Pub Date : 2024-12-28DOI: 10.1016/j.soilbio.2024.109702
Caroline Krug Vieira, Matheus Nicoletti Marascalchi, Martin Rozmoš, Oldřich Benada, Valeriia Belova, Jan Jansa
Arbuscular mycorrhizal (AM) fungal structures, such as spores, vesicles, extra- and intra- radical hyphae, are home to diverse communities of prokaryotic (bacterial and archaeal) taxa and can have significant impact on the movement and behavior of those microbes within the soil. The ability to disperse via fungal hyphae, known as the fungal highway effect, was first observed in ectomycorrhiza and later in other fungal groups. This effect may benefit soil prokaryotes allowing them to explore new microhabitats in soil, offering advantages such as improved nutrient access, enhanced dispersal and colonization. Although the term “fungal highways” is well established, there still are only few studies that address the partner interactions and movement of microorganisms through the hyphal networks when referring to AM fungi. Bacteria can colonize the surfaces of hyphae and form biofilms that provide protection for both the bacteria and the fungus, influence the nutrient cycles, giving the bacteria access to resources transported by the fungus. Bacteria movement on AM fungal hyphae is facilitated by several mechanisms, including physical transport along the hyphal networks, swimming within the continuous water films that develop along the hyphal surfaces, and chemotaxis, where the bacteria move towards or away from specific chemical signals. Overall, the interactions between bacteria and AM fungi appears as a dynamic and complex process. Yet, we still do not know much about the influence of soil properties, plant age and species, seasonality, soil management and different climate with respect to AM fungal highways and microbiomes. Here, we review the current knowledge on prokaryotic movement through AM fungal hyphosphere and the possible factors that could affect it. Future research needs to elucidate mechanisms involved in the recruitment and/or migration of microbes in the AM fungal hyphosphere. Understanding these interactions may eventually help developing more sustainable agricultural practices and/or support environmental conservation.
{"title":"Arbuscular mycorrhizal fungal highways – what, how and why?","authors":"Caroline Krug Vieira, Matheus Nicoletti Marascalchi, Martin Rozmoš, Oldřich Benada, Valeriia Belova, Jan Jansa","doi":"10.1016/j.soilbio.2024.109702","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109702","url":null,"abstract":"Arbuscular mycorrhizal (AM) fungal structures, such as spores, vesicles, extra- and intra- radical hyphae, are home to diverse communities of prokaryotic (bacterial and archaeal) taxa and can have significant impact on the movement and behavior of those microbes within the soil. The ability to disperse via fungal hyphae, known as the fungal highway effect, was first observed in ectomycorrhiza and later in other fungal groups. This effect may benefit soil prokaryotes allowing them to explore new microhabitats in soil, offering advantages such as improved nutrient access, enhanced dispersal and colonization. Although the term “fungal highways” is well established, there still are only few studies that address the partner interactions and movement of microorganisms through the hyphal networks when referring to AM fungi. Bacteria can colonize the surfaces of hyphae and form biofilms that provide protection for both the bacteria and the fungus, influence the nutrient cycles, giving the bacteria access to resources transported by the fungus. Bacteria movement on AM fungal hyphae is facilitated by several mechanisms, including physical transport along the hyphal networks, swimming within the continuous water films that develop along the hyphal surfaces, and chemotaxis, where the bacteria move towards or away from specific chemical signals. Overall, the interactions between bacteria and AM fungi appears as a dynamic and complex process. Yet, we still do not know much about the influence of soil properties, plant age and species, seasonality, soil management and different climate with respect to AM fungal highways and microbiomes. Here, we review the current knowledge on prokaryotic movement through AM fungal hyphosphere and the possible factors that could affect it. Future research needs to elucidate mechanisms involved in the recruitment and/or migration of microbes in the AM fungal hyphosphere. Understanding these interactions may eventually help developing more sustainable agricultural practices and/or support environmental conservation.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"30 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-28DOI: 10.1016/j.soilbio.2024.109704
Chongyang Li, Jordon Wade, Kelly Vollbracht, Diane G. Hooper, Skye A. Wills, Andrew J. Margenot
Buffers are commonly employed in soil enzyme assays to maintain a constant pH during the assay incubation, but soils are already buffered and buffer can alter apparent Vmax and Km. To test for potential artifacts of buffer on soil enzyme activities, we selected 32 soils to furnish a broad range of physiochemical characteristics and assayed soil β-glucosidase (BG) and phosphomonoesterase (PME) activities at varied substrate concentrations either in water or in modified universal buffer (MUB). The pH of assays was different (up to 1.6 units) from the measured soil pH (1:2, m/v in water), but MUB did not maintain pH better than water. Compared to water, MUB generally suppressed activities (by∼31%), apparent Vmax (by∼32%) and Km (by∼52%) of PME, but yielded similar activities (by∼4% difference) and apparent Vmax (by∼9% difference) for BG. Soils with higher pH tended to have larger degree of suppressed PME actvities in MUB compared to assays in water. Based on the best practice of using a substrate concentration that is 5×Km for substrate saturation of the enzyme, the median substrate requirement to assay PME in these 32 soils was ≈ 50 mM g-1 in water and 25 mM g-1 in MUB. Regardless of matrix type, the commonly employed PME substrate concentration of 10 mM g-1 (e.g., Tabatabai, 1994) is insufficient for accurate activity assays. In contrast, for BG assays the commonly used pNP-linked substrate concentration of 10 mM g-1 appears appropriate for most soils with a median substrate requirement of ∼4 mM g-1 in water and ∼6 mM g-1 in MUB. Our results support previous claims that buffers are unnecessary for assaying soil enzyme activities and can alter apparent kinetic parameters (Km, Vmax). Potential soil- and enzyme-specific substrate requirements should be determined a priori to ensure accurate measurements of enzyme activities in soils.
