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Potential of natural language processing for metadata extraction from environmental scientific publications 自然语言处理在环境科学出版物元数据提取中的潜力
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-03-14 DOI: 10.5194/soil-9-155-2023
G. Blanchy, Lukas Albrecht, J. Koestel, S. Garré
Abstract. Summarizing information from large bodies of scientific literature is anessential but work-intensive task. This is especially true in environmentalstudies where multiple factors (e.g., soil, climate, vegetation) cancontribute to the effects observed. Meta-analyses, studies thatquantitatively summarize findings of a large body of literature, rely onmanually curated databases built upon primary publications. However, giventhe increasing amount of literature, this manual work is likely to requiremore and more effort in the future. Natural language processing (NLP)facilitates this task, but it is not clear yet to which extent theextraction process is reliable or complete. In this work, we explore threeNLP techniques that can help support this task: topic modeling, tailoredregular expressions and the shortest dependency path method. We apply thesetechniques in a practical and reproducible workflow on two corpora ofdocuments: the Open Tension-diskInfiltrometer Meta-database (OTIM) and the Meta corpus. The OTIM corpus contains the sourcepublications of the entries of the OTIM database of near-saturated hydraulicconductivity from tension-disk infiltrometer measurements(https://github.com/climasoma/otim-db, last access: 1 March 2023). The Meta corpus is constituted ofall primary studies from 36 selected meta-analyses on the impact ofagricultural practices on sustainable water management in Europe. As a firststep of our practical workflow, we identified different topics from theindividual source publications of the Meta corpus using topic modeling.This enabled us to distinguish well-researched topics (e.g., conventionaltillage, cover crops), where meta-analysis would be useful, from neglectedtopics (e.g., effect of irrigation on soil properties), showing potentialknowledge gaps. Then, we used tailored regular expressions to extractcoordinates, soil texture, soil type, rainfall, disk diameter and tensionsfrom the OTIM corpus to build a quantitative database. We were able toretrieve the respective information with 56 % up to 100 % of allrelevant information (recall) and with a precision between 83 % and100 %. Finally, we extracted relationships between a set of driverscorresponding to different soil management practices or amendments (e.g.,“biochar”, “zero tillage”) and target variables (e.g., “soilaggregate”, “hydraulic conductivity”, “crop yield”) from thesource publications' abstracts of the Meta corpus using the shortestdependency path between them. These relationships were further classifiedaccording to positive, negative or absent correlations between the driverand the target variable. This quickly provided an overview of the differentdriver–variable relationships and their abundance for an entire body ofliterature. Overall, we found that all three tested NLP techniques were ableto support evidence synthesis tasks. While human supervision remainsessential, NLP methods have the potential to support auto
摘要从大量科学文献中总结信息是一项必要但又需要大量工作的任务。在环境研究中尤其如此,因为多种因素(如土壤、气候、植被)可能导致观察到的影响。荟萃分析,即定量总结大量文献发现的研究,依赖于建立在主要出版物基础上的人工管理数据库。然而,鉴于文献数量的增加,这种手工工作在未来可能需要越来越多的努力。自然语言处理(NLP)促进了这项任务,但目前尚不清楚提取过程在多大程度上是可靠或完整的。在这项工作中,我们探索了三种可以帮助支持这项任务的enlp技术:主题建模、定制正则表达式和最短依赖路径方法。我们将这些技术应用于两个文档语料库上的实用和可重复的工作流:开放张力磁盘过滤计元数据库(OTIM)和元语料库。OTIM语料包含OTIM近饱和水力导电性数据库条目的源出版物,这些条目来自张力盘渗透计测量(https://github.com/climasoma/otim-db,最后访问时间:2023年3月1日)。该Meta语料库由36项精选的关于欧洲农业实践对可持续水资源管理影响的Meta分析的所有主要研究组成。作为我们实际工作流程的第一步,我们使用主题建模从元语料库的单个源出版物中识别不同的主题。这使我们能够区分研究充分的主题(例如,传统耕作,覆盖作物)和被忽视的主题(例如,灌溉对土壤特性的影响),其中元分析是有用的,这显示了潜在的知识差距。然后,我们使用定制的正则表达式从OTIM语料库中提取坐标、土壤质地、土壤类型、降雨量、圆盘直径和张力,建立定量数据库。我们能够以56%到100%的相关信息(召回率)检索相应的信息,准确率在83%到100%之间。最后,我们从Meta语料库的源出版物摘要中提取了与不同土壤管理实践或修订(例如,“生物炭”,“零耕作”)相对应的一组驱动因素与目标变量(例如,“土壤团聚体”,“水力导电性”,“作物产量”)之间的关系,使用它们之间的最短依赖路径。这些关系进一步根据驱动程序和目标变量之间的正相关、负相关或不相关进行分类。这很快为整个文献提供了不同的驱动变量关系及其丰富程度的概述。总的来说,我们发现所有三种测试的NLP技术都能够支持证据合成任务。虽然人类监督仍然是必不可少的,但NLP方法有可能支持自动证据合成,随着新出版物的出现,自动证据合成可以不断更新。
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引用次数: 1
Wetting and drying cycles, organic amendments, and gypsum play a key role in structure formation and stability of sodic Vertisols 干湿循环、有机改进剂和石膏对钠基垂直溶胶的结构形成和稳定性起着关键作用
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-03-03 DOI: 10.5194/soil-9-141-2023
S. Niaz, J. Wehr, R. Dalal, P. Kopittke, N. Menzies
