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Summary: Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non‐ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron‐chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC‐ESI‐HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild‐type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non‐acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering. [ABSTRACT FROM AUTHOR]

Summary: Minerals and rocks represent essential reservoirs of nutritive elements for the long‐lasting functioning of forest ecosystems developed on nutrient‐poor soils. While the presence of effective mineral weathering bacteria was evidenced in the rhizosphere of different plants, the molecular mechanisms involved remain uncharacterized. To fill this gap, we combined transcriptomic, proteomics, geo‐chemical and physiological analyses to decipher the potential molecular mechanisms explaining the mineral weathering effectiveness of strain PML1(12) of Caballeronia mineralivorans. Considering the early‐stage of the interaction between mineral and bacteria, we identified the genes and proteins differentially expressed when: (i) the environment is depleted of certain essential nutrients (i.e., Mg and Fe), (ii) a mineral is added and (iii) the carbon source (i.e., glucose vs mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of (i) mobilizing iron through the production of a non‐ribosomal peptide synthetase‐independent siderophore, (ii) inducing chemotaxis and motility in response to nutrient availability and (iii) strongly acidifying its environment in the presence of glucose using a suite of GMC oxidoreductases to weather mineral. These results provide new insights into the molecular mechanisms involved in mineral weathering and their regulation and highlight the complex sequence of events triggered by bacteria to weather minerals. [ABSTRACT FROM AUTHOR]

The role of forest vegetation in the silicon (Si) cycle has been widely examined. However, to date, little is known about the specific role of fine roots. The main objective of our study was to assess the influence of fine roots on the Si cycle in a temperate forest in north-eastern France. Silicon pools and fluxes in vegetal solid and solution phases were quantified within each ecosystem compartment, i.e. in the atmosphere, above-ground and below-ground tree tissues, forest floor and different soil layers, on three plots, each with different soil types, i.e. Dystric Cambisol (DC), Eutric Cambisol (EC) and Rendzic Leptosol (RL). In this study, we took advantage of a natural soil gradient, from shallow calcic soil to deep moderately acidic soil, with similar climates, atmospheric depositions, species compositions and management. Soil solutions were measured monthly for 4 years to study the seasonal dynamics of Si fluxes. A budget of dissolved Si (DSi) was also determined for the forest floor and soil layers. Our study highlighted the major role of fine roots in the Si cycle in forest ecosystems for all soil types. Due to the abundance of fine roots mainly in the superficial soil layers, their high Si concentration (equivalent to that of leaves and 2 orders higher than that of coarse roots) and their rapid turnover rate (approximately 1 year), the mean annual Si fluxes in fine roots in the three plots were 68 and 110 kgha-1 yr-1 for the RL and the DC, respectively. The turnover rates of fine roots and leaves were approximately 71 and 28% of the total Si taken up by trees each year, demonstrating the importance of biological recycling in the Si cycle in forests. Less than 1% of the Si taken up by trees each year accumulated in the perennial tissues. This study also demonstrated the influence of soil type on the concentration of Si in the annual tissues and therefore on the Si fluxes in forests. The concentrations of Si in leaves and fine roots were approximately 1.5-2.0 times higher in the Si-rich DC compared to the Si-poor RL. In terms of the DSi budget, DSi production was large in the three plots in the forest floor (9.9 to 12.7 kgha-1 yr-1), as well as in the superficial soil layer (5.3 to 14.5 kgha-1 yr-1) and decreased with soil depth. An immobilization of DSi was even observed at 90 cm depth in plot DC (-1.7 kgha-1 yr-1). The amount of Si leached from the soil profile was relatively low compared to the annual uptake by trees (13% in plot DC to 29% in plot RL). The monthly measurements demonstrated that the seasonal dynamics of the DSi budget were mainly linked to biological activity. Notably, the peak of dissolved Si production in the superficial soil layer occurred during winter and probably resulted from fine-root decomposition. Our study reveals that biological processes, particularly those involving fine roots, play a predominant role in the Si cycle in temperate forest ecosystems, while the geochemical processes appear to be limited. [ABSTRACT FROM AUTHOR]

