptibility, hazard, multi-hazard, and risk maps and assessments for an area of interest is key for scientists devoted to understanding soil dynamics and in helping land-use planners, managers, and decision-makers. 122,123 These assessments can be valuable for each community before, during, and after the occurrence of a given event. To accomplish this, statistical, probability, metaheuristic, machine learning, and ensemble-based GIS (geographic information system) and RS (remote sensing) models are being tested and improved in the most recent research studies. [124][125][126] However, the selection of the best model for application is challenging. There are various advantages and disadvantages to each of the above-mentioned algorithms. One of the most important problems with traditional models is related to the absence of precise border/class for categorical factors including lithological units, soil texture, and land use types in nature. 127 On the other hand, determining a natural border for continuous and numerical factors such as slope, elevation, distance from rivers, faults, and roads is very difficult, or even its mere description. So, determining natural disaster

10

Air, Soil and Water Research assessments with a high level of accuracy and considering simple effective factors that might predict natural disaster occurrence is an important previous step. In response to these issues, we can suggest machine learning approaches to increase model accuracy when dealing with complex and uncertain problems while also developing new methods and theories. 128 On the other hand, conducting in situ measurements or field experiments is also indispensable to understand the activation of initial soil erosion processes and runoff results obtained under laboratory (controlled) or real (semi-controlled) conditions, as well as machine learning outputs. A rainfall simulator device, which is one approach to obtain such information, is shown in Figure 4C. To obtain meaningful results, experimental design procedures must be appropriate, 129 adequate, and standardized methods need to be used. 130 Enough events must be observed with sufficient repetitions to adequately characterize the system. The use of rainfall, wind, and runoff simulations 131 has to become a standard technique to confirm model applications or test plot variations at different points on hillslopes or in watersheds. Sediment tracers (eg, fallout radionuclides, rare earth elements, magnetic substances) allow the collection of erosion data that considers spatial distribution and the identification of sediment sources (fingerprinting), which is essential for characterizing soil erosion processes and validating soil erosion models. 132 Another hot topic is the use of biomarkers or biological indicators to understand past and current soil erosion and driving factors such as crusts or soil mobilization. Among these, dendrochronological methods and the improved stock unearthing methods are used in agricultural areas. [133][134][135] Finally, a new object of study is related to weather types and soil erosion, using erosion plots and accurate climate data. [136][137][138]

Watering ponds and soil quality due to livestock and overgrazing

Livestock husbandry is a key economic activity for both the survivorship of many rural areas and the preservation of cultural ecosystems with a high natural value (Figure 4D). Its sustainability depends on the efficient management of natural resources such as pasture and water through empiric knowledge of natural cycles (eg, climate, phenology of pasture species, livestock breeding). 139 The scarcity of fertile soils and water has traditionally been superseded by strategies based on animal movement (transhumance). Nowadays, many farms are self-sufficient because of the construction of watering ponds and conservation of grass, among other infrastructures and actions. 140 Nevertheless, this natural-based solution is also causing health problems due to a reduction in soil and water quality and transmission of diseases via wildlife. 141,142 The origin of watering ponds is very ancient, probably from the times of the Roman Empire, although their broad dissemination is linked to the arrival of heavy machinery in the second half of the 20th century. 143 They are constructed to store water from different sources: direct rainfall and sub/surface runoff. They are designed taking into account geometrical parameters such as pond and basin surface, maximum depth, and so on. Marín-Comitre et al 144 summarized the hydrological response of different ponds to precedent rainfall. They concluded a pond must have a minimum surface of 2000 m 2 and a storage capacity rate of 100 m 3 ha -1 to guarantee water for livestock during drought periods. Other concerns for farmers and stakeholders include water quality in their ponds; more than 75% of them have admitted using water from wells under particular circumstances; these ponds also function as biodiversity preserves (eg, amphibians). 145 Soil and water quality are key issues for livestock health and possible transmission of diseases from animals to humans via meat consumption because of pathogens and chemical residues present in low-quality water, soil, and plants. 146 This quality largely depends on appropriate land management because overstocking animals can produce an increase in soil erosion and compaction and loss of biodiversity and soil organic carbon, 147,148 meaning more contaminants arrive in surface water. In addition, livestock is considered a major water polluter because they can defecate directly into the pond and their excreta can arrive in water via runoff.