Abstract. In the natural environment, soils undergo wetting and drying (WD) cycles dueto precipitation and evapotranspiration. The WD cycles have a profoundimpact on soil physical, chemical, and biological properties and drive thedevelopment of structure in soils. Degraded soils are often lackingstructure, and the effect of organic amendments and WD cycles on structureformation of these soils is poorly understood. The aim of this study was toevaluate the role of biotic and abiotic factors on aggregate formation andstabilization of sodic soils after the addition of gypsum and organicamendments (feedlot manure, chicken manure, lucerne pallets, and anionicpoly acrylamide). Amended soils were incubated at 25 ∘C over fourWD cycles, with assessment of soil microbial respiration, electricalconductivity, pH, sodium adsorption ratio (SAR), aggregate stability inwater (ASWAT), aggregate size distribution, and mean weight diameter. Ourresults demonstrate that WD cycles can improve aggregate stability after theaddition of amendments in sodic Vertisols, but this process depends on thetype of organic amendment. Lucerne pellets resulted in highest soilmicrobial respiration, proportions of large macroaggregates (>2000 µm), and mean weight diameter. In contrast, dispersion wassignificantly reduced when soils were treated with chicken manure, whilstanionic polyacrylamide only had a transient effect on aggregate stability.When these organic amendments were applied together with gypsum, thestability of aggregates was further enhanced, and dispersion becamenegligible after the second WD cycle. The formation and stability of smallmacroaggregates (2000–250 µm) was less dependent on the type oforganic amendments and more dependent on WD cycles as the proportion ofsmall macroaggregates also increased in control soils after four WD cycles,highlighting the role of WD cycles as one of the key factors that improvesaggregation and stability of sodic Vertisols.
摘要在自然环境中,由于降水和蒸散作用,土壤经历了干湿循环。WD循环对土壤的物理、化学和生物特性有着深远的影响,并驱动着土壤结构的发展。退化土壤通常缺乏结构,有机改良剂和WD循环对这些土壤结构形成的影响尚不清楚。本研究的目的是评价添加石膏和有机改进剂(饲养场粪肥、鸡粪、苜蓿草和阴离子聚丙烯酰胺)后,生物和非生物因素对碱土团聚体形成和稳定性的作用。将改良过的土壤在25°C下培养4个周期,评估土壤微生物呼吸、电导率、pH、钠吸附比(SAR)、水中团聚体稳定性(ASWAT)、团聚体粒径分布和平均重量直径。我们的研究结果表明,WD循环可以提高在添加了有机改性剂后的聚类稳定性,但这一过程取决于有机改性剂的类型。Lucerne颗粒导致最高的土壤微生物呼吸,大团聚体比例(>2000µm)和平均重量直径。相比之下,鸡粪处理显著降低了土壤的分散性,而阴离子聚丙烯酰胺对团聚体稳定性只有短暂的影响。当这些有机改进剂与石膏一起使用时,集料的稳定性进一步提高,并且在第二次WD循环后分散性变得可以忽略不计。小团聚体(2000-250µm)的形成和稳定性对有机修正类型的依赖程度较低,而对WD循环的依赖程度较高,在4个WD循环后,对照土壤中小团聚体的比例也有所增加,这表明WD循环是改善土壤聚类和稳定性的关键因素之一。
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引用次数: 1
Quality assessment of meta-analyses on soil organic carbon 土壤有机碳荟萃分析质量评价
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-02-21 DOI: 10.5194/soil-9-117-2023
Julia Fohrafellner, S. Zechmeister-Boltenstern, Rajasekaran Murugan, Elena Valkama
Abstract. Soil organic carbon (SOC) plays a vital role in theglobal carbon cycle and is a potential sink for carbon dioxide. Agriculturalmanagement practices can support carbon sequestration and, therefore, offerpotential removal strategies whilst also improving overall soil quality.Meta-analysis allows one to summarize results from primary articles bycalculating an overall effect size and to reveal the source of variationacross studies. The number of meta-analyses published in the field ofagriculture is continuously rising. At the same time, more and more articlesrefer to their synthesis work as a meta-analysis, despite applying less thanrigorous methodologies. As a result, poor-quality meta-analyses arepublished and may lead to questionable conclusions and recommendations toscientists, policymakers, and farmers. This study aims at quantitatively analyzing 31 meta-analyses, publishedbetween the years of 2005 and 2020, studying the effects of different managementpractices on SOC. We compiled a set of quality criteria suitable for soil andagricultural sciences by adapting existing meta-analytical guidelines fromother disciplines. The set is supported by a scoring scheme that allows for aquantitative analysis. The retrieved meta-analyses were structured accordingto 11 management categories, such as tillage, cover crops, crop residuemanagement, and biochar application, which allowed us to assess thestate of knowledge on these categories. Major deficiencies were found in theuse of standard metrics for effect size calculation, independence of effectsizes, standard deviation extraction for each study, and study weighting bythe inverse of variance. Only 1 out of 31 SOC meta-analyses, which studiedthe effects of no tillage/reduced tillage compared with conventional tillage, wasfound to be of high quality. Therefore, improved meta-analyses on theeffects of organic agriculture, biochar, fertilization, or cropdiversification on SOC are urgently needed. We conclude that, despite efforts over the last 15 years, the quality ofmeta-analyses on SOC research is still low. Thus, in order for the scientificcommunity to provide high-quality synthesis work and to make advancements inthe sustainable management of agricultural soils, we need to adapt rigorousmethodologies of meta-analysis as quickly as possible.