缓冲液通常用于土壤酶测定，以在测定孵育期间保持恒定的pH值，但土壤已经被缓冲，缓冲液可以改变表观Vmax和Km。为了测试缓冲液对土壤酶活性的潜在影响，我们选择了32种土壤，提供了广泛的理化特征，并在不同的底物浓度下测定了土壤β-葡萄糖苷酶（BG）和磷酸单酯酶（PME）的活性，这些底物浓度分别是在水中或改性通用缓冲液（MUB）中。测定的pH值与测定的土壤pH值（1:2，m/v在水中）不同（高达1.6个单位），但MUB并不比水更好地维持pH值。与水相比，MUB通常抑制PME的活性（减少~ 31%）、表观Vmax（减少~ 32%）和Km（减少~ 52%），但对BG的活性（减少~ 4%）和表观Vmax（减少~ 9%）相似。与水中相比，pH值较高的土壤中MUB中PME活性的抑制程度较大。根据使用底物浓度5×Km作为酶的底物饱和度的最佳实践，在这32种土壤中测定PME的中位底物要求在水中≈50 mM g-1，在MUB中为25 mM g-1。无论基质类型如何，通常使用的PME底物浓度为10 mM g-1（例如，Tabatabai, 1994）不足以进行准确的活性测定。相比之下，对于BG分析，通常使用的10 mM g-1的pNP-linked底物浓度似乎适用于大多数土壤，水中和MUB中对底物的中值要求分别为~ 4 mM g-1和~ 6 mM g-1。我们的研究结果支持了先前的观点，即缓冲液对于测定土壤酶活性是不必要的，并且可以改变表观动力学参数（Km, Vmax）。潜在的土壤和酶特异性底物要求应事先确定，以确保准确测量土壤中的酶活性。
{"title":"Do chromogenic assays of soil enzyme activities need buffers? More disadvantages than advantages of modified universal buffer in the para-nitrophenyl-based assay of phosphomonoesterase and β-glucosidase","authors":"Chongyang Li, Jordon Wade, Kelly Vollbracht, Diane G. Hooper, Skye A. Wills, Andrew J. Margenot","doi":"10.1016/j.soilbio.2024.109704","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109704","url":null,"abstract":"Buffers are commonly employed in soil enzyme assays to maintain a constant pH during the assay incubation, but soils are already buffered and buffer can alter apparent V<sub>max</sub> and K<sub>m</sub>. To test for potential artifacts of buffer on soil enzyme activities, we selected 32 soils to furnish a broad range of physiochemical characteristics and assayed soil β-glucosidase (BG) and phosphomonoesterase (PME) activities at varied substrate concentrations either in water or in modified universal buffer (MUB). The pH of assays was different (up to 1.6 units) from the measured soil pH (1:2, m/v in water), but MUB did not maintain pH better than water. Compared to water, MUB generally suppressed activities (by∼31%), apparent V<sub>max</sub> (by∼32%) and K<sub>m</sub> (by∼52%) of PME, but yielded similar activities (by∼4% difference) and apparent V<sub>max</sub> (by∼9% difference) for BG. Soils with higher pH tended to have larger degree of suppressed PME actvities in MUB compared to assays in water. Based on the best practice of using a substrate concentration that is 5×K<sub>m</sub> for substrate saturation of the enzyme, the median substrate requirement to assay PME in these 32 soils was ≈ 50 mM g<sup>-1</sup> in water and 25 mM g<sup>-1</sup> in MUB. Regardless of matrix type, the commonly employed PME substrate concentration of 10 mM g<sup>-1</sup> (e.g., Tabatabai, 1994) is insufficient for accurate activity assays. In contrast, for BG assays the commonly used <em>p</em>NP-linked substrate concentration of 10 mM g<sup>-1</sup> appears appropriate for most soils with a median substrate requirement of ∼4 mM g<sup>-1</sup> in water and ∼6 mM g<sup>-1</sup> in MUB. Our results support previous claims that buffers are unnecessary for assaying soil enzyme activities and can alter apparent kinetic parameters (K<sub>m</sub>, V<sub>max</sub>). Potential soil- and enzyme-specific substrate requirements should be determined <em>a priori</em> to ensure accurate measurements of enzyme activities in soils.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"62 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-28DOI: 10.1016/j.soilbio.2024.109701
Chongyang Li, Jordon Wade, Andrew J. Margenot
Predicting soil phosphorus (P) bioavailability requires an understanding of organic P mineralization (Pmin) but assessing Pmin rates is challenging. Recent advances in the use of radioisotopic P labeling enable estimates of Pmin rates in soil. However, there is yet no standardization of radioisotopic dilution methods, potentially compromising comparison of results among studies. We conducted a systematic literature search to (1) synthesize the varying procedures among different studies, (2) compare the soil Pmin results obtained via two most commonly used approaches, isotopically exchangeable kinetics (IEK) and isotope pool dilution (IPD), and (3) address the methodological advantages and limitations of IEK and IPD. We identified and analyzed 98 studies, and found large discrepancies in study-specific radioisotope spike level, soil incubation period and extraction methods used to estimate the soil available P pool. On average, a spike level of 10-20 kBq g-1 soil was used among studies but empirical assessments are required to confirm that this assumed range of spike level is sufficient to measure exchangeable P. We found that incubation duration should be ≤14 d because there is an increasing possibility of measuring declining cumulative gross Pmin values beyond 14 d, even though reduced cumulative rate with additional time is theoretically impossible. Gross Pmin rates were lower by IPD compared to IEK. However, 18 studies reported undetectable gross Pmin, possibly due to the unverified but widely made assumption that biotic and abiotic process rates are additive. The complexity of the methodological issues necessitated a more nuanced approach via an advanced statistical approach (e.g., decision tree) to select a method based on trade-offs. To address the methodological issues identified in this review, a greater quantity and quality of observations need to be collected (e.g., well-designed experiments, data quality assurance such as quenching correction).
