Biogeosciences最新文献

{"title":"Dark septate endophytic fungi associated with pioneer grass inhabiting volcanic deposits and their functions in promoting plant growth","authors":"Han Sun, T. Nishizawa, Hiroyuki Ohta, K. Narisawa","doi":"10.5194/bg-20-4737-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4737-2023","url":null,"abstract":"Abstract. Growth of the pioneer grass Miscanthus condensatus, one of the first vegetation types to be established on volcanic deposits, is promoted by root-associated fungi, particularly dark septate endophytes (DSEs). Fungal taxa within DSEs colonize the root of Miscanthus condensatus in oligotrophic Andosol, and their function in plant growth promotion remains largely unknown. We, therefore, comprehensively assessed the composition of the DSE community associated with Miscanthus condensatus root in volcanic ecosystems using the approaches of both metabarcoding (next-generation sequencing) and isolation (culturing). Also, the promotion effects of DSEs on plant growth (rice as a proxy) were evaluated by inoculation of core isolates to rice roots. Here, we found the following: (i) 70 % of culturable fungi that colonized Miscanthus condensatus phylogenetically belonged to DSEs; (ii) seven orders were identified by both sequencing and culturing methods; and (iii) inoculation of DSE isolates (Phialocephala fortinii, P. helvetica, and Phialocephala sp.) validated their effects on rice growth, particularly under an extremely low pH condition (compared to the control without inoculation, rice biomass was enhanced 7.6-fold after inoculation of P. fortinii). This study helps improve our understanding of the community of Miscanthus condensatus-associated DSE fungi and their functions in promoting plant growth.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139209328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal dynamics and annual budget of dissolved inorganic carbon in the northwestern Mediterranean deep-convection region","authors":"C. Ulses, C. Estournel, P. Marsaleix, K. Soetaert, M. Fourrier, L. Coppola, D. Lefèvre, F. Touratier, C. Goyet, V. Guglielmi, F. Kessouri, P. Testor, X. Durrieu de Madron","doi":"10.5194/bg-20-4683-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4683-2023","url":null,"abstract":"Abstract. Deep convection plays a key role in the circulation, thermodynamics, and biogeochemical cycles in the Mediterranean Sea, which is considered to be a hotspot of biodiversity and climate change. In the framework of the DEWEX (Dense Water Experiment) project, the seasonal and annual budgets of dissolved inorganic carbon in the deep-convection area of the northwestern Mediterranean Sea are investigated over the period September 2012–September 2013 using a 3D coupled physical–biogeochemical–chemical modeling approach. At the annual scale, we estimate that the northwestern Mediterranean Sea's deep-convection region was a moderate sink of 0.5 mol C m−2 yr−1 of CO2 for the atmosphere. The model results show the reduction of oceanic CO2 uptake during deep convection and its increase during the abrupt spring phytoplankton bloom following the deep-convection events. We highlight the major roles in the annual dissolved inorganic carbon budget of both the biogeochemical and physical fluxes, which amount to −3.7 and 3.3 mol C m−2 yr−1, respectively, and are 1 order of magnitude higher than the air–sea CO2 flux. The upper layer (from the surface to 150 m depth) of the northwestern deep-convection region gained dissolved inorganic carbon through vertical physical transport and, to a lesser extent, oceanic CO2 uptake, and it lost dissolved inorganic carbon through lateral transport and biogeochemical fluxes. The region, covering 2.5 % of the Mediterranean, acted as a source of dissolved inorganic carbon for the surface and intermediate water masses of the Balearic Sea and southwestern Mediterranean Sea and could represent up to 22 % and 11 %, respectively, of the CO2 exchanges with the Atlantic Ocean at the Strait of Gibraltar.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139219167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imaging of the electrical activity in the root zone under limited-water-availability stress: a laboratory study for Vitis vinifera","authors":"B. Mary, Veronika Iván, F. Meggio, Luca Peruzzo, Guillaume Blanchy, C. Chou, B. Ruperti, Yuxin Wu, Giorgio Cassiani","doi":"10.5194/bg-20-4625-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4625-2023","url":null,"abstract":"Abstract. Understanding root signals and their consequences for the whole plant physiology is one of the keys to tackling the water-saving challenge in agriculture. The implementation of water-saving irrigation strategies, such as the partial root zone drying (PRD) method, is part of a comprehensive approach to enhance water use efficiency. To reach this goal tools are needed for the evaluation of the root's and soil water dynamics in time and space. In controlled laboratory conditions, using a rhizotron built for geoelectrical tomography imaging, we monitored the spatio-temporal changes in soil electrical resistivity (ER) for more than a month corresponding to eight alternating water inputs cycles. Electrical resistivity tomography (ERT) was complemented with electrical current imaging (ECI) using plant-stem-induced electrical stimulation. To estimate soil water content in the rhizotron during the experiment, we incorporated Archie's law as a constitutive model. We demonstrated that under mild water stress conditions, it is practically impossible to spatially distinguish the limited-water-availability effects using ECI. We evidenced that the current source density spatial distribution varied during the course of the experiment with the transpiration demand but without any significant relationship to the soil water content changes. On the other hand, ERT showed spatial patterns associated with irrigation and, to a lesser degree, to RWU (root water uptake) and hydraulic redistribution. The interpretation of the geoelectrical imaging with respect to root activity was strengthened and correlated with indirect observations of the plant transpiration using a weight monitoring lysimeter and direct observation of the plant leaf gas exchanges.