摘要土壤有机碳(SOC)在全球碳循环中起着至关重要的作用,是二氧化碳的潜在汇。农业管理实践可以支持碳固存,因此可以提供潜在的去除策略,同时还可以改善整体土壤质量。荟萃分析允许人们通过计算总体效应大小来总结主要文章的结果,并揭示研究间差异的来源。农业领域发表的荟萃分析的数量在不断增加。与此同时,越来越多的文章将他们的综合工作称为荟萃分析,尽管使用的方法并不严格。因此,发表的低质量的荟萃分析可能会导致科学家、政策制定者和农民得出可疑的结论和建议。本研究旨在定量分析2005年至2020年间发表的31项荟萃分析,研究不同管理实践对SOC的影响。我们通过调整来自不同学科的现有元分析指南,编制了一套适合土壤和农业科学的质量标准。该集合由允许定量分析的评分方案支持。检索到的荟萃分析根据11个管理类别进行结构化,例如耕作,覆盖作物,作物残留物管理和生物炭应用,这使我们能够评估这些类别的知识状况。主要缺陷是在使用标准度量来计算效应量、效应量的独立性、每项研究的标准差提取以及方差逆加权等方面。在31项研究免耕/免耕与常规耕作效果的有机碳荟萃分析中,只有1项发现质量高。因此,迫切需要改进有机农业、生物炭、施肥或作物多样化对有机碳影响的meta分析。我们得出的结论是,尽管过去15年做出了努力,但SOC研究的元分析质量仍然很低。因此,为了使科学界能够提供高质量的综合工作,并在农业土壤的可持续管理方面取得进展,我们需要尽快适应严格的元分析方法。
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引用次数: 5
The role of long-term mineral and manure fertilization on P species accumulation and phosphate-solubilizing microorganisms in paddy red soils 长期矿肥施肥对水稻红壤磷素积累和溶磷微生物的影响
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-02-16 DOI: 10.5194/soil-9-101-2023
Shuiqing Chen, Ju-sheng Gao, Huaihai Chen, Zeyuan Zhang, Jing Huang, Lefu Lv, Jinfang Tan, Xiaoqian Jiang
Abstract. Understanding soil phosphorus (P) transformation and turnover under various fertilization managements is important for evaluating sustainable P fertility and potential bioavailability in agriculture managements. Thus, long-term fertilization experiments (∼ 38 years) with the application of different inorganic and organic fertilizers in paddy red soils wereconducted to determine the effect of different fertilizer applications on Ppool accumulation and microbial communities, especially for phosphate-solubilizing microorganisms (PSMs). Long-term inorganic P (IP) fertilization increased the concentrations of total P (TP) (∼ 479 mg kg−1), available P (AP) (∼ 417 mg kg−1) andinorganic P (∼ 18 mg kg−1), but manurefertilization accelerated the accumulation of organic P, especially fororthophosphate monoesters (e.g., myo-IHP, ∼ 12 mg kg−1). Long-term mineral fertilization decreased bacterial richness,evenness and complexation of bacterial networks. In contrast, long-termmanure fertilization and rhizosphere accumulated more amounts of totalcarbon, total nitrogen, and organic carbon, as well as regulated the soilpH, thus improving the separation of bacterial communities. Furthermore, PSM compositions were greatly influenced by fertilization managements andrhizosphere. For example, inorganic P fertilization increased the abundanceof Thiobacillus (i.e., the most abundant phosphate-solubilizing bacteria (PSB) in this study) and shifted the community structure of PSB. Correspondingly, the concentrations of inorganic and total P were the key factors for the variation of the PSB community structure. These findings are beneficial for understanding the variation of inorganic and organic P pools and the microbial community, especially for PSMs under long-term inorganic and/or organic fertilization.