Some countries with a long farming tradition (eg, the United States, Argentina, Australia, New Zealand, South Africa) have developed specific legislation to guarantee water quality for consumption by their livestock and, subsequently, for soil/water interactions. The EU (Regulation (EC) No 183/2005-requirements for feed hygiene) only mentions that water for animals should have the same quality as for human consumption, but it does not provide any information about indicators that can be assessed by farmers (E coli, nutrient contents, color, the turbidity of the water, etc) despite the 30 directives and regulations which have set up the EU policy to limit degradation and pollution of aquatic environments since 1975 (eg, directive 2000/60/CE).

Therefore, further research on soil and water for livestock from different perspectives is still needed. It is relevant to pay attention to how the water for livestock, stored in watering ponds, moves through soil and how soil influences the quality of water in the pond, both as a potential source of contaminates and as a filter system. Some important research questions have not been solved yet include (1) how exactly soil management influences the amount and quality of the stored water, (2) will the current infrastructures be able to face future challenges in soil management caused by climate change, and (3) which parameters should be used as indicators of soil quality and the quality of water and plants used for animal consumption?

Digital Soil Mapping (DSM)

Soil maps support many research fields including, but not limited to, pedology, soil classification, soil survey, landscape modeling, natural resources management, land use planning, carbon storage, land use/land cover change, and environmental risk assessment. [149][150][151][152] Numerous assessments have defined and criticized current soil mapping techniques. [START_REF]International Soil Classification System for Naming Soils and Creating Legends for Soil Maps[END_REF]153,154 DSM involves 3 main components: (1) input data (field and laboratory soil observations), (2) the process (building mathematical or statistical models to better fit the soil-environment relationships), and (3) output (continuous thematic or raster maps), and the associated uncertainties. The first recognized soil maps were produced in the mid-19th century to determine the suitability of land use for agricultural purposes. Vast growth occurred in this field in the 20th century due to the development of computers and information technology, [130][131][132] including exponential development in geographic information systems (GIS), global positioning systems (GPS), remote sensing (RS), and geostatistics. The availability of satellite images, digital elevation models (DEMs), Light Detection and Ranging of Laser Imaging Detection and Ranging (LIDAR), and radio detection and ranging (RADAR) are key to understanding the increasing research on digital soil mapping. The utilization of proximity sensors such as portable X-ray fluorescence (PXRF) spectrometry, gamma-ray radiometry, UV-visible fluorescence measurements, and visible near-infrared reflectance (Vis-NIR) spectroscopy, as well as computational algorithms, represent new horizons to be explored. [155][156][157][158][159][160][161][162] The availability of soil maps is fundamental to underpin sustainable soil management decisions at local, regional, national, and global scales, but currently faces 3 main issues: (1) soil surveys, carried out either conventionally by experienced pedologists and/or using DSM approaches, 163,164 are still far from covering many parts of the planet, particularly at detailed scales higher than 1/50 000; (2) soil surveys are costly and time-consuming, therefore they are scarce; and (3) several soil properties, such as topsoil nitrogen content, may vary over short to medium temporal ranges (5-10 years) and need to be periodically updated. Over the last two decades, DSM has gained more and more recognition linking field, laboratory, and proximal soil observations with quantitative spatial and geostatistical methods to infer soil spatial patterns. 165 The GlobalSoilMap program, which aims to provide a fine resolution global grid of soil functional properties, is emblematic of the challenges raised by DSM. 163 In addition to specifications to harmonize soil profile properties (eg, by using spline functions 166 ), it has provided international standards for output maps, including the requirement of estimates of the uncertainties associated with mapped properties. [167][168][169] The availability of increasing amounts of remote sensing data, notably the Sentinel satellite series, is promising for enabling not only updates to existing maps but also a wider coverage of digital soil maps of soil properties. Remote sensing reflectance spectra of bare soil pixels are likely to predict several topsoil properties 170 while reproducing spatial structure [171][172][173][174] and may also contribute to infer uncertainty. 175 To date, few authors have incorporated satellite imagery as covariates within DSM models. 176 As the widely available Sentinel-2 series have recently exhibited promising capacities to predict soil properties spectrally, [177][178][179][180] this is a new challenge for the coming years.