{"title":"In pursuit of soil P mineralization: a review and synthesis of radioisotopic labeling techniques","authors":"Chongyang Li, Jordon Wade, Andrew J. Margenot","doi":"10.1016/j.soilbio.2024.109701","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109701","url":null,"abstract":"Predicting soil phosphorus (P) bioavailability requires an understanding of organic P mineralization (P<sub>min</sub>) but assessing P<sub>min</sub> rates is challenging. Recent advances in the use of radioisotopic P labeling enable estimates of P<sub>min</sub> rates in soil. However, there is yet no standardization of radioisotopic dilution methods, potentially compromising comparison of results among studies. We conducted a systematic literature search to (1) synthesize the varying procedures among different studies, (2) compare the soil P<sub>min</sub> results obtained via two most commonly used approaches, isotopically exchangeable kinetics (IEK) and isotope pool dilution (IPD), and (3) address the methodological advantages and limitations of IEK and IPD. We identified and analyzed 98 studies, and found large discrepancies in study-specific radioisotope spike level, soil incubation period and extraction methods used to estimate the soil available P pool. On average, a spike level of 10-20 kBq g<sup>-1</sup> soil was used among studies but empirical assessments are required to confirm that this assumed range of spike level is sufficient to measure exchangeable P. We found that incubation duration should be ≤14 d because there is an increasing possibility of measuring declining cumulative gross P<sub>min</sub> values beyond 14 d, even though reduced cumulative rate with additional time is theoretically impossible. Gross P<sub>min</sub> rates were lower by IPD compared to IEK. However, 18 studies reported undetectable gross P<sub>min</sub>, possibly due to the unverified but widely made assumption that biotic and abiotic process rates are additive. The complexity of the methodological issues necessitated a more nuanced approach via an advanced statistical approach (e.g., decision tree) to select a method based on trade-offs. To address the methodological issues identified in this review, a greater quantity and quality of observations need to be collected (e.g., well-designed experiments, data quality assurance such as quenching correction).","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"30 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-24DOI: 10.1016/j.soilbio.2024.109699
Shangqi Xu, Meng Na, Yongjie Huang, Jie Zhang, Jihai Zhou, Lu-Jun Li
Saline-alkali soils are widely distributed worldwide and pose significant threats to food security and environmental safety. Rice cultivation is an effective strategy for ameliorating saline-alkali soils, increasing grain productivity, promoting soil organic carbon (SOC) accumulation and sustaining soil health in the Songnen Plain of Northeast China. This study investigated changes in microbial carbon cycling functions along rice cultivation chronosequences at two saline-alkali sites, Daan and Qianan. Rice cultivation improved soil health of the saline-alkali soils by neutralizing the pH and increasing the SOC content. Initial soil nutrient levels differed significantly at the two sites, but the nutrient dynamics were consistent, e.g., available nitrogen (AN) gradually increased, while available phosphorus (AP) initially increased and then decreased during rice cultivation. The diversity of carbon cycling genes increased with the duration of rice cultivation, while the relative abundance of genes associated with carbon decomposition decreased, which could promote carbon accumulation. These changes were primarily driven by the reduction in soil pH, followed by nutrient availability. Interestingly, at the Daan site, where AP and AN levels were relatively low, these nutrients significantly influenced carbon cycling genes. Conversely, at the Qianan site, where AP and AN levels were higher, there was less impact of nutrients than SOC on carbon cycling genes. This suggests that nutrient stoichiometry may be regulating carbon cycling genes. The soil succession process can be divided into two stages: less than 15 years of rice cultivation and more than 15 years. With longer-term rice cultivation, first the nitrogen limitation and then the phosphorus availability constrained microbial carbon cycling functions, and nutrient availability became more important than the soil pH effect. The soil nutrient and pH dynamics, together with flooding conditions in rice paddies, may limit microbial carbon decomposition, thereby promoting SOC accumulation in saline-alkali soils.