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"252 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139228031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromophoric dissolved organic matter dynamics revealed through the optimization of an optical–biogeochemical model in the northwestern Mediterranean Sea","authors":"Eva Álvarez, G. Cossarini, A. Teruzzi, J. Bruggeman, Karsten Bolding, S. Ciavatta, Vincenzo Vellucci, F. D’Ortenzio, David Antoine, P. Lazzari","doi":"10.5194/bg-20-4591-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4591-2023","url":null,"abstract":"Abstract. Chromophoric dissolved organic matter (CDOM) significantly contributes to the non-water absorption budget in the Mediterranean Sea. The absorption coefficient of CDOM, aCDOM(λ), is measurable in situ and can be retrieved remotely, although ocean-colour algorithms do not distinguish it from the absorption of detritus. These observations can be used as indicators for the concentration of other relevant biogeochemical variables in the ocean, e.g. dissolved organic carbon. However, our ability to model the biogeochemical processes that determine CDOM concentrations is still limited. Here we propose a novel parameterization of the CDOM cycle that accounts for the interplay between the light- and nutrient-dependent dynamics of local CDOM production and degradation, as well as its vertical transport. The parameterization is included in a one-dimensional (1D) configuration of the Biogeochemical Flux Model (BFM), which is here coupled to the General Ocean Turbulence Model (GOTM) through the Framework for Aquatic Biogeochemical Models (FABM). Here the BFM is augmented with a bio-optical component that resolves spectrally the underwater light transmission. We run this new GOTM-(FABM)-BFM configuration to simulate the seasonal aCDOM(λ) cycle at the deep-water site of the Bouée pour l'acquisition de Séries Optiques à Long Terme (BOUSSOLE) project in the northwestern Mediterranean Sea. Our results show that accounting for both nutrient and light dependence of CDOM production improves the simulation of the seasonal and vertical dynamics of aCDOM(λ), including a subsurface maximum that forms in spring and progressively intensifies in summer. Furthermore, the model consistently reproduces the higher-than-average concentrations of CDOM per unit chlorophyll concentration observed at BOUSSOLE. The configuration, outputs, and sensitivity analyses from this 1D model application will be instrumental for future applications of BFM to the entire Mediterranean Sea in a three-dimensional configuration.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"33 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139240085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing impacts of coastal warming, acidification, and deoxygenation on Pacific oyster (Crassostrea gigas) farming: a case study in the Hinase area, Okayama Prefecture, and Shizugawa Bay, Miyagi Prefecture, Japan","authors":"Masahiko Fujii, Ryuji Hamanoue, L. P. C. Bernardo, Tsuneo Ono, Akihiro Dazai, Shigeyuki Oomoto, M. Wakita, Takehiro Tanaka","doi":"10.5194/bg-20-4527-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4527-2023","url":null,"abstract":"Abstract. Coastal warming, acidification, and deoxygenation are progressing primarily due to the increase in anthropogenic CO2. Coastal acidification has been reported to have effects that are anticipated to become more severe as acidification progresses, including inhibiting the formation of shells of calcifying organisms such as shellfish, which include Pacific oysters (Crassostrea gigas), one of the most important aquaculture resources in Japan. Moreover, there is concern regarding the combined impacts of coastal warming, acidification, and deoxygenation on Pacific oysters. However, spatiotemporal variations in acidification and deoxygenation indicators such as pH, the aragonite saturation state (Ωarag), and dissolved oxygen have not been observed and projected in oceanic Pacific oyster farms in Japan. To assess the present impacts and project future impacts of coastal warming, acidification, and deoxygenation on Pacific oysters, we performed continuous in situ monitoring, numerical modeling, and microscopic examination of Pacific oyster larvae in the Hinase area of Okayama Prefecture and Shizugawa Bay in Miyagi Prefecture, Japan, both of which are famous for their Pacific oyster farms. Our monitoring results first found Ωarag values lower than the critical level of acidification for Pacific oyster larvae in Hinase, although no impact of acidification on larvae was identified by microscopic examination. Our modeling results suggest that Pacific oyster larvae are anticipated to be affected more seriously by the combined impacts of coastal warming and acidification, with lower pH and Ωarag values and a prolonged spawning period, which may shorten the oyster shipping period and lower the quality of oysters.