Soil Organic Carbon Sequestration in Climate-Smart Agriculture Need for soil organic carbon sequestration

Soil degradation, which includes several processes such as soil erosion, salinization, acidification, compaction, nutrient depletion, and soil organic carbon (SOC) depletion, is a threat to soil fertility (Figure 5A), and hence, food security-especially in developing countries. 181 Currently, 33% of global soils have lost much of their SOC through the historical expansion of agriculture and pastoralism. 182 This has resulted in increased erosion risks and reduced water storage and nutrient supplies. However, this trend may be reversed by implementing management practices that enhance soil carbon sequestration by increasing C input or reducing C losses from the soil. In agriculture, several practices (such as green manuring, increased cereal use in rotation schemes, use or substitution of mineral with organic fertilizers, the use of organic amendments (Figure 5B), crop residue incorporation and reduced tillage) provide a valuable alternative to conventional systems, without compromising food production. 183,184 The sequestration of SOC has become part of the global carbon agenda for climate change mitigation and adaptation through the launch of the "4 per mille" initiative at COP21 by UNFCC in Paris in 2015. The idea behind the initiative is that an annual increase of 4‰ of the global SOC stocks in the top 0.3 to 0.4 m of all non-permafrost soils would counteract the annual global rise in atmospheric CO 2 . 185 Increases in SOC are, however, only realistic in actively managed soils including agricultural soils and managed forestry in the first 0.3 to 0.4 m soil depth. This would require an annual increase of 4.7 Gt C y -1 in agricultural soils to compensate for the net annual increase of atmospheric C, averaged over the years 2005 to 2014. 186 Various studies estimated the technical potential for SOC sequestration and, in a broader sense, SOC storage171 by improved (1) cropland and grazing land management, (2) livestock and manure management, (3) restoration of degraded lands and cultivated organic soils, and (4) agroforestry. [187][188][189][190][191] Global-scale SOC sequestration rates have thus been estimated at 2 to 3 Gt C y -1 , but those estimates are likely far too high due to a lack of nutrients like N and P necessary to sequester the suggested amount of carbon in extensive grasslands and croplands with low fertilization rates. This follows from stoichiometric considerations, ie, the need for sequestering N and P given the C/N and C/P ratios in stored SOC. 192,193 Despite its limitations and the need for further research, the implementation of management practices that increase SOC contents can improve soil quality, fertility, and functioning.

Challenges for soil organic carbon sequestration

The major potential for significant carbon sequestration is in the world's cropland soils, especially in those with large yield gaps 191 and/or large historic soil organic carbon (SOC) losses. 182 Closing the gaps between the current and water-limited yields can be achieved mostly by a more balanced nutrient supply, which is intimately linked to SOC sequestration, by enhanced crop residue return in support of SOC sequestration. 183,194 Rising SOC values may also increase agricultural yields in areas with low SOC or high salinity (Figure 5C and D) contents due to associated improvements in nutrient supplies, water-holding capacity, and soil structural stability. 195,196 However, there is a price to SOC sequestration as it also implies immobilization of N in SOC and the elevated N inputs that are needed to enhance plant uptake and N immobilization may cause trade-offs with nitrous oxide (N 2 O) emissions. 197,198 The challenge is to close the yield gap sustainably, with low

