Résumé
Abstract. The activity of microorganisms in soil is important for a robust
functioning of soil and related ecosystem services. Hence, there is a
necessity to identify the composition, diversity, and function of the soil
microbiome in order to determine its natural properties, functioning, and
operating range as well as to assess ecotoxicological effects due to
anthropogenic activities. Numerous microbiological methods currently exist
in the literature and new, more advanced methods continue to be developed;
however, only a limited number of these methods are standardised.
Consequently, there is a need to identify the most promising
non-standardised methods for assessing soil quality and to transform them
into standards. In agreement with the “Ecosystem Service Approach”, new
methods should focus more on soil microbial functions, including nutrient
cycling and greenhouse gas emission, pest control and plant growth
promotion, carbon cycling and sequestration, as well as soil structure
development and filter function. The few existing standardised methods
available that focus on the function of the soil microbiome mostly include
measurements, like basal respiration, enzyme activities, and biodegradation
of organic matter, under well-defined conditions in the lab. This paper sets
out to summarise and expand on recent discussions within the International
Organization for Standardization (ISO), Soil Quality – Biological
Characterization sub-committee (ISO TC 190/SC 4), where a need was identified
to develop scientifically sound methods which would best fulfil the
practical needs of future users for assessing soil quality, going beyond the
existing test systems. Of particular note is the current evolution of
molecular methods in microbial ecology that use quantitative real-time PCR
(qPCR) to produce a large number of new functional endpoints which are more
sensitive as compared to “classical” methods. Quantitative PCR assesses the
abundance of microbes that catalyse major transformation steps in nitrogen
and phosphorus cycling, greenhouse gas emissions, chemical transformations
including pesticide degradation, and plant growth promotion pathways based
on the assessment of marker gene sequences that drive the related processes.
In the assessment of soil quality methods, it was found that most methods
focus on bacteria and related endpoints. Techniques to describe fungal
communities as well as their functional traits are far less represented. As
such, techniques to analyse fungal enzyme activities are proposed.
Additionally, methods for the determination of microbial growth rates and
efficiencies, including the use of glomalin as a biochemical marker for soil
aggregation, are discussed. Furthermore, field methods indicative of carbon
turnover, including the litter bag test and a modification to the tea bag
test, are presented. However, it is obvious that with increasing
developments in high throughput sequencing technologies and big data
analyses, including metagenomics analysis, it will be possible to implement
these technologies into the standardisation process for assessing the
functions of the soil microbiome. Overall, it is suggested that endpoints
should represent a potential function of soil microorganisms rather than
actual activity levels, as the latter can largely be dependent on short-term
variable soil properties such as pedoclimatic conditions, nutrient
availability, and anthropogenic soil cultivation activities.
Auteurs, date et publication :
Auteurs Sören Thiele-Bruhn , Michael Schloter , Berndt-Michael Wilke , Lee A. Beaudette , Fabrice Martin-Laurent , Nathalie Cheviron , Christian Mougin , Jörg Römbke
Publication : SOIL
Date : 2020
Volume : 6
Issue : 1
Pages : 17-34
Catégorie(s)
#BiochemEnv #INRAERésumé
Biomineralization is a common process in most vascular plants, but poorly investigated for trees. Although the presence of calcium oxalate and silica accumulation has been reported for some tree species, the chemical composition, abundance, and quantification of biominerals remain poorly documented. However, biominerals may play important physiological and structural roles in trees, especially in forest ecosystems, which are characterized by nutrient-poor soils. In this context, our study aimed at investigating the morphology, distribution, and relative abundance of biominerals in the different vegetative compartments (foliage, branch, trunk, and root) of Fagus sylvatica L. and Acer pseudoplatanus L. using a combination of scanning electron microscopy and tomography analyses. Biomineral crystallochemistry was assessed by X-ray diffraction and energy-dispersive X-ray analyses, while calcium, silicon, and oxalic acid were quantified in the compartments and at the forest scale. Our analyses revealed that biominerals occurred as crystals or coating layers mostly in bark and leaves and were identified as opal, whewellite, and complex biominerals. In both tree species, opal was mostly found in the external tissues of trunk, branch, and leaves, but also in the roots of beech. In the stand, opal represents around 170 kg/ha. Whewellite was found to suit to conductive tissues (i.e., axial phloem parenchyma, vascular bundles, vessel element) in all investigated compartments of the two tree species. The shape of whewellite was prismatic and druses in beech, and almost all described shapes were seen in sycamore maple. Notably, the amount of whewellite was strongly correlated with the total calcium in all investigated compartments whatever the tree species is, suggesting a biologic control of whewellite precipitation. The amount of whewellite in the aboveground biomass of Montiers forest was more important than that of opal and was around 1170 kg/ha. Therefore, biominerals contribute in a substantial way to the biogeochemical cycles of silicon and calcium.