摘要了解不同施肥管理下土壤磷的转化和周转对评价土壤磷的可持续肥力和潜在生物有效性具有重要意义。因此,在水稻红壤上进行了长期施肥试验(~ 38年),施用不同的无机和有机肥料,以确定不同肥料用量对池积累和微生物群落的影响,特别是对磷肥溶解微生物(psm)的影响。长期无机磷(IP)施肥增加了总磷(TP) (~ 479 mg kg - 1)、速效磷(~ 417 mg kg - 1)和无机磷(~ 18 mg kg - 1)的浓度,但施肥加速了有机磷的积累,特别是正磷酸盐单酯(例如,myo-IHP, ~ 12 mg kg - 1)。长期矿物施肥降低了细菌丰富度、均匀度和细菌网络的复杂性。相反,长期施肥和根际积累了更多的总碳、总氮和有机碳,并调节了土壤ph,从而促进了细菌群落的分离。此外,PSM组成受施肥管理和根际影响较大。例如,无机磷肥增加了硫杆菌(即本研究中最丰富的磷酸盐溶解菌)的丰度,并改变了PSB的群落结构。相应的,无机磷和全磷浓度是影响PSB群落结构变化的关键因素。这些发现有助于了解长期无机和/或有机施肥条件下psm土壤无机和有机磷库及微生物群落的变化。
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引用次数: 4
Semantics about soil organic carbon storage: DATA4C+, a comprehensive thesaurus and classification of management practices in agriculture and forestry 土壤有机碳储量语义:DATA4C+,农业和林业管理实践的综合词库和分类
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-02-10 DOI: 10.5194/soil-9-89-2023
K. Fujisaki, T. Chevallier, A. Bispo, J. Laurent, François Thevenin, L. Chapuis-Lardy, R. Cardinael, C. Le Bas, V. Freycon, F. Bénédet, V. Blanfort, Michel Brossard, M. Tella, J. Demenois
Abstract. Identifying the drivers of soil organic carbon (SOC) stock changes is of theutmost importance to contribute to global challenges like climate change,land degradation, biodiversity loss, or food security. Evaluating the impactsof land use and management practices in agriculture and forestry on SOC isstill challenging. Merging datasets or making databases interoperable is apromising way, but still has several semantic challenges. So far, acomprehensive thesaurus and classification of management practices inagriculture and forestry has been lacking, especially while focusing on SOCstorage. Therefore, the aim of this paper is to present a firstcomprehensive thesaurus for management practices driving SOC storage(DATA4C+). The DATA4C+ thesaurus contains 224 classified and definedterms related to land management practices in agriculture and forestry. Itis organized as a hierarchical tree reflecting the drivers of SOC storage.It is oriented to be used by scientists in agronomy, forestry, and soilsciences with the aim of uniformizing the description of practicesinfluencing SOC in their original research. It is accessible in Agroportal(http://agroportal.lirmm.fr/ontologies/DATA4CPLUS, last access: 24 March 2022) to enhanceits findability, accessibility, interoperability, and reuse by scientistsand others such as laboratories or land managers. Future uses of theDATA4C+ thesaurus will be crucial to improve and enrich it, but also toraise the quality of meta-analyses on SOC, and ultimately help policymakersto identify efficient agricultural and forest management practices toenhance SOC storage.
摘要确定土壤有机碳(SOC)储量变化的驱动因素对于应对气候变化、土地退化、生物多样性丧失或粮食安全等全球挑战至关重要。评估农业和林业土地利用和管理实践对有机碳的影响仍然具有挑战性。合并数据集或使数据库可互操作是一种很有前途的方法,但仍然存在一些语义挑战。到目前为止,缺乏一个全面的农业和林业管理实践的词典和分类,特别是在关注SOCstorage时。因此,本文的目的是为驱动SOC存储(DATA4C+)的管理实践提供第一个综合词典。DATA4C+词典包含224个与农业和林业土地管理实践相关的分类和定义术语。它被组织成反映SOC存储驱动程序的层次树。它面向农学、林业和土壤科学的科学家使用,目的是在他们的原始研究中统一影响SOC的实践描述。可通过Agroportal(http://agroportal.lirmm.fr/ontologies/DATA4CPLUS,最后一次访问:2022年3月24日)访问,以提高科学家和实验室或土地管理者等其他人的可查找性、可访问性、互操作性和重用性。未来对data4c +词库的使用将是改进和丰富它的关键,同时也将提高SOC元分析的质量,并最终帮助政策制定者确定有效的农业和森林管理实践,以增强SOC存储。
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引用次数: 2
Does soil thinning change soil erodibility? An exploration of long-term erosion feedback systems 土壤变薄会改变土壤的可蚀性吗?长期侵蚀反馈系统的探索
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-01-23 DOI: 10.5194/soil-9-71-2023
P. Batista, D. Evans, B. Cândido, P. Fiener
Abstract. Soil erosion rates on arable land frequently exceed the pace atwhich new soil is formed. This imbalance leads to soil thinning (i.e.truncation), whereby subsoil horizons and their underlying parent materialbecome progressively closer to the land surface. As soil erosion is aselective process and subsurface horizons often have contrasting propertiesto the original topsoil, truncation-induced changes to soil properties might affect erosion rates and runoff formation through a soil erosion feedback system. However, the potential interactions between soil erosion and soil truncation are poorly understood due to a lack of empirical data and the neglection of long-term erodibility dynamics in erosion simulation models. Here, we present a novel model-based exploration of the soil erosion feedback system over a period of 500 years using measured soil properties from a diversified database of 265 agricultural soil profiles in the UK. For this, we adapted the Modified Morgan–Morgan–Finney model (MMMF) to perform a modelling experiment in which topography, climate, land cover, and crop management parameters were held constant throughout the simulation period. As selective soil erosion processes removed topsoil layers, the model gradually mixed subsurface soil horizons into a 0.2 m plough layer and updated soil properties using mass-balance mixing models. Further, we estimated the uncertainty in model simulations with a forward error assessment. We found that modelled erosion rates in 99 % of the soil profiles were sensitive to truncation-induced changes in soil properties. The soil losses in all except one of the truncation-sensitive profiles displayed a decelerating trend, which depicted an exponential decay in erosion rates over the simulation period. This was largely explained by decreasing silt contents in the soil surface due to selective removal of this more erodible particle size fraction and the presence of clayey or sandy substrata. Moreover, the soil profiles displayed an increased residual stone cover, which armoured the land surface and reduced soil detachment. Contrastingly, the soils with siltier subsurface horizons continuously replenished the plough layer with readily erodible material, which prevented the decline of soil loss rates over time. Although our results are limited by the edaphoclimatic conditions represented in our data, as by our modelling assumptions, we have demonstrated how modelled soil losses can be sensitive to erosion-induced changes in soil properties. These findings are likely to affect how we calculate soil lifespans and make long-termprojections of land degradation.