Conclusions

This review aimed to present and discuss some challenges and possible ideas associated with recent advancements in soil research. Twenty experts belonging to the editorial board of Air, Soil and Water Research gave examples that illustrate some of the diverse and complex that affect soils. A summary of the main conclusions is shown in Figure 6, where a pyramidal diagram shows the main threats and challenges discussed in this article. Many of the soil-related challenges (compaction, erosion, contamination) have been around for decades and the underlying processes have been studied extensively by the scientific community. New aims are primarily the technologies that became available and affordable over the last few decades (computational capacities, GIS, remote sensing, bioremediation etc) that provide us with new opportunities to better address some of these challenges. Emerging new technologies based on geographic information systems and remote sensing combined with models, new computational capabilities and algorithms or in situ measurements provide new opportunities to understand soil processes and interactions at diverse spatiotemporal scales. Micro-plastics are an emerging potential pollutant with the potential to negatively affect the world's soils, and now are even more relevant due to the residues of face masks (produced from polymers) used during the COVID-19 pandemic. Still, studies on microplastics in soil systems are scarce; therefore, it highlights the urgent need for future studies to fill the important knowledge gaps related to microplastics in soil systems. Also, more research must be conducted, especially in field conditions and over the medium to long term, on the development and application of green technologies to mitigate pollution and other degradation factors of soils. Impacts from wildfires and human activities (urbanization, industrialization, transportation, agriculture) on soil microorganisms (biodiversity) and thereby on biogeochemical cycles, especially organic carbon, nutrients and pollutants, and water availability should be major objectives of the investigation by the scientific community. Data sharing and more open data access between soil scientists are also important. This can further facilitate modeling, increase knowledge and accelerate collaboration between peers. All the above topics and more are important and related to the influence of soils on human health. Manuscripts on these emerging topics are highly welcomed in Air, Soil and Water Research.

Figure 1 .

 1 Figure 1. Soil scientists and soil profiles: (A and B) Dr Manuel Pulido performing soil bulk density measurements; (C) Terric Anthrosol with colluvic materials 1 in the vineyards of the Celler del Roure, Valencia, Spain; (D) Eutric Gypsisol, 1 Málaga city, Spain; (E) Entisols 2 soil order with calcium carbonate concretions in deep horizon, Western desert, Egypt; (F) Aridisols 2 soil order with vertic features (slickenside, wedge-shaped aggregates, and high clay content), Northern Nile Delta, Egypt. Photos were taken by Jesús Barrena and Manuel Pulido (Extremadura University), Jesús Rodrigo-Comino (Valencia and Trier Universities), and Noura Bakr (National Research Centre, Cairo).

Figure 2 .

 2 Figure 2. Soil degradation by contamination and overexploitation: (A) soil contaminated with jet fuel and pesticides, North Dakota, USA; (B) contamination from an iron and steel scrap storage yard, central Poland; (C) irrigated and tilled fields in Jalandhar, Punjab, India; (D) agricultural terraces in abandoned fields in Bierge, Spain; (E and F) plastic items found in soils from an old greenhouse field, Portugal. Photos were taken by Eric C. Brevik (Dickinson State University), Maja Radziemska (Warsaw University of Life Sciences), Manuel López-Vicente (Wageningen University), and Andrés Rodríguez-Seijo (University of Porto).

Figure 3 .

 3 Figure 3. Wildfire effects on soil: (A and B) A landscape of Karst Garbin Basin (Xibeile Town, Mengzi City, Yunnan Province) where took place the field experiment for restoration areas (2016-2020); (C) non-rehabilitated burned soils in Fars, Iran; (D) grassland wildfire, Karcag, Hungary; (E and F) January-February 2017 at Pumanque, Chile. Photos were taken by Hamid Reza Pourghasemi (Shiraz University), Orsolya Valkó (Hungarian Academy of Sciences), Daniel Bahamondes (Universidad de O'Higgins), and Yang Yu (Beijing Forestry University.

  118,119 Specific current challenges in the development and application of soil erosion models include (1 the non-linear relationships and thresholds between factors and processes; (2) the heterogeneity of model outputs obtained with different approaches at the same site; (3) the identification of stable areas; (4) the refinement of model predictions with accurate independent metrics of soil loss and deposition;(5) improved indicators of vegetation changes at a high temporal resolution using remote sensing; (6) upscaling model findings from the local scale to larger ones; and (7) integrating soil erosion processes with carbon sequestration, nutrient fluxes, diffuse contamination, and climate change scenarios.

Figure 4 .