Context In the current context of land use and climate change, there is a need to precisely quantify the carbon (C) balance of forest ecosystems, and more specifically, of C allocation to tree compartments. Aims We quantified the seasonal changes in the aboveground biomass production (aBP) of a beech forest growing on two different soils: an alocrisol and a calci-brunisol. In addition, for the alocrisol ecosystem, we assessed the existence and degree of intra-annual variability in the ratio of wood aBP to gross primary production (GPP), i.e., the wood aBP efficiency. Methods The study site is a 60-year-old beech forest in northeastern France. An eddy covariance tower records continuously net ecosystem exchange. To investigate the temporal changes in aBP, mini-cores were drilled and diameter at breast height measurements were taken on a monthly basis from 45 trees for both stands studied over 2014. Results A clear difference in aBP was observed between the two soils with the alocrisol being more productive than the calcibrunisol. For the alocrisol, both woody aBP and GPP changed over the course of the year, reaching peak values during June (6 and 12.5 gC m−2 day−1, respectively). Wood applied bias photon-to-current efficiency aboveground Biomass Production Efficiency (aBPE) also showed important intra-annual variations, ranging from 0.09 in September to 0.58 in July. Wood density varied throughout the year, and not taking it into account would have led to an overestimation of aBP by as much as 20% in April and May. Conclusion Our study highlights the importance of taking wood density into account for intra-annual studies of aBP. Wood aBPE cannot be considered as constant as it fluctuated from 0.09 to 0.58 throughout the year for an annual value of 0.34. The potential error in wood aBPE stemming from not taking these changes into account amounts to 15%. [ABSTRACT FROM AUTHOR]

Boron concentrations and isotopic compositions of atmospheric dust and dissolved depositions were monitored over a two-year period (2012-2013) in the forest ecosystem of Montiers (Northeastern France). This time series allows the determination of the boron atmospheric inputs to this forest ecosystem and contributes to refine our understanding of the sources and processes that control the boron atmospheric cycle. Mean annual dust and dissolved boron atmospheric depositions are comparable in size (13 g⋅ ha-1⋅yr-1 and 16 g⋅ha-1⋅yr-1, respectively), which however show significant intra- and interannual variations. Boron isotopes in dust differ from dissolved inputs, with an annual mean value of +1 ‰ and +18‰ for, respectively. The notable high boron contents (190-390 µg⋅g[sup -1]) of the dust samples are interpreted as resulting from localized spreading of boron-rich fertilizers, thus indicating a significant local impact of regional agricultural activities. Boron isotopes in dissolved depositions show a clear seasonal trend. The absence of correlation with marine cyclic solutes contradicts a control of atmospheric boron by dissolution of seasalts. Instead, the boron data from this study are consistent with a Rayleigh-like evolution of the atmospheric gaseous boron reservoir with possible but limited anthropogenic and/or biogenic contributions [ABSTRACT FROM AUTHOR]