摘要耕地的土壤侵蚀速度经常超过新土壤形成的速度。这种不平衡导致土壤变薄(即截断),从而使底土层及其下面的母质逐渐接近陆地表面。由于土壤侵蚀是一个选择性过程,地下层通常与原始表土具有截然不同的特性,截断引起的土壤特性变化可能通过土壤侵蚀反馈系统影响侵蚀速率和径流形成。然而,由于缺乏经验数据和在侵蚀模拟模型中忽略了长期可蚀性动力学,土壤侵蚀与土壤截断之间的潜在相互作用知之甚少。在这里,我们提出了一种新的基于模型的土壤侵蚀反馈系统的探索,在500年的时间里,使用从英国265个农业土壤剖面的多样化数据库中测量的土壤特性。为此,我们采用修正Morgan-Morgan-Finney模型(MMMF)进行建模实验,其中地形、气候、土地覆盖和作物管理参数在整个模拟期间保持不变。随着选择性土壤侵蚀过程去除表层土壤,该模型逐渐将地下土壤层混合成0.2 m耕层,并使用质量平衡混合模型更新土壤性质。此外,我们用前向误差评估来估计模型模拟中的不确定性。我们发现,99%的土壤剖面模拟侵蚀率对截断引起的土壤性质变化敏感。除截断敏感剖面外,其余剖面的土壤流失量均呈下降趋势,表明侵蚀率在模拟期间呈指数衰减。这在很大程度上可以解释为土壤表面泥沙含量的减少,这是由于选择性地去除了这种更容易被侵蚀的粒度部分以及粘土或砂质基质的存在。此外,土壤剖面显示出残留的石头覆盖物增加,覆盖了陆地表面,减少了土壤分离。相比之下,具有粉质地下层的土壤不断地向犁层补充易于侵蚀的物质,这阻止了土壤流失率随时间的下降。虽然我们的结果受到我们数据中所代表的气候条件的限制,正如我们的建模假设一样,我们已经证明了模拟的土壤损失如何对侵蚀引起的土壤性质变化敏感。这些发现可能会影响我们计算土壤寿命和对土地退化进行长期预测的方式。
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引用次数: 1
Forest liming in the face of climate change: the implications of restorative liming for soil organic carbon in mature German forests 面对气候变化的森林石灰化:恢复性石灰化对德国成熟森林土壤有机碳的影响
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-01-12 DOI: 10.5194/soil-9-39-2023
O. van Straaten, L. Kulp, Guntars O. Martinson, D. P. Zederer, U. Talkner
Abstract. Forest liming is a management tool that has and continues to be usedextensively across northern Europe to counteract acidification processesfrom anthropogenic sulfur and nitrogen (N) deposition. In this study, wequantified how liming affects soil organic carbon (SOC) stocks and attemptto disentangle the mechanisms responsible for the often contrastingprocesses that regulate net soil carbon (C) fluxes. Using a paired plotexperimental design we compared SOC stocks in limed plots with adjacentunlimed control plots at 28 experimental sites to 60 cm soil depth in maturebroadleaf and coniferous forests across Germany. Historical soil data from asubset of the paired experiment plots were analyzed to assess how SOC stocksin both control and limed plots changed between 1990 and 2019. Overall, we found that forest floor C stocks have been accumulating overtime in the control plots. Liming however largely offset organic layerbuildup in the L/Of layer, and forest floor C stocks remained unchangedover time in the limed plots. This, in turn, meant that nutrients remainedmobile and were not bound in soil organic matter complexes. Results from thepaired plot analysis showed that forest floor C stocks were significantlylower in limed plots than the control (−34 %, −8.4 ± 1.7 Mg C ha−1) but did not significantly affect SOC stocks in themineral soil, when all sites are pooled together. In the forest floorlayers, SOC stocks exhibited an exponential decrease with increasing pH,highlighting how lime-induced improvements in the biochemical environmentstimulate organic matter (OM) decomposition. Nevertheless, for both forestfloor and mineral soils, the magnitude and direction of the belowground Cchanges hinged directly on the inherent site characteristics, namely, foresttype (conifer versus broadleaf), soil pH, soil texture, and the soil SOCstocks. On the other hand, SOC stock decreases were often offset by otherprocesses that fostered C accumulation, such as improved forest productivityor increased carbon stabilization, which correspondingly translated to anoverall variable response by SOC stocks, particularly in the mineral soil. Lastly, we measured soil carbon dioxide (CO2) and soil methane(CH4) flux immediately after a re-liming event at three of theexperimental sites. Here, we found that (1) liming doubles CH4 uptakein the long-term; (2) soil organic matter mineralizationprocesses respond quickly to liming, even though the duration and size ofthe CO2 flush varied between sites; and (3) lime-derived CO2contributed very little to total CO2 emissions over the measurementperiod (determined using stable isotope approaches).