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"44 31","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139240371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-term additions of ammonium nitrate to montane forest ecosystems may cause limited soil acidification, even in the presence of soil carbonate","authors":"T. Baer, G. Furrer, S. Zimmermann, P. Schleppi","doi":"10.5194/bg-20-4577-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4577-2023","url":null,"abstract":"Abstract. Nitrogen (N) deposition has decreased in the last decades in Europe but in many cases remains higher than the critical loads, i.e., higher than what could be considered safe for biodiversity and ecosystem functioning. The main concerns about N deposition are eutrophication and acidification. In a long-term experiment (1994 to present) in a montane (1200 m a.s.l.) coniferous forest in Alptal, central Switzerland, we simulated increased N deposition by adding NH4NO3 to rainwater. This treatment consisted of an additional N input of 22 kg ha−1 yr−1 to the 12 kg ha−1 yr−1 ambient bulk deposition rate or 17 kg N ha−1 yr−1 throughfall rate. The treatment was applied simultaneously to a small catchment area and to plots in a replicated block experiment (n=5). The site has a carbonate-rich parent material and is thus not particularly at risk of acidification. Nevertheless, we examined soil acidification as affected both by ambient and experimentally increased N deposition. In the 2.5 decades since the beginning of the study, nitrate (NO3-) and especially sulfate (SO42-) concentrations decreased in precipitation, while pH increased by slightly more than 1 unit. In the same time period a reduction in pH of the soil was measured. The exchangeable acidity in the soil increased, especially in the N-addition treatment. This was mainly observed on small mounds because the drier mounds are less well buffered than wet depressions. This trend, however, was limited in time, as exchangeable acidity later declined again to reach values not much higher than 26 years before. This was also the case in the N-addition treatment and can be considered a progressive recovery mainly due to the reduced acid inputs and, at this site with a carbonate-rich subsoil, to the biological cycling of base cations. The pH of the runoff from the experimental catchments decreased by 0.3 units, both in the control and under N addition. Decreasing Ca2+ and increasing Al3+ and Fe2+ concentrations in runoff also show that the recovery observed in the exchangeable soil acidity is not yet able to stop the slow acidification of water leaving the catchments. However, with the runoff water pH remaining above 7, this trend is not alarming for water quality or for the health of water bodies. Future monitoring will be necessary to see if and when a recovery takes place in the soil and runoff pH.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139242742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward coherent space–time mapping of seagrass cover from satellite data: an example of a Mediterranean lagoon","authors":"Guillaume Goodwin, M. Marani, S. Silvestri, L. Carniello, A. D’Alpaos","doi":"10.5194/bg-20-4551-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4551-2023","url":null,"abstract":"Abstract. Seagrass meadows are a highly productive and economically important shallow coastal habitat. Their sensitivity to natural and anthropogenic disturbances, combined with their importance for local biodiversity, carbon stocks, and sediment dynamics, motivate a frequent monitoring of their distribution. However, generating time series of seagrass cover from field observations is costly, and mapping methods based on remote sensing require restrictive conditions on seabed visibility, limiting the frequency of observations. In this contribution, we examine the effect of accounting for environmental factors, such as the bathymetry and median grain size (D50) of the substrate as well as the coordinates of known seagrass patches, on the performance of a random forest (RF) classifier used to determine seagrass cover. Using 148 Landsat images of the Venice Lagoon (Italy) between 1999 and 2020, we trained an RF classifier with only spectral features from Landsat images and seagrass surveys from 2002 and 2017. Then, by adding the features above and applying a time-based correction to predictions, we created multiple RF models with different feature combinations. We tested the quality of the resulting seagrass cover predictions from each model against field surveys, showing that bathymetry, D50, and coordinates of known patches exert an influence that is dependent on the training Landsat image and seagrass survey chosen. In models trained on a survey from 2017, where using only spectral features causes predictions to overestimate seagrass surface area, no significant change in model performance was observed. Conversely, in models trained on a survey from 2002, the addition of the out-of-image features and particularly coordinates of known vegetated patches greatly improves the predictive capacity of the model, while still allowing the detection of seagrass beds absent in the reference field survey. Applying a time-based correction eliminates small temporal variations in predictions, improving predictions that performed well before correction. We conclude that accounting for the coordinates of known seagrass patches, together with applying a time-based correction, has the most potential to produce reliable frequent predictions of seagrass cover. While this case study alone is insufficient to explain how geographic location information influences the classification process, we suggest that it is linked to the inherent spatial auto-correlation of seagrass meadow distribution. In the interest of improving remote-sensing classification and particularly to develop our capacity to map vegetation across time, we identify this phenomenon as warranting further research.