{"title":"Changes in microbial carbon cycling functions along rice cultivation chronosequences in saline-alkali soils","authors":"Shangqi Xu, Meng Na, Yongjie Huang, Jie Zhang, Jihai Zhou, Lu-Jun Li","doi":"10.1016/j.soilbio.2024.109699","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109699","url":null,"abstract":"Saline-alkali soils are widely distributed worldwide and pose significant threats to food security and environmental safety. Rice cultivation is an effective strategy for ameliorating saline-alkali soils, increasing grain productivity, promoting soil organic carbon (SOC) accumulation and sustaining soil health in the Songnen Plain of Northeast China. This study investigated changes in microbial carbon cycling functions along rice cultivation chronosequences at two saline-alkali sites, Daan and Qianan. Rice cultivation improved soil health of the saline-alkali soils by neutralizing the pH and increasing the SOC content. Initial soil nutrient levels differed significantly at the two sites, but the nutrient dynamics were consistent, e.g., available nitrogen (AN) gradually increased, while available phosphorus (AP) initially increased and then decreased during rice cultivation. The diversity of carbon cycling genes increased with the duration of rice cultivation, while the relative abundance of genes associated with carbon decomposition decreased, which could promote carbon accumulation. These changes were primarily driven by the reduction in soil pH, followed by nutrient availability. Interestingly, at the Daan site, where AP and AN levels were relatively low, these nutrients significantly influenced carbon cycling genes. Conversely, at the Qianan site, where AP and AN levels were higher, there was less impact of nutrients than SOC on carbon cycling genes. This suggests that nutrient stoichiometry may be regulating carbon cycling genes. The soil succession process can be divided into two stages: less than 15 years of rice cultivation and more than 15 years. With longer-term rice cultivation, first the nitrogen limitation and then the phosphorus availability constrained microbial carbon cycling functions, and nutrient availability became more important than the soil pH effect. The soil nutrient and pH dynamics, together with flooding conditions in rice paddies, may limit microbial carbon decomposition, thereby promoting SOC accumulation in saline-alkali soils.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"23 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142884214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-21DOI: 10.1016/j.soilbio.2024.109698
Ahmet Kürşad Sırcan, Thilo Streck, Andrea Schnepf, Mona Giraud, Adrian Lattacher, Ellen Kandeler, Christian Poll, Holger Pagel
Understanding the feedback mechanisms between roots and soil, and their effects on microbial communities, is crucial for predicting carbon cycling processes in agroecosystems. Process-based modeling is a valuable tool for quantifying biogeochemical processes and identifying regulatory mechanisms in the rhizosphere. A novel one-dimensional axisymmetric rhizosphere model is used to simulate the spatially resolved dynamics of microorganisms and soil organic matter turnover around a single root segment. The model accounts for two functional groups with different life history strategies (copiotrophs and oligotrophs), reflecting trade-offs in functional microbial traits related to substrate utilization and microbial metabolism. It considers differences in the accessibility of soil organic matter by including the microbial utilization of low and high molecular weight organic carbon compounds (LMW-OC, HMW-OC). The model was conditioned using Bayesian inference with constraint-based parameter sampling, which enabled the identification of parameter sets resulting in plausible model predictions in agreement with experimental evidence.Mimicking the behavior of growing roots, the model assumed 15 days of rhizodeposition for LMW-OC. The simulations show a decreasing pattern of dissolved LMW-OC away from the root surface. We observed a dominance of copiotrophs close to the root surface (0-0.1 mm). Spatial patterns of functional microbial groups persisted after rhizodeposition ended, indicating a legacy effect of rhizodeposition on microbial communities, particularly on oligotrophic activity. Simulated microbial biomass exhibits a very rapid change within 0-0.2 mm away from the root surface, which points to the importance of resolving soil properties and states at sub-millimeter resolution. Microbial-explicit rhizosphere modeling thus facilitates elucidating spatiotemporal patterns of microorganisms and carbon turnover in the rhizosphere. The identified legacy effect of rhizodeposition on soil microorganisms might be leveraged for rhizosphere-based carbon stabilization strategies in agroecosystems.