Auteurs, date et publication :
Auteurs C. Krieger , C. Calvaruso , C. Morlot , S. Uroz , L. Salsi , M.-P. Turpault
Publication : Geobiology
Date : 2025
Volume : 15
Issue : 2
Pages : 296-310
Catégorie(s)
#FORET Montiers #INRAEAuteurs, date et publication :
Auteurs O. Sauzet , C. Cammas , P. Barbillon , M.P. Étienne , D. Montagne
Publication : Geoderma
Date : 2025
Volume : 266
Pages : 46-57
Catégorie(s)
#INRAE #PRO #PRO ColmarRésumé
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
Auteurs, date et publication :
Auteurs Julien Genitoni , Danièle Vassaux , Alain Delaunay , Sylvie Citerne , Luis Portillo Lemus , Marie-Pierre Etienne , David Renault , Solenn Stoeckel , Dominique Barloy , Stéphane Maury
Publication : Physiologia Plantarum
Date : 2025
Volume : 170
Issue : 2
Pages : 280-298
Catégorie(s)
#INRAE #PEARLRésumé
In forest ecosystems, the silicon (Si) mass-balance at the watershed scale can be strongly influenced by readily soluble Si components, such as dissolved Si, adsorbed Si, amorphous silica (biogenic and pedogenic opal) and short-range ordered aluminosilicates. The aim of the present study is to (a) identify the components of the readily soluble Si pool in the Cambisol found below three tree species, under homogeneous soil and climate conditions, and (b) study the impact of Si recycling by tree species on the Si pools. We therefore measured the concentrations of Si extracted by Na2CO3 (Si-alk), oxalate (Si-ox) and CaCl2. The Si-alk concentration decreased from the humus layer to 15 cm depth and then slightly increased until a depth of 75 cm. In the humus layer, the Si-alk concentration consisted mainly of phytoliths and differed significantly between tree species (expressed as mg SiO2 g(-1)): Douglas fir (14.5 +/- 0.65) > European beech (11.8 +/- 0.30) > Black pine (5.4 +/- 0.31). Below 7.5 cm, the Si-alk content did not differ significantly between tree species, and the Si-ox content, increasing significantly, was mainly comprised of Si adsorbed onto amorphous Fe oxides. These results suggest that (a) tree species can impact the readily soluble Si content in the topsoil, through different rates of Si uptake and phytolith restitution by the vegetation, and (b) the soil's readily soluble Si pool is mainly comprised of phytoliths and adsorbed Si. Here, the readily soluble Si pool is thus controlled by both the iron dynamics and Si biocycling.
Auteurs, date et publication :
Auteurs Jean-Thomas Cornelis , Hugues Titeux , Jacques Ranger , Bruno Delvaux
Publication : Plant and Soil
Date : 2011
Volume : 342
Issue : 1-2
Pages : 369-378
Catégorie(s)
#FORET Breuil #INRAERésumé
The exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58 to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals.