 4 Figure 4. Soil erosion processes affecting urban, rural, and natural ecosystems: (A) floods in Mazandaran Province (Kelardasht), Iran; (B) landslides in Tehran, Iran; (C) rainfall simulation experiments in abandoned areas in SE Spain; (D) grazing areas of SW Spain. Photos were taken by Hamid Reza Pourghasemi (Shiraz University), Jesús Barrena and Manuel Pulido (Extremadura University), and Jesús Rodrigo-Comino (Valencia and Trier Universities).

  N 2 O emissions, to contribute to climate change mitigation. This calls for a spatially diversified strategy for climate change mitigation from agricultural soils, focusing on efforts to (1) improve N use efficiency and reduce N 2 O emissions in soils with a low C sequestration potential and (2) sequester carbon in soils with a low C stock and a high C sequestration potential. 192

Figure 5 .

 5 Figure 5. Need for soil organic carbon storage: (A) differences in winter wheat development due to the presence of a slaking crust in Luvisols1 from loess with low topsoil organic carbon content; (B) green waste compost about to be spread over fields; (C and D) salinization processes, Northern Nile Delta, Egypt. Photographs taken in the Versailles Plain (France) by Emmanuelle Vaudour (AgroParisTech) and Noura Bakr (National Research Centre, Cairo).

Acknowledgements

We thank the scientific community cited in this review and other researchers who are trying to understand soils. This article is dedicated to all the stakeholders who are facing delicate environmental situations characterized by climate change, water and soil degradation, migration from rural and marginal areas, and non-deserved low prices and incomes for their produced resources and goods.

Photos were taken by Jesús Rodrigo-Comino (Valencia

Author Contributions

All authors contributed equally to this work.


Evolution -Le Moulon

Présentation générale des données

* Raw data are acquired on dedicated work stations using conventional hard disks (RAID) into data files. * Raw data files are transfered using ssh encrypted connection to the servers in IDEEV computer room. File storage is distributed on a ceph cluster (distributed file system). Ceph guarantees reliability using erasure code (protection against hardware failures) and performance. * Raw data files are converted into Open data formats (mzML, mzXML) on the data storage system. * So called "generated files", processed data from raw data files are also produced and stored on the ceph data storage system. * To ensure data safety, data files backups are made every day through dedicated RAID file servers.

Raw data produced by the mass spectrometer Mode d'obtention des données

Données générées par la structure Raw data are unprocessed data output by the instruments (mainly mass spectrometers) hosted at PAPPSO. We convert these raw data into an open format for mass spectrometry. The files output by the conversion process (formats: mzXML or mzML) are also stored without modification of the mass data in them.

Origine

Observation Instruments hosted at PAPPSO.

Nature des données

Proteomics data (LC-MS/MS analyses on protein extracts)

Format des données

.tdf (Bruker's format) .raw (Thermo's format) .mzXML (open format for raw data)

.mzML (open format for raw data)

Scientific software projects developped by PAPPSO Mode d'obtention des données

Données générées par la structure Données produites par un tiers

As the codes of our software are open, third parties can contribute to them and add new functionalities.

Type de données

Software

The softwares that we develop are:

-X!TandemPipeline implemented in C++ for the peptide identification and protein inference -MassChroq implemented in C++ for peptide quantification -MCQR implemented in R for data analysis -msXpertSuite implemented in C++ for modelling, simulating and analyzing ionized flying species Nature des données programming language (C++, Python, R, perl, Java, Javascript, PHP...)

Format des données text files

Droits de propriété intellectuelle

Raw data produced by the mass spectrometer

Qui détiendra les droits sur les données et les autres informations créées ?

The users and their respective institutions are the owners of the produced data.

Scientific software projects developped by PAPPSO

Qui détiendra les droits sur les données et les autres informations créées ?

The institutions that paid for the development of the code have the intellectual property rights (mainly INRAE and CNRS).

Confidentialité

Raw data produced by the mass spectrometer

Identification des jeux de données contenant des données confidentielles PAPPSO guarantees the confidentiality of all the datasets produced, as described in its charter. The decision of data publication is taken with the users.

Quelles sont les mesures prises et les normes auxquelles il est nécessaire de se conformer pour garantir cette confidentialité ?