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"45 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139256043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leaf carbon and nitrogen stoichiometric variation along environmental gradients","authors":"Huiying Xu, Han Wang, I. Prentice, S. Harrison","doi":"10.5194/bg-20-4511-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4511-2023","url":null,"abstract":"Abstract. Leaf stoichiometric traits are central to ecosystem function and biogeochemical cycling, yet no accepted theory predicts their variation along environmental gradients. Using data in the China Plant Trait Database version 2, we aimed to characterize variation in leaf carbon and nitrogen per unit mass (Cmass, Nmass) and their ratio and to test an eco-evolutionary optimality model for Nmass. Community-mean trait values were related to climate variables by multiple linear regression. Climatic optima and tolerances of major genera were estimated; Pagel's λ was used to quantify phylogenetic controls, and Bayesian phylogenetic linear mixed models to assess the contributions of climate, species identity, and phylogeny. Optimality-based predictions of community-mean Nmass were compared to observed values. All traits showed strong phylogenetic signals. Climate explained only 18 % of C:N ratio variation among species but 45 % among communities, highlighting the role of taxonomic replacement in mediating community-level responses. Geographic distributions of deciduous taxa were separated primarily by moisture and evergreens by temperature. Cmass increased with irradiance but decreased with moisture and temperature. Nmass declined with all three variables. C:N ratio variations were dominated by Nmass. The coefficients relating Nmass to the ratio of maximum carboxylation capacity at 25 ∘C (Vcmax25) and leaf mass per area (Ma) were influenced by leaf area index. The optimality model captured 68 % and 53 % of variation between communities for Vcmax25 and Ma, respectively, and 21 % for Nmass. We conclude that stoichiometric variations along climate gradients are achieved largely by environmental selection among species and clades with different intraspecific trait values. Variations in leaf C:N ratio are mainly determined by Nmass, and optimality-based modelling shows useful predictive ability for community-mean Nmass. These findings should help to improve the representation of C:N coupling in ecosystem models.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"38 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139262723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coordination of rooting, xylem, and stomatal strategies explains the response of conifer forest stands to multi-year drought in the southern Sierra Nevada of California","authors":"Junyan Ding, P. Buotte, R. Bales, B. Christoffersen, R. Fisher, Michael Goulden, Ryan Knox, Lara Kueppers, J. Shuman, Chonggang Xu, Charles D. Koven","doi":"10.5194/bg-20-4491-2023","DOIUrl":"https://doi.org/10.5194/bg-20-4491-2023","url":null,"abstract":"Abstract. Extreme droughts are a major determinant of ecosystem disturbance that impacts plant communities and feeds back into climate change through changes in plant functioning. However, the complex relationships between aboveground and belowground plant hydraulic traits and their role in governing plant responses to drought are not fully understood. In this study, we use a model, the Functionally Assembled Terrestrial Ecosystem Simulator in a configuration that includes plant hydraulics (FATES-Hydro), to investigate ecosystem responses to the 2012–2015 California drought in comparison with observations at a site in the southern Sierra Nevada that experienced widespread tree mortality during this drought. We conduct a sensitivity analysis to explore how different plant water sourcing and hydraulic strategies lead to differential responses during normal and drought conditions. The analysis shows the following. Deep roots that sustain productivity through the dry season are needed for the model to capture observed seasonal cycles of evapotranspiration (ET) and gross primary productivity (GPP) in normal years, and deep-rooted strategies are nonetheless subject to large reductions in ET and GPP when the deep soil reservoir is depleted during extreme droughts, in agreement with observations. Risky stomatal strategies lead to greater productivity during normal years as compared to safer stomatal control, but they also lead to a high risk of xylem embolism during the 2012–2015 drought. For a given stand density, stomatal and xylem traits have a stronger impact on plant water status than on ecosystem-level fluxes. Our study highlights the significance of resolving plant water sourcing strategies to represent drought impacts on plants and consequent feedbacks in models.","PeriodicalId":502171,"journal":{"name":"Biogeosciences","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139265101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}