Auteurs, date et publication :
Auteurs Laura Picard , Marie-Pierre Turpault , P. Oger , Stephane Uroz
Publication : FEMS Microbiology Ecology
Date : 2025
Catégorie(s)
#FORET Breuil #INRAERésumé
We evaluated whether and how rapidly temperate forest tree species able to stimulate or inhibit nitrification (through biological nitrification inhibition, BNI) also influence denitrifier activity and abundance in soil and identified the main determinants of changes in denitrification. A reciprocal soil core transfer approach was implemented at a long-term experimental site between Douglas fir, a species assumed to stimulate nitrification, and stands of tree species with (spruce and Nordmann fir) or without (Corsican pine and beech) BNI capacity. Sixteen months after soil transfer, potential denitrification decreased in soils transferred from Douglas fir to another tree species and increased in soil cores transferred from any species to Douglas fir. The change in denitrification was not related to the BNI capacity of the tree species ‘receiving’ the soil cores. Structural equation modelling revealed that in soil cores transferred between Douglas fir and BNI species, changes in denitrification were mainly correlated to nitrifier abundances, i.e. AOA and Nitrobacter, nitrification rates, and soil N O3− availability, whereas in soil cores transferred between Douglas fir and non-BNI species denitrification changes were well correlated to C availability and the abundance of nirK-harbouring denitrifiers. Overall, our results indicate that denitrification rates can change strongly and quickly following soil transfers between tree stands. Particularly, when Douglas fir replaces BNI tree species, this quickly results in both increased nitrification and denitrification rates, thus exacerbating the ensuing risk of increased NO3− leaching and N2O emission from soil.
Auteurs, date et publication :
Auteurs A. Florio , C. Bréfort , C. Creuze des Chatelliers , J. Gervaix , F. Poly , B. Zeller , X. Le Roux
Publication : Biology and Fertility of Soils
Date : 2025
Volume : 57
Issue : 8
Pages : 1089-1101
Catégorie(s)
#ANR-Citation #FORET Breuil #INRAE #M-POETERésumé
To evaluate the aquatic ecosystem's quality and ensure the sustainable management of fisheries, it is important to monitor fish populations. Hydroacoustics uses sound waves to noninvasively scan and gather information on waterbodies including fish abundance and distribution. Unmanned surface vehicles (USV) have been increasingly used in marine and freshwater environments to enable data collection. We provide a detailed description of a new USV called Hydroacoustic Autonomous boat for Remote fish detection in LakE (HARLE), which is devoted to hydroacoustic studies in freshwater. The USV is electrically powered and equipped with the most modern fishery scientific echosounder, suitable for broadband applications, the EK80 (SIMRAD). The USV was used for a conventional hydroacoustic survey in a peri-alpine lake to investigate its potential to monitor fish populations in lakes. In the lower layer of the lake where there were numerous targets and comparisons were possible, hydroacoustic metrics and fish biomass values (kg ha−1) from the SIMRAD EK80 on board the USV and EK60 on board the research vessel were similar. We showed that the HARLE has great potential to be used as a tool for fish monitoring and hydroacoustic survey in freshwater.
Auteurs, date et publication :
Auteurs Chloé Goulon , Olivier Le Meaux , Romain Vincent-Falquet , Jean Guillard
Publication : Limnology and Oceanography: Methods
Date : 2025
Volume : 19
Issue : 4
Pages : 280-292
Catégorie(s)
#INRAE #OLAAuteurs, date et publication :
Auteurs Taise Robinson Kunrath , Christophe de Berranger , Xavier Charrier , François Gastal , Paulo César de Faccio Carvalho , Gilles Lemaire , Jean-Claude Emile , Jean-Louis Durand
Publication : Agricultural Water Management
Date : 2025
Volume : 150
Pages : 46–56
Catégorie(s)
#ACBB #ACBB Lusignan #INRAEAuteurs, date et publication :
Auteurs Timothée Bonnet , Laurent Crespin , Adrien Pinot , Laurent Bruneteau , Vincent Bretagnolle , Bertrand Gauffre
Publication : Agriculture, ecosystems & environment
Date : 2025
Volume : 177
Pages : 21–27