Access to the instruments is regulated and monitored. The data are directly transmitted to the storage cluster through a secure shell (ssh) link. The server is protected by a firewall filtering connections by IP number ranges and accessible only by encrypted ssh key to the PAPPSO agents. Even if the desktop and laptop computers of the PAPPSO agents are encrypted (following the recommendations of the CNRS under the responsibility of the CSSI), it is not allowed to copy data elsewhere than on the cluster. All PAPPSO agents sign a charter for the use of computer resources specifying the confidentiality of all data produced. In the event of an incident, the data is recovered from the PAPPSO backup servers or from the regularly archived LTO tapes.

Scientific software projects developped by PAPPSO Identification des jeux de données contenant des données confidentielles

The codes of our softwares are not confidential, but the master branches of their repositories are restricted for some actions.

Quelles sont les mesures prises et les normes auxquelles il est nécessaire de se conformer pour garantir cette confidentialité ?

The code of our software are versioned on the GitLab forge hosted by INRAE's MATHNUM department forgemia. We use the application's functionalities to manage the repositories access and grants.

Le cas échéant, comment la confidentialité de données fournies par des personnes sera garantie lorsque les données seront partagées ou rendues disponibles pour une analyse de second niveau ?

Not relevant

Partage des données

Raw data produced by the mass spectrometer Y a t'il une obligation de partage (ou à l'inverse une interdiction ou une restriction) ?

The user is committed to publicly open the data. An embargo period can be defined with respect to the scientific community usage. The decision of data publication is taken with the user.

Quelles sont les réutilisations potentielles de ces données ?

Re-use for new research purposes Re-use to apply different methods of analysis Support for public policy, expertise Trainings

Scientific software projects developped by PAPPSO Y a t'il une obligation de partage (ou à l'inverse une interdiction ou une restriction) ?

All our software are licensed under the GNU GPL v3. Any modification is allowed as long as the modified code is available under the same conditions.

Quelles sont les réutilisations potentielles de ces données ?

Improvement of existing functionalities Addition of new functionalities to answer new needs

La lecture des données nécessite-t-elle le recours à un logiciel ou un outil spécifique ? Si oui, lequel ?

Any software produced by PAPPSO only requires publicly available standard compilers, runtimes, operating systems to run.

Comment les données seront-elles partagées ?

All our softwares are versioned on private repositories of the GitLab forge forgemia and are available publicly or upon request.

Sous quelle licence ?

Autre (à préciser dans la zone d'Informations supplémentaires All our sofwares are under the GNU General Public Licence version 3.

Organisation et documentation des données

Raw data produced by the mass spectrometer

Quels méthodes et outils sont utilisés pour acquérir et traiter les données, depuis leur acquisition jusqu'à leur mise à disposition, leur archivage ou leur destruction ? Utiliser éventuellement un lien vers un schéma illustrant les processus

Raw data are acquired by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). If necessary, they may be converted to the mzXML/mzML formats by using the msConvert software. They can be visualized and explored by using mineXpert2. Raw data can be processed by using X!TandemPipeline for peptide identification, protein inference and protein quantification based on spectral counts. When processed by using MassChroQ, together with identification results, they allow to produce peptide quantification results. Finally, quantification results can be analysed and interpreted by using MCQR. A schematic overview of the data processing is available here. The raw data produced by the mass spectrometers (proprietary format) are archived on LTO8 tape in two copies, one stored on the Jouy site, the other on the Moulon site. The files transformed to open formats (mzXML or mzML) as well as all subsequent analysis data are stored on a distributed, fault-tolerant and resilient file system (ceph) (erasure code). To prevent manipulation errors, the data is archived with BURP software in multiple copies every day on dedicated servers (RAID5), guaranteeing a storage time of one month. The PAPPSO storage system is hosted in our secure computer room at IDEEV (controlled access, air conditioning, fire protection system). At the end of the analyses, the data stored on the cluster are archived on LTO8 tapes in 2 copies (one in Jouy, the other in IDEEV). The content of the tapes is referenced and the tapes are labelled.