The role of forest vegetation in the silicon (Si) cycle has been widely examined. However, to date, no study has investigated the specific role of fine roots. The main objectives of our study were to assess the influence of fine roots as well as the impact of soil properties on the Si cycle in a temperate forest in northeastern France. Silicon pools and fluxes in solid and solution phases were quantified within each ecosystem compartment, i.e., the atmosphere, aboveground and belowground tree tissues, forest floor, and different soil horizons, on three plots, each with different soil types, i.e., Dystric Cambisol (plot S1), Eutric Cambisol (plot S2), and Rendzic Leptosol (plot S3). In this study, we took advantage of a natural soil gradient, from shallow calcic soil to deep moderately acidic soil, with similar climates, atmospheric depositions, species composition and management. Soil solutions were measured monthly for four years to study the seasonal dynamics of Si fluxes. A budget of dissolved Si was also determined for the forest floor and soil layers. Our study highlighted the major role of fine roots in the Si cycle in forest ecosystems for all soil types. Because of the abundance of fine roots mainly in the superficial soil horizons, their high Si concentration (equivalent to that of leaves and two orders higher than that of coarse roots) and their rapid turnover rate (approximately one year), the mean annual Si fluxes in fine roots in the three plots ranged from 68 to 110 kg ha-1 y-1 for the Rendzic Leptosol and the Dystric Cambisol, respectively. The turnover of fine roots and leaves was approximately 71 % and 28 % of the total Si taken up by trees each year, respectively, demonstrating the importance of biological recycling in the Si cycle in forests. Less than 1 % of the Si taken up by trees each year accumulated in the perennial tissues. This study also demonstrated the influence of soil type on the concentration of Si in the annual tissues and therefore on the Si fluxes in forests. The concentrations of Si in leaves and fine roots were approximately 1.5-2.0 times higher in the Si-rich Dystric Cambisol compared to the Si poor Rendzic Leptosol. In terms of the dissolved Si budget, there were large amounts of dissolved Si in the three plots on the forest floor (9.9 to 12.7 kg ha-1 y-1) and in the superficial soil horizon (5.3 to 14.5 kg ha-1 y-1), and Si decreased with depth in plot S1 (1.7 kg ha-1 y-1). The amount of Si leached from the soil profile was relatively low compared to the annual uptake by trees (13 % in plot S1 to 29 % in plot S3). The monthly measurements demonstrated that the seasonal dynamics of the dissolved Si budget were mainly linked to biological activity. Notably, the peak of dissolved Si production in the superficial soil horizon was during the winter and probably resulted from fine root decomposition. Our study reveals that biological processes, particularly those of fine roots, play a predominant role in the Si cycle in temperate forest ecosystems, while the geochemical processes appear to be limited. [ABSTRACT FROM AUTHOR]

Metals can be immobilized on biochars by precipitation with carbonate. The distribution of metal-carbonate phases at the surface of biochars and the conditions of their formation, however, are unknown. Electron microscopy and X-photon spectroscopy were used to characterize carbonate phases in various morphological groups of particles of a wood-derived biochar, both before and after a metal-sorption experiment. Our results showed that the distribution of metals at the surface of biochar particles depended on the corresponding wood tissues and the presence of carbonate phases. Metals were particularly concentrated (i) within calcium carbonate crystals in bark-derived particles, which originated from calcium oxalate crystals formed prior to pyrolysis, and (ii) as new phases formed by the reprecipitation of carbonate on specific tissues of biochar. The formation of biochar carbonate phases and their redistribution by dissolution-precipitation mechanisms may primarily control the localization of metals on biochar particles and the durability of metals immobilization. [ABSTRACT FROM AUTHOR]

Climate change and particularly increasing frequency of drought events during the vegetation period may threaten tree vitality and forest biomass productivity in many temperate regions in the future. In that context, the identification of critical environmental factors and a better understanding of their impact on forests are decisive. The water balance is recognized as one of the most important soil factors for stand productivity in temperate forests. Hence, the consequences of short or long term climate change might vary considerably spatially in function of soil type within a given forest. Our study objective was to assess the impact of contrasting soil types on the water balance and stand growth of a beech ( Fagus sylvatica ) forest ecosystem of similar age and management during four climatically contrasting years. The experimental forest site of Montiers presents different soils with contrasting physicochemical properties (Dystric Cambisol, Eutric Cambisol and Rendzic Leptosol) monitored to quantify water fluxes and stand biomass increment. Using data collected over the period 2012–2015, including a particularly dry year (−24% precipitations in 2015), we also quantified the impact of water shortage on stand productivity at the annual scale as a function of soil type. We evidenced important differences in soil water holding capacities (SWHC) along the studied soil sequence, ranging between 57 mm for the Rendzic Leptosol downhill over limestone and 205 mm for the Dystric Cambisol uphill over detrital sediments. The results show that the canopy intercepted the same amount of incident rainfall in the three plots and that there were no significant differences in annual soil moisture dynamics among the studied soils. We evidenced different rooting patterns depending on soil type. Under a same climate and with stand, site exposition and solar radiation equivalency, trees transpiration was the evident primary driver of the stand potential to produce aboveground biomass. Soil water holding capacity, annual trees transpiration and aboveground biomass production increased in that order: Rendzic Leptosol < Eutric Cambisol < Dystric Cambisol. During the drier year 2015, the decrease in aboveground biomass productivity was of similar amplitude on the three soil types. [ABSTRACT FROM AUTHOR]