摘要森林石灰化是一种管理工具,已经并将继续在北欧广泛使用,以抵消人为硫和氮(N)沉积造成的酸化过程。在本研究中,我们量化了石灰如何影响土壤有机碳(SOC)储量,并试图理清调节土壤净碳(C)通量的经常相互矛盾的过程的机制。采用配对样地试验设计,对德国各地成熟阔叶林和针叶林28个试验点在60 cm土壤深度上有石灰样地与相邻无石灰样地的土壤有机碳储量进行了比较。分析了配对试验区子集的历史土壤数据,以评估1990年至2019年对照和石灰样地有机碳储量的变化情况。总体而言,我们发现在对照样地,森林地面C储量是随时间积累的。然而,石灰化在很大程度上抵消了L/Of层中有机层的积累,并且在石灰化样地,森林地面碳储量随时间保持不变。反过来,这意味着养分保持流动,而不是束缚在土壤有机质复合体中。配对样地分析结果表明,石灰样地的森林地面碳储量显著低于对照(−34%,−8.4±1.7 Mg C ha−1),但对矿质土的有机碳储量影响不显著。在森林底层,有机碳储量随着pH值的增加呈指数下降,这表明石灰诱导的生化环境改善促进了有机质的分解。然而,对于林地和矿质土壤,地下变化的幅度和方向直接取决于固有的立地特征,即森林类型(针叶林与阔叶)、土壤pH、土壤质地和土壤SOCstocks。另一方面,有机碳储量的减少通常被促进碳积累的其他过程所抵消,如森林生产力的提高或碳稳定性的增加,这相应地转化为有机碳储量的整体可变响应,特别是在矿质土壤中。最后,我们在三个试验点测量了土壤二氧化碳(CO2)和土壤甲烷(CH4)通量。在这里,我们发现(1)石灰在长期内使CH4吸收加倍;(2)土壤有机质矿化过程对石灰化反应迅速,尽管不同地点CO2冲刷的持续时间和大小不同;(3)在测量期间(使用稳定同位素方法确定),石灰产生的二氧化碳对二氧化碳总排放量的贡献很小。
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引用次数: 0
Soil depth as a driver of microbial and carbon dynamics in a planted forest (Pinus radiata) pumice soil 土壤深度对人工林(辐射松)浮石土壤微生物和碳动态的影响
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-01-12 DOI: 10.5194/soil-9-55-2023
Alexa-Kate Byers, L. Garrett, C. Armstrong, F. Dean, S. Wakelin
Abstract. Forest soils are fundamental in regulating the global carbon (C)cycle; their capacity to accumulate large stores of C means they form avital role in mitigating the effects of climate change. Understanding theprocesses that regulate forest soil C dynamics and stabilisation isimportant to maximise the capacity and longevity of C sequestration.Compared with surface soil layers, little is known about soil C dynamics insubsoil layers, sensu those below 30 cm depth. This knowledge gap creates largeuncertainties when estimating the distribution of global soil C stocks andassessing the vulnerability of soil C reserves to climate change. This studyaimed to dive deep into the subsoils of Puruki Experimental Forest (NewZealand) and characterise the changes in soil C dynamics and the soilmicrobiome down to 1 m soil depth. ITS and 16S rRNA sequencing andquantitative real-time PCR were used to measure changes in soil microbialdiversity, composition, and abundance. Stable (δ13C) andradioactive (14C) C analyses were performed to assess depth-drivenchanges in the stability and age of soil C. Our research identified largedeclines in microbial diversity and abundance with soil depth, alongsidesignificant structural shifts in community membership. Importantly, weconservatively estimate that more than 35 % of soil C stocks are present insubsoil layers below 30 cm. Although the age of soil C steadily increasedwith depth, reaching a mean radiocarbon age of 1571 yr BP (years beforepresent) in the deepest soil layers, the stability of soil C varied betweendifferent subsoil depth increments. These research findings highlight theimportance of quantifying subsoil C stocks for accurate C accounting. Byperforming a broad range of analytical measures, this research hascomprehensively characterised the abiotic and biotic properties of a subsoilenvironment – a frequently understudied but significant component of forestecosystems.