Quelles métadonnées seront utilisées pour accompagner le jeu de données

Comment les fichiers de données sont-ils gérés et organisés : contrôle des versions, conventions de nommage des fichiers, organisation des fichiers

By essence, the raw data files need no version control system, because these files are only stored and never modified. Raw data files are stored on our file system using a naming convention (by site, instrument, date, experiment). This complete path is conserved from the initial acquisition to the final archive location. The intermediate files (xpip files, for example) are so-called "generated" data files, which means that they can be regenerated using the same raw data set and the same software program. We do store these intermediate files along with the raw data files. Generated files contains the name and version of software used to process data.

Quel est le processus de contrôle qualité des données ?

The quality of the proteomics data is controlled at several stages: a visual control of the chromatograms as well as numerical indicators (number of identified peptides and proteins, percentage of assigned spectra) allow to ensure that the data were correctly acquired by the mass spectrometer. In addition, graphical representations such as distribution density, boxplot or PCA are used to check the alignment of retention times, the dispersion and distribution of data in each sample, the variability between samples.

Utiliser éventuellement un lien vers un schéma illustrant les processus

Standard text editor to produce programming language code. Version control is provided by git. We use general naming convention for R code as well as the directory name scheme. We use the debian package policy for other sofware : each file is described and stored in standard places.

Quelles

Quel est le processus de contrôle qualité des données ?

Our development process is test driven. Our debian packages can only be released if tests are successful. We also use test datasets and controls are made for each software version to guarantee reliability.

Stockage et sécurité des données

  La lecture des données nécessite-t-elle le recours à un logiciel ou un outil spécifique ? Si oui, lequel ? -Bruker data (directory-based raw data format): readable by DataAnalysis software(Bruker) or free and open source PAPPPSO's implementation (PAPPSOms++ library); -Thermo Fisher Scientific raw data: readable by Qual Browser (Thermo) or Free Style (Thermo); -mzXML or mzML: readable by the mineXpert2, mzMine2 free and open source software or any other proteomics open source software.Comment les données seront-elles partagées ?The data will be deposited in the reference repositories like MASSIVE or PRIDE, on the Data INRAE portal.Avec qui ?Autre Public data are shared with anyone (open access) Private data are shared with identified users (academic and/or private partners)Sous quelle licence ?Autre (à préciser dans la zone d'Informations supplémentaires A DOI will be automatically associated to the data deposited on reference repositories like MASSIVE or PRIDE. Otherwise, we encourage the users to associate a DOI to the dataset with INRAE's open data repository service. It allows to discuss the license associated to the data. By default, public data are under the CC-BY V4.0 license. We can provide support if needed.

  métadonnées seront utilisées pour accompagner le jeu de données ? Quels seront les standards, vocabulaires, taxonomies... utilisés pour décrire et représenter les données et éléments de métadonnées ? Comment les métadonnées seront-elles produites et mises à jour ? Our source code is documented using standards : Doxygen for C++, R documentation... Une documentation complémentaire aux métadonnées est-elle nécessaire pour décrire les données et assurer leur réutilisabilité sur le long terme ? Not relevant Comment les fichiers de données sont-ils gérés et organisés : contrôle des versions, conventions de nommage des fichiers, organisation des fichiers

  Scientific software projects developped by PAPPSOQuels sont les types de flux empruntés par les données et les supports utilisés pour les stocker ? (Faire éventuellement un lien vers un schéma)Git repositories are used on local file systems and then pushed to the central git repository in ForgeMIA gitlab.Quelle est la volumétrie actuelle et prévisionnelle ?500Mb maximum per year.Sécurité -Confidentialité : les données font-elles l'objet d'échange ou de partage avec de tiers acteurs et selon quelles modalités ? comment sont déterminés les droits d'accès aux données avant leur publication ?Source code are available publicly under the terms of the GPLv3. Access is granted by the ForgeMIA Gitlab repository.Sécurité -Intégrité -Tracabilité : Quelles sont les mesures de protection mises en oeuvre pour suivre la production et l'analyse des

? Quels seront les standards, vocabulaires, taxonomies... utilisés pour décrire et représenter les données et éléments de métadonnées ? Comment les métadonnées seront-elles produites et mises à jour ? Metadata Metadata origin and production mode (e.g. manual input, automatic annotation...) Standard and associated vocabularies Conditions or frequency update (if applicable) (e.g. change in accessibility)