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In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities. [ABSTRACT FROM AUTHOR]

Abstract: Compared to conifers, broadleaf forests are less prone to soil and water acidification, because (1) they often have soils with larger exchangeable base cation pools, (2) the pollution scavenging capacity of deciduous trees is lower, and (3) they grow more slowly and are often less intensively managed. Since the 1980s, atmospheric deposition acidity has strongly decreased in forest ecosystems, so that the present acidification status of broadleaf forests should be improving. We used a 35year-old beech plot in the Morvan Mountains (Burgundy, France) to question past and present acidification processes in broadleaf ecosystems. Soil exchangeable Mg, Ca and K pools measured from samples collected in 1974 and 2001 were compared and input–output budgets were computed over the 2003–2008 period. The objectives were (i) to assess Mg and Ca pool size changes over 1974–2008, (ii) to discuss the potential causes of these changes and, (iii) discuss the limits of conventional methods to study nutrient pool size changes (soil data comparison and nutrient budgets). Soil exchangeable Mg pools decreased during the 1974–2001 period while Ca and K pools remained constant, and very small. Soil solution monitoring and input–output budgets over the 2003–2008 period suggested an ongoing loss of exchangeable Ca and Mg, partly due to the desorption of sulphate from the soil which induced Mg, Ca and K depletion. Given the very low concentration in exchangeable base cations, and assuming no change in soil spatial variability, we computed that resampling soils at 10years intervals may not unequivocally demonstrate a gain/loss of exchangeable base cations. Foliar Mg concentrations were continuously below the deficiency level, K and N concentrations decreased but Ca did not. From this, we discuss the validity/limits of the different approaches used, how the ecosystem can cope with such low levels of nutrients, and the fluxes and processes within the ecosystem that should be investigated in this perspective. [Copyright &y& Elsevier]

Abstract: Keeping European temperate forests on acidic soils sustainable is challenging for forest management and wood production. Nutrient budgets are a diagnostic tool that assesses forest sustainability by adding up nutrient inputs (atmospheric dissolved deposition and soil weathering) and outputs (losses in drainage water and by wood harvesting). In these forests, nutrient budgets of essential nutrients are often unbalanced, especially for the base cations Ca, Mg and K, meaning that these nutrients deplete from the ecosystem, what threatens forest sustainability. Whereas Aeolian dust deposition (ADD) is recognized as a significant nutrient input in various ecosystems, particularly in oceans, it is not taken into account in usual nutrient budgets of European forests. ADD has been characterized in different places in the world, however, little is known in European forests and about ADD impacts on their biogeochemical cycles. To fill this gap, this review aims at (i) synthesizing data on ADD characteristics in European forests to put forward a deposition model over Europe and calculate nutrient fluxes, (ii) highlighting the contribution of ADD to plant tissues in two ecosystems with an isotopic approach, (iii) evaluating the contribution of ADD to the total nutrient inputs, and (iv) assessing the impacts of ADD on European nutrient budgets of forests concerning Ca, Mg and K. Aeolian dust in Europe is either long-distance transported from arid regions such as Sahara or short-distance from the erosion of local soils. It was estimated to deposit between 41 and 129kgha−1 year−1 throughout Europe. Its mineralogical composition reveals nutrient bearing minerals, silicates and nonsilicates (carbonates, oxides, hydroxides, sulphates, phosphates, halides). This suggests Aeolian dust may contribute as high as 30% of total nutrient inputs, so that it may significantly shift upwards nutrient budgets of European forests under latitude 52°N. Further investigations are therefore needed to inform about accurate ADD rates below the tree canopy and to take account of the total nutrient inputs. [Copyright &y& Elsevier]

In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scieroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials. [ABSTRACT FROM AUTHOR]