摘要森林土壤是调节全球碳(C)循环的基础;它们积累大量碳的能力意味着它们在缓解气候变化的影响方面发挥着至关重要的作用。了解调节森林土壤碳动态和稳定的过程对于最大限度地提高碳固存能力和寿命至关重要。与表层土壤相比,我们对深层(即30 cm以下土层)的土壤碳动态知之甚少。在估计全球土壤C储量分布和评估土壤C储量对气候变化的脆弱性时,这种知识差距造成了很大的不确定性。本研究旨在深入新西兰普鲁基实验森林的底土,并表征土壤C动态和土壤微生物组的变化,直至土壤深度1 m。采用ITS、16S rRNA测序和实时荧光定量PCR检测土壤微生物多样性、组成和丰度的变化。稳定(δ13C)和放射性(14C) C分析用于评估深度驱动的土壤C稳定性和年龄的变化。我们的研究发现,随着土壤深度的增加,微生物多样性和丰度大幅下降,同时群落成员的结构也发生了重大变化。重要的是,我们保守估计,超过35%的土壤C储量存在于30厘米以下的地下土层中。尽管土壤C的年龄随着深度的增加而稳步增加,在最深的土层中达到1571年BP(距今多年)的平均放射性碳年龄,但土壤C的稳定性在不同的底土深度增量之间存在差异。这些研究结果强调了量化地下碳储量对准确计算碳的重要性。通过执行广泛的分析措施,本研究全面表征了地下土壤环境的非生物和生物特性-这是森林生态系统中经常未得到充分研究但重要的组成部分。
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引用次数: 1
Shapley values reveal the drivers of soil organic carbon stock prediction Shapley值揭示了土壤有机碳储量预测的驱动因素
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-01-11 DOI: 10.5194/soil-9-21-2023
A. Wadoux, N. Saby, M. Martin
Abstract. Insights into the controlling factors of soil organic carbon (SOC) stock variation are necessary both for our scientific understanding of the terrestrial carbon balance and to support policies that intend to promote carbon storage in soils to mitigate climate change. In recent years, complex statistical and algorithmic tools from the field of machine learning have become popular for modelling and mapping SOC stocks over large areas. In this paper, we report on the development of a statistical method for interpreting complex models, which we implemented for the study of SOC stock variation. We fitted a random forest machine learning model with 2206 measurements of SOC stocks for the 0–50 cm depth interval from mainland France and used a set of environmental covariates as explanatory variables. We introduce Shapley values, a method from coalitional game theory, and use them to understand how environmental factors influence SOC stock prediction: what is the functional form of the association in the model between SOC stocks and environmental covariates, and how does the covariate importance vary locally from one location to another and between carbon-landscape zones? Results were validated both in light of the existing and well-described soil processes mediating soil carbon storage and with regards to previous studies in the same area. We found that vegetation and topography were overall the most important drivers of SOC stock variation in mainland France but that the set of most important covariates varied greatly among locations and carbon-landscape zones. In two spatial locations with equivalent SOC stocks, there was nearly an opposite pattern in the individual covariate contribution that yielded the prediction – in one case climate variables contributed positively, whereas in the second case climate variables contributed negatively – and this effect was mitigated by land use. We demonstrate that Shapley values are a methodological development that yield useful insights into the importance of factors controlling SOC stock variation in space. This may provide valuable information to understand whether complex empirical models are predicting a property of interest for the right reasons and to formulate hypotheses on the mechanisms driving the carbon sequestration potential of a soil.