	Experimental design manual input	text tabulated file format
	Protein sequence data	automatic annotation from genome sequence or RNAseq information	FASTA files	Latest available version at the moment of the analysis
			Minimal
	Phenotyping experiment	manual input	Informations About Plant Phenotyping Experiments
			(MIAPPE)
	Protein functionnal	automatic or manual annotations from trEMBL, SwissProt,	GO, KEGG	Latest available version at the moment
	annotation	mapMan, KEGG, GO	annotations	of the analysis

Une documentation complémentaire aux métadonnées est-elle nécessaire pour décrire les données et assurer leur réutilisabilité sur le long terme ? Metadata Documentation

	Experimental design	self explanatory (biological or technical repetitions, experimental conditions...)
	Protein sequence data	Publicly available databases
	Phenotyping experiment	Publicly available biological ontologies
	Protein functionnal annotation	Publicly available ontologies

Raw data produced by the mass spectrometer Quels sont les types de flux empruntés par les données et les supports utilisés pour les stocker ? (Faire éventuellement un lien vers un schéma) Quelle est la volumétrie actuelle et prévisionnelle ?

  In 2022, annual data production is 20Tb. Previsional production for 2024 is 30Tb.

L'

entité hébergeant physiquement les données a-t-elle une politique de sécurité pour son système d'information ? politique locale, charte des infrastructures de recherche...

	Charte des infrastructures de recherche à l'Inra
	Sécurité -Confidentialité :

les données font-elles l'objet d'échange ou de partage avec de tiers acteurs et selon quelles modalités ? comment sont déterminés les droits d'accès aux données avant leur publication ?

  As already discussed, all data produced by PAPPSO are confidential, only available to PAPPSO members. Upon demand from data owners, raw data or generated files are sent directly or uploaded to a data repository for Open Access purpose or confidential access if needed.

	Sécurité -Intégrité

-Tracabilité : Quelles sont les mesures de protection mises en oeuvre pour suivre la production et l'analyse des données ?

  PAPPSO is certified ISO 9001. Our production processes are traced in our Quality Management System.

Scientific software projects developped by PAPPSOQuels méthodes et outils sont utilisés pour acquérir et traiter les données, depuis leur acquisition jusqu'à leur mise à disposition, leur archivage ou leur destruction ?

se reporter à l'annuaire INRAE) Validé par Validé le 16/06/2021 1 unpublished Mélisande Blein-Nicolas UMR Génétique Quantitative et

* Finally, raw data files and generated files are archived

données ?

git system and debian quality assurance team.

Archivage et conservation des données

Raw data produced by the mass spectrometer Quelles sont les données à conserver sur le moyen ou le long terme et quelles sont les données à détruire ?

All the elaborated and derived data are preserved in the long term as well as the useful raw data (for a later re-exploitation). Only temporary files needed to generate elaborated data can be destroyed.

Sur quelle plateforme d'archivage pérenne seront archivées les données à conserver sur le long terme ? Sinon, quelles procédures seront mises en place pour la conservation à long terme ?

The data stored are archived on LTO8 tapes in 2 copies (one in Jouy, the other in Le Moulon). The content of the tapes is referenced and the tapes are labelled.

Quelle est la durée de conservation des données ?

At least 2 years.

Quelles garanties de financements couvriront les coûts associés à la conservation à long terme ?

Long term conservation is guaranteed as long as PAPPSO is financially supported.

Scientific software projects developped by PAPPSO

Quelles sont les données à conserver sur le moyen ou le long terme et quelles sont les données à détruire ?

all source codes and all versions are kept.

Sur quelle plateforme d'archivage pérenne seront archivées les données à conserver sur le long terme ? Sinon, quelles procédures seront mises en place pour la conservation à long terme ?

Long term support is provided by the ForgeMIA.

All our software are also conserved by the Debian project.

Quelle est la durée de conservation des données ? no limit

Quelles garanties de financements couvriront les coûts associés à la conservation à long terme ?

Financial support is guaranteed by institutional support of ForgeMIA and international support of the Debian project.