{"title":"Trait-based Modeling of Microbial Interactions and Carbon Turnover in the Rhizosphere","authors":"Ahmet Kürşad Sırcan, Thilo Streck, Andrea Schnepf, Mona Giraud, Adrian Lattacher, Ellen Kandeler, Christian Poll, Holger Pagel","doi":"10.1016/j.soilbio.2024.109698","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109698","url":null,"abstract":"Understanding the feedback mechanisms between roots and soil, and their effects on microbial communities, is crucial for predicting carbon cycling processes in agroecosystems. Process-based modeling is a valuable tool for quantifying biogeochemical processes and identifying regulatory mechanisms in the rhizosphere. A novel one-dimensional axisymmetric rhizosphere model is used to simulate the spatially resolved dynamics of microorganisms and soil organic matter turnover around a single root segment. The model accounts for two functional groups with different life history strategies (copiotrophs and oligotrophs), reflecting trade-offs in functional microbial traits related to substrate utilization and microbial metabolism. It considers differences in the accessibility of soil organic matter by including the microbial utilization of low and high molecular weight organic carbon compounds (LMW-OC, HMW-OC). The model was conditioned using Bayesian inference with constraint-based parameter sampling, which enabled the identification of parameter sets resulting in plausible model predictions in agreement with experimental evidence.Mimicking the behavior of growing roots, the model assumed 15 days of rhizodeposition for LMW-OC. The simulations show a decreasing pattern of dissolved LMW-OC away from the root surface. We observed a dominance of copiotrophs close to the root surface (0-0.1 mm). Spatial patterns of functional microbial groups persisted after rhizodeposition ended, indicating a legacy effect of rhizodeposition on microbial communities, particularly on oligotrophic activity. Simulated microbial biomass exhibits a very rapid change within 0-0.2 mm away from the root surface, which points to the importance of resolving soil properties and states at sub-millimeter resolution. Microbial-explicit rhizosphere modeling thus facilitates elucidating spatiotemporal patterns of microorganisms and carbon turnover in the rhizosphere. The identified legacy effect of rhizodeposition on soil microorganisms might be leveraged for rhizosphere-based carbon stabilization strategies in agroecosystems.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"31 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-17DOI: 10.1016/j.soilbio.2024.109697
Lin Xu, Yongping Kou, Qian Mao, Xiangzhen Li, Chaonan Li, Bo Tu, Jiabao Li, Lihua Tu, Lixia Wang, Hongwei Xu, Chengming You, Han Li, Sining Liu, Li Zhang, Bo Tan, Jiao Li, Yaling Yuan, Kai Wei, Zhenfeng Xu
Alkaline phosphatase (phoD) gene-encoding bacterial (phoD-harbouring) communities are crucial for organic phosphorus (P) mineralisation in agroecosystems. However, the relative contributions of natural factors (e.g., climate) and anthropogenic influences (e.g., fertilisation) to these communities remain unclear, particularly at large spatial scales. To address this, we analysed phoD amplicon sequence data from 290 samples across 15 independent cropland studies, spanning diverse climatic zones and soil types from central to eastern Asia. Our results reveal that climatic factors exert stronger effects than fertiliser regimes on soil phoD-harbouring communities. Specifically, the richness of soil phoD-harbouring communities decreased by approximately three times as mean annual precipitation increased from 160 mm to 1800 mm, and mean annual temperature rose from 9°C to 18°C. Compared to the control, chemical nitrogen (N) + P + organic fertiliser doubled richness, while the control’s richness was 10 times higher than that of chemical N + P + potassium fertiliser. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the most dominant phoD-harbouring taxa, collectively accounting for 65.3% of the relative abundance. Precipitation explained up to 96.3% of the variance in community composition, while fertiliser regimes explained approximately 40%. Notably, excessive potassium fertilisation was linked to reduced richness and abundance of dominant phoD-harbouring taxa, potentially limiting the availability of plant-accessible P. This suggests that the amount of potassium fertiliser should be carefully considered in future agricultural practices, as it may reduce plant-available P by inhibiting soil phoD-harbouring communities.
{"title":"Climate outweighs fertiliser effects on soil phoD-harbouring communities in agroecosystems","authors":"Lin Xu, Yongping Kou, Qian Mao, Xiangzhen Li, Chaonan Li, Bo Tu, Jiabao Li, Lihua Tu, Lixia Wang, Hongwei Xu, Chengming You, Han Li, Sining Liu, Li Zhang, Bo Tan, Jiao Li, Yaling Yuan, Kai Wei, Zhenfeng Xu","doi":"10.1016/j.soilbio.2024.109697","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109697","url":null,"abstract":"Alkaline phosphatase (<em>phoD</em>) gene-encoding bacterial (<em>phoD</em>-harbouring) communities are crucial for organic phosphorus (P) mineralisation in agroecosystems. However, the relative contributions of natural factors (e.g., climate) and anthropogenic influences (e.g., fertilisation) to these communities remain unclear, particularly at large spatial scales. To address this, we analysed <em>phoD</em> amplicon sequence data from 290 samples across 15 independent cropland studies, spanning diverse climatic zones and soil types from central to eastern Asia. Our results reveal that climatic factors exert stronger effects than fertiliser regimes on soil <em>phoD</em>-harbouring communities. Specifically, the richness of soil <em>phoD</em>-harbouring communities decreased by approximately three times as mean annual precipitation increased from 160 mm to 1800 mm, and mean annual temperature rose from 9°C to 18°C. Compared to the control, chemical nitrogen (N) + P + organic fertiliser doubled richness, while the control’s richness was 10 times higher than that of chemical N + P + potassium fertiliser. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the most dominant <em>phoD</em>-harbouring taxa, collectively accounting for 65.3% of the relative abundance. Precipitation explained up to 96.3% of the variance in community composition, while fertiliser regimes explained approximately 40%. Notably, excessive potassium fertilisation was linked to reduced richness and abundance of dominant <em>phoD</em>-harbouring taxa, potentially limiting the availability of plant-accessible P. This suggests that the amount of potassium fertiliser should be carefully considered in future agricultural practices, as it may reduce plant-available P by inhibiting soil <em>phoD</em>-harbouring communities.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"76 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-15DOI: 10.1016/j.soilbio.2024.109692