摘要深入了解土壤有机碳(SOC)储量变化的控制因素,对于科学理解陆地碳平衡和支持旨在促进土壤碳储存以减缓气候变化的政策是必要的。近年来,机器学习领域的复杂统计和算法工具已成为建模和绘制大面积SOC库存的流行工具。在本文中,我们报告了一种用于解释复杂模型的统计方法的发展,我们将其用于研究有机碳储量的变化。我们拟合了一个随机森林机器学习模型,在法国大陆0-50 cm深度范围内测量了2206个SOC储量,并使用了一组环境协变量作为解释变量。我们引入联合博弈论中的Shapley值方法,并利用它来理解环境因素如何影响碳储量预测:碳储量与环境协变量之间的关联在模型中的功能形式是什么,协变量的重要性如何在不同地点和不同碳景观带之间发生局部变化?根据现有的和描述良好的土壤过程介导土壤碳储存,以及在同一地区的先前研究,验证了结果。研究发现,植被和地形总体上是法国大陆土壤有机碳储量变化的最重要驱动因素,但最重要的协变量集在不同地点和碳景观带之间差异很大。在土壤有机碳储量相当的两个空间点上,产生预测的个体协变量贡献模式几乎相反——在一种情况下,气候变量贡献为正,而在另一种情况下,气候变量贡献为负——这种影响被土地利用所缓解。我们证明Shapley值是一种方法发展,对控制SOC储量空间变化的因素的重要性产生有用的见解。这可能提供有价值的信息,以了解复杂的经验模型是否出于正确的原因预测感兴趣的特性,并就驱动土壤碳固存潜力的机制提出假设。
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引用次数: 5
Soil and crop management practices and the water regulation functions of soils: a qualitative synthesis of meta-analyses relevant to European agriculture 土壤和作物管理实践和土壤的水调节功能:与欧洲农业相关的荟萃分析的定性综合
4区 农林科学 Q2 Agricultural and Biological Sciences Pub Date : 2023-01-04 DOI: 10.5194/soil-9-1-2023
G. Blanchy, G. Bragato, C. Di Bene, N. Jarvis, M. Larsbo, Katharina H. E. Meurer, S. Garré
Abstract. Adopting soil and crop management practices that conserve or enhance soil structure is critical for supporting the sustainable adaptation of agriculture to climate change, as it should help maintain agricultural production in the face of increasing drought or water excess without impairing environmental quality. In this paper, we evaluate the evidence for this assertion by synthesizing the results of 34 published meta-analyses of the effects of such practices on soil physical and hydraulic properties relevant for climate change adaptation in European agriculture. We also review an additional 127 meta-analyses that investigated synergies and trade-offs or help to explain the effects of soil and crop management in terms of the underlying processes and mechanisms. Finally, we identify how responses to alternative soil–crop management systems vary under contrasting agro-environmental conditions across Europe. This information may help practitioners and policymakers to draw context-specific conclusions concerning the efficacy of management practices as climate adaptation tools. Our synthesis demonstrates that organic soil amendments and the adoption of practices that maintain “continuous living cover” result in significant benefits for the water regulation function of soils, mostly arising from the additional carbon inputs to soil and the stimulation of biological processes. These effects are clearly related to improved soil aggregation and enhanced bio-porosity, both of which reduce surface runoff and increase infiltration. One potentially negative consequence of these systems is a reduction in soil water storage and groundwater recharge, which may be problematic in dry climates. Some important synergies are reductions in nitrate leaching to groundwater and greenhouse gas emissions for nonleguminous cover crop systems. The benefits of reducing tillage intensity appear much less clear-cut. Increases in soil bulk density due to traffic compaction are commonly reported. However, biological activity is enhanced under reduced tillage intensity, which should improve soil structure and infiltration capacity and reduce surface runoff and the losses of agro-chemicals to surface water. However, the evidence for these beneficial effects is inconclusive, while significant trade-offs include yield penalties and increases in greenhouse gas emissions and the risks of leaching of pesticides and nitrate. Our synthesis also highlights important knowledge gaps on the effects of management practices on root growth and transpiration. Thus, conclusions related to the impacts of management on the crop water supply and other water regulation functions are necessarily based on inferences derived from proxy variables. Based on these knowledge gaps, we outlined several key avenues for future research on this topic.
摘要采用保护或加强土壤结构的土壤和作物管理做法对于支持农业可持续适应气候变化至关重要,因为它应有助于在面临日益严重的干旱或水资源过剩的情况下保持农业生产,同时不损害环境质量。在本文中,我们通过综合34项已发表的荟萃分析结果来评估这一论断的证据,这些荟萃分析是关于此类做法对欧洲农业中与气候变化适应相关的土壤物理和水力特性的影响。我们还回顾了另外127项荟萃分析,这些分析调查了协同作用和权衡,或有助于解释土壤和作物管理在潜在过程和机制方面的影响。最后,我们确定了在欧洲不同的农业环境条件下,对替代土壤作物管理系统的反应是如何变化的。这些信息可以帮助从业者和决策者就管理实践作为气候适应工具的有效性得出具体情况下的结论。我们的综合研究表明,有机土壤改良和采用保持“连续生物覆盖”的做法对土壤的水调节功能有显著的好处,主要来自土壤的额外碳输入和生物过程的刺激。这些效应明显与土壤聚集性的改善和生物孔隙度的增加有关,两者都减少了地表径流,增加了入渗。这些系统的一个潜在负面后果是减少土壤储水量和地下水补给,这在干燥气候下可能会造成问题。一些重要的协同作用是减少硝酸盐对地下水的淋滤和非豆科覆盖作物系统的温室气体排放。减少耕作强度的好处似乎不那么明确。由于交通压实导致的土壤容重增加是常见的报道。然而,减少耕作强度可以增强生物活性,从而改善土壤结构和入渗能力,减少地表径流和农用化学品对地表水的损失。然而,这些有益影响的证据是不确定的,而重要的权衡包括产量损失和温室气体排放的增加以及农药和硝酸盐浸出的风险。我们的综合还突出了管理实践对根系生长和蒸腾作用影响方面的重要知识空白。因此,有关管理对作物供水和其他水调节功能的影响的结论必须基于代理变量的推断。基于这些知识差距,我们概述了未来研究该主题的几个关键途径。
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引用次数: 4
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Soil Science
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