Camilo Castillo-Avila, Dennis Castillo-Figueroa, Juan M. Posada
Soils harbor more than half of Earth's biodiversity, with soil fauna representing one of the most diverse groups. However, understanding the drivers influencing their biodiversity remains limited. Upper Andean tropical forests are among Earth's most biodiverse ecosystems, but have undergone large-scale historical transformations, resulting in landscapes with different forest successional stages. In this study, we aimed to analyze soil fauna communities along a successional gradient in Colombia's Eastern Andean forests and identify key microclimatic, soil, and forest structural drivers. We collected soil fauna from 168 samples (30x30x5 cm), in dry and wet seasons, in 14 permanent plots (20x20 m) located in four sites. Data on microclimate, nutrients, productivity, plant diversity, and litter functional richness were gathered from these permanent plots. We observed significant soil fauna biodiversity turnover among Andean montane forest sites, mirroring the distinctive floristic composition between them. We also found that soil fauna richness and abundance increased with succession, attributed to higher productivity and more suitable microclimatic conditions in old-growth forests. Our findings suggest that the primary driver of soil fauna richness in tropical mountain Andean forests is the amount of energy (i.e, forest productivity), while soil fauna abundance is mainly influenced by thermal conditions. Additionally, factors framed within the physiological tolerance hypothesis (i.e., calcium, aluminum) and within the habitat heterogeneity hypothesis (i.e., litter functional richness, plant diversity) also play a role, albeit to a lesser extent. This study emphasizes the importance of examining forest recovery including soil fauna groups to understand successional patterns in tropical mountain forests.
{"title":"Drivers of soil fauna communities along a successional gradient in upper Andean tropical forests","authors":"Camilo Castillo-Avila, Dennis Castillo-Figueroa, Juan M. Posada","doi":"10.1016/j.soilbio.2024.109692","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109692","url":null,"abstract":"Soils harbor more than half of Earth's biodiversity, with soil fauna representing one of the most diverse groups. However, understanding the drivers influencing their biodiversity remains limited. Upper Andean tropical forests are among Earth's most biodiverse ecosystems, but have undergone large-scale historical transformations, resulting in landscapes with different forest successional stages. In this study, we aimed to analyze soil fauna communities along a successional gradient in Colombia's Eastern Andean forests and identify key microclimatic, soil, and forest structural drivers. We collected soil fauna from 168 samples (30x30x5 cm), in dry and wet seasons, in 14 permanent plots (20x20 m) located in four sites. Data on microclimate, nutrients, productivity, plant diversity, and litter functional richness were gathered from these permanent plots. We observed significant soil fauna biodiversity turnover among Andean montane forest sites, mirroring the distinctive floristic composition between them. We also found that soil fauna richness and abundance increased with succession, attributed to higher productivity and more suitable microclimatic conditions in old-growth forests. Our findings suggest that the primary driver of soil fauna richness in tropical mountain Andean forests is the amount of energy (i.e, forest productivity), while soil fauna abundance is mainly influenced by thermal conditions. Additionally, factors framed within the physiological tolerance hypothesis (i.e., calcium, aluminum) and within the habitat heterogeneity hypothesis (i.e., litter functional richness, plant diversity) also play a role, albeit to a lesser extent. This study emphasizes the importance of examining forest recovery including soil fauna groups to understand successional patterns in tropical mountain forests.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"12 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-15DOI: 10.1016/j.soilbio.2024.109693
Sara G. Cazzaniga, Philippe Belliard, Joris van Steenbrugge, Sven van den Elsen, Carin Lombaers, Johnny Visser, Leendert Molendijk, Jose G. Macia-Vicente, Joeke Postma, Liesje Mommer, Johannes Helder
Plant-parasitic nematodes are harmful pathogens for many agricultural crops. Within this category, root-knot nematodes (RKN, Meloidogyne spp.) are worldwide regarded as the most impactful because of their wide geographical distribution and their polyphagous nature. Host plant resistances against RKN have been successfully introduced in a few crops only. As the use of nematicides is becoming increasingly restricted because of environmental and human health concerns, there is a need for alternative strategies to control RKN. One such approach is the stimulation of local nematode antagonists. We investigated this in an experimental field setting with two main variables: density of the Columbia root-knot nematode Meloidogyne chitwoodi, and the type of cover crop. For each of the three M. chitwoodi densities, the effects of ten cover crop treatments were tested on both the resident (DNA) and the active (RNA) fractions of the bacterial and fungal communities. In our analyses, we focused on changes in the abundance of plant-parasitic nematode antagonists. From the eight bacterial and 26 fungal genera known from global literature to harbour potential antagonists of plant-parasitic nematodes, we detected respectively five and 14 genera in our agricultural field. Among the bacterial genera, four genera were shown to comprise bacterial species for which nematode antagonism has been documented. The fungal genera included facultative nematode parasites (e.g., Arthrobotrys spp.), endophytes strengthening host defences (e.g., Acremonium spp.), as well as multiple obligatory nematophagous species. This study revealed that conventionally managed arable fields may harbour an unexpectedly high diversity of nematode antagonists. Multiple antagonists were stimulated by cover crops in a cover crop-specific manner, and, to a lesser extent, by increased RKN densities. The richness in putative nematode antagonists did not translate into M. chitwoodi suppression, and we currently investigating whether this relates to the facultative nematophagous lifestyle of most of these antagonists.
{"title":"On the diversity of nematode antagonists in an agricultural soil, and their steerability by root-knot nematode density and cover crops","authors":"Sara G. Cazzaniga, Philippe Belliard, Joris van Steenbrugge, Sven van den Elsen, Carin Lombaers, Johnny Visser, Leendert Molendijk, Jose G. Macia-Vicente, Joeke Postma, Liesje Mommer, Johannes Helder","doi":"10.1016/j.soilbio.2024.109693","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109693","url":null,"abstract":"Plant-parasitic nematodes are harmful pathogens for many agricultural crops. Within this category, root-knot nematodes (RKN, <em>Meloidogyne</em> spp.) are worldwide regarded as the most impactful because of their wide geographical distribution and their polyphagous nature. Host plant resistances against RKN have been successfully introduced in a few crops only. As the use of nematicides is becoming increasingly restricted because of environmental and human health concerns, there is a need for alternative strategies to control RKN. One such approach is the stimulation of local nematode antagonists. We investigated this in an experimental field setting with two main variables: density of the Columbia root-knot nematode <em>Meloidogyne chitwoodi</em>, and the type of cover crop. For each of the three <em>M. chitwoodi</em> densities, the effects of ten cover crop treatments were tested on both the resident (DNA) and the active (RNA) fractions of the bacterial and fungal communities. In our analyses, we focused on changes in the abundance of plant-parasitic nematode antagonists. From the eight bacterial and 26 fungal genera known from global literature to harbour potential antagonists of plant-parasitic nematodes, we detected respectively five and 14 genera in our agricultural field. Among the bacterial genera, four genera were shown to comprise bacterial species for which nematode antagonism has been documented. The fungal genera included facultative nematode parasites (<em>e.g</em>., <em>Arthrobotrys</em> spp.), endophytes strengthening host defences (<em>e.g</em>., <em>Acremonium</em> spp.), as well as multiple obligatory nematophagous species. This study revealed that conventionally managed arable fields may harbour an unexpectedly high diversity of nematode antagonists. Multiple antagonists were stimulated by cover crops in a cover crop-specific manner, and, to a lesser extent, by increased RKN densities. The richness in putative nematode antagonists did not translate into <em>M. chitwoodi</em> suppression, and we currently investigating whether this relates to the facultative nematophagous lifestyle of most of these antagonists.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"85 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Global change may change plant carbon input, which may in turn accelerate or retard the mineralization of soil organic matter (SOM), a phenomenon known as priming effect. However, deep soil priming effect on large geographic scale is poorly understood, hindering a complete understanding of the response of whole-soil carbon dynamics to plant carbon input. Across a 2000 km grassland transect in Inner Mongolia, China, this study showed that soil priming effects at 0-200 cm depth varied systematically with climate and soil properties. The intensity of priming effect varied with depth. Averaged across 10 sites along the transect, glucose addition increased native SOM decomposition by 5.1% in surface soil (0-10 cm), while decreased it by 12.9% and 25.7% in middle (30-50 cm) and deep (150-200 cm) soils, respectively. Interestingly, the regulating factors of priming at different depths were significantly different. The priming effect in surface soil was primarily regulated by SOM stability represented by content of soil minerals and (clay+silt) %, whereas that in middle soil was mainly regulated by soil substrates, SOM stability and soil pH, and that in deep soil was mainly controlled by soil substrates. This study demonstrates distinct controls of the priming effect across soil depths at the regional scale, and contributes to improving our understanding of how whole-soil carbon dynamics respond to global change.
全球变化可能会改变植物的碳输入，进而加速或延缓土壤有机质（SOM）的矿化，这种现象被称为引物效应。然而，人们对大地理尺度上的深层土壤引诱效应知之甚少，这阻碍了人们全面了解全土碳动态对植物碳输入的响应。这项研究在中国内蒙古2000公里的草原横断面上发现，0-200厘米深度的土壤引诱效应随气候和土壤特性的变化而系统地变化。引诱效应的强度随深度而变化。对横断面上的 10 个地点进行平均，添加葡萄糖可使表层土壤（0-10 厘米）中的原生 SOM 分解增加 5.1%，而中层土壤（30-50 厘米）和深层土壤（150-200 厘米）中的原生 SOM 分解分别减少 12.9% 和 25.7%。有趣的是，不同深度的打底调节因子存在显著差异。表层土壤的引诱效果主要受以土壤矿物质含量和（粘土+淤泥）%为代表的 SOM 稳定性的调控，而中层土壤的引诱效果主要受土壤基质、SOM 稳定性和土壤 pH 的调控，深层土壤的引诱效果主要受土壤基质的调控。这项研究表明，在区域尺度上，不同土壤深度的启动效应受不同的控制，有助于加深我们对整个土壤碳动态如何响应全球变化的理解。
{"title":"Depth-dependent regulations of soil priming effects along a 2000 km grassland transect","authors":"Yunlong Hu, Jiguang Feng, Shuai Zhang, Zhongkui Luo, Biao Zhu","doi":"10.1016/j.soilbio.2024.109696","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109696","url":null,"abstract":"Global change may change plant carbon input, which may in turn accelerate or retard the mineralization of soil organic matter (SOM), a phenomenon known as priming effect. However, deep soil priming effect on large geographic scale is poorly understood, hindering a complete understanding of the response of whole-soil carbon dynamics to plant carbon input. Across a 2000 km grassland transect in Inner Mongolia, China, this study showed that soil priming effects at 0-200 cm depth varied systematically with climate and soil properties. The intensity of priming effect varied with depth. Averaged across 10 sites along the transect, glucose addition increased native SOM decomposition by 5.1% in surface soil (0-10 cm), while decreased it by 12.9% and 25.7% in middle (30-50 cm) and deep (150-200 cm) soils, respectively. Interestingly, the regulating factors of priming at different depths were significantly different. The priming effect in surface soil was primarily regulated by SOM stability represented by content of soil minerals and (clay+silt) %, whereas that in middle soil was mainly regulated by soil substrates, SOM stability and soil pH, and that in deep soil was mainly controlled by soil substrates. This study demonstrates distinct controls of the priming effect across soil depths at the regional scale, and contributes to improving our understanding of how whole-soil carbon dynamics respond to global change.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"10 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-15DOI: 10.1016/j.soilbio.2024.109694
Akeem T. Shorunke, Bobbi L. Helgason, Richard E. Farrell
Crop residues are an important source of N for subsequent crops and contribute to cropping system nitrous oxide (N2O) emissions. Oilseed residues, particularly canola (Brassica napus L.), can instigate higher N2O emissions compared to pulse and wheat crop residues but the reason for this disproportionate emission response is unknown. To determine the quantity and source of N2O emissions, we conducted an incubation experiment (84 d) using 15N and 13C labelled residues of canola, wheat ,flax, pea and investigated key N-cycling gene abundances, microbial abundance and community structure using PLFA and soil C and N dynamics. Residue addition of all types significantly increased microbial abundance and abundances of denitrification and nitrification genes. Canola residue resulted in significantly greater nosZI abundance. Lower incorporation of canola residue 13C into PLFA and higher 13CO2 emissions suggests that canola residue C was used less efficiently (i.e., less for growth and more for respiration), depleting O2 and stimulating denitrification. The magnitude of N2O emission from residue-amended soils was significantly higher (p < 0.05) than the unamended control soil and differed with residue type: canola > pea = wheat > flax > control. The canola residue emission factor was 1.56% of residue N – significantly higher than that of wheat (0.99%), pea (0.95%) and flax (0.18%). This higher canola emission factor resulted from greater residue-derived (1.47%) N2O as well as residue-induced (0.65%) soil emissions. The combined use of stable isotope tracing of 15N2O and 13CO2 and microbial characterization quantified differences in residue-derived N2O emissions from common crops that were linked to differences in microbial abundance, community structure and activity.
{"title":"Evidence of the need for crop-specific N2O emission factors","authors":"Akeem T. Shorunke, Bobbi L. Helgason, Richard E. Farrell","doi":"10.1016/j.soilbio.2024.109694","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109694","url":null,"abstract":"Crop residues are an important source of N for subsequent crops and contribute to cropping system nitrous oxide (N<sub>2</sub>O) emissions. Oilseed residues, particularly canola (<em>Brassica napus</em> L.), can instigate higher N<sub>2</sub>O emissions compared to pulse and wheat crop residues but the reason for this disproportionate emission response is unknown. To determine the quantity and source of N<sub>2</sub>O emissions, we conducted an incubation experiment (84 d) using <sup>15</sup>N and <sup>13</sup>C labelled residues of canola, wheat ,flax, pea and investigated key N-cycling gene abundances, microbial abundance and community structure using PLFA and soil C and N dynamics. Residue addition of all types significantly increased microbial abundance and abundances of denitrification and nitrification genes. Canola residue resulted in significantly greater <em>nosZI</em> abundance. Lower incorporation of canola residue <sup>13</sup>C into PLFA and higher <sup>13</sup>CO<sub>2</sub> emissions suggests that canola residue C was used less efficiently (i.e., less for growth and more for respiration), depleting O<sub>2</sub> and stimulating denitrification. The magnitude of N<sub>2</sub>O emission from residue-amended soils was significantly higher (<em>p <</em> 0.05) than the unamended control soil and differed with residue type: canola > pea = wheat > flax > control. The canola residue emission factor was 1.56% of residue N – significantly higher than that of wheat (0.99%), pea (0.95%) and flax (0.18%). This higher canola emission factor resulted from greater residue-derived (1.47%) N<sub>2</sub>O as well as residue-induced (0.65%) soil emissions. The combined use of stable isotope tracing of <sup>15</sup>N<sub>2</sub>O and <sup>13</sup>CO<sub>2</sub> and microbial characterization quantified differences in residue-derived N<sub>2</sub>O emissions from common crops that were linked to differences in microbial abundance, community structure and activity.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"14 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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