Pub Date : 2024-12-06DOI: 10.1016/j.soilbio.2024.109683
Alexander H. Krichels, Robert A. Sanford, Joanne C. Chee-Sanford, Lynn Connor, Rachel Van Allen, Angela D. Kent, Wendy H. Yang
Climate change is increasing the frequency and intensity of large precipitation events that flood soils and establish anoxic conditions that promote microbial denitrification, a predominant source of atmospheric nitrous oxide (N2O, a strong greenhouse gas). Denitrification may be favored within topographic depressions in otherwise flat fields that are prone to ponding, establishing “hotspots” of N2O emissions. The location of N2O hotspots may also depend on the distribution of soil microbial communities that are responsible for the production and consumption of N2O in soils. Yet, relating soil microbial community composition to N2O emissions remains challenging. To assess how spatial variation in soil microbial communities affects N2O emissions, we measured the community composition of active microorganisms using amplicon-based sequencing of cDNA generated from mRNA transcripts associated with N-cycling processes in response to experimentally flooding and draining soils in the lab. We also used stable isotope tracers to relate microbial communities to process rates. Consistent with the hypothesis that denitrifying microbial communities are not functionally redundant, we found that the diversity of microbial taxa expressing nitrite reduction genes (nirK) and N2O reduction genes (Clade I nosZ) were correlated with denitrifier-derived N2O emissions. Depressional soils had more diverse active N2O consuming communities (assessed using Clade I nosZ) under flooded conditions, limiting net N2O emissions compared to upslope soils. Our results show that depressional soils maintain distinct microbial communities that likely promote higher rates of N2O reduction compared to upslope soils. Soil microtopography can, therefore, select for distinct microbial communities that emit different amount of N2O in response to large precipitation events.
气候变化正在增加大降水事件的频率和强度，这些大降水事件会淹没土壤，并建立促进微生物反硝化的缺氧条件，微生物反硝化是大气一氧化二氮（N2O，一种强温室气体）的主要来源。在地形洼地中，反硝化作用可能更有利，否则平坦的田地容易积水，从而建立N2O排放的“热点”。N2O热点的位置也可能取决于土壤中负责N2O生产和消耗的土壤微生物群落的分布。然而，将土壤微生物群落组成与N2O排放联系起来仍然具有挑战性。为了评估土壤微生物群落的空间变化对N2O排放的影响，我们利用基于扩增子的cDNA测序方法测量了活性微生物的群落组成，这些cDNA是由与实验室土壤淹水和排水实验中n循环过程相关的mRNA转录本产生的。我们还使用稳定同位素示踪剂将微生物群落与加工速率联系起来。与反硝化微生物群落不存在功能冗余的假设一致，我们发现表达亚硝酸盐还原基因（nirK）和N2O还原基因（Clade I nosZ）的微生物分类群的多样性与反硝化菌衍生的N2O排放相关。洼地土壤在淹水条件下具有更多样化的活性N2O消耗群落（使用Clade I nosZ进行评估），与上坡土壤相比，限制了N2O的净排放。我们的研究结果表明，与上坡土壤相比，洼地土壤保持着独特的微生物群落，可能促进更高的N2O还原速率。因此，土壤微地形可以选择不同的微生物群落，这些微生物群落在大降水事件中释放不同数量的N2O。
{"title":"Distinct N-cycling microbial communities contribute to microtopographic variation in soil N2O emissions from denitrification","authors":"Alexander H. Krichels, Robert A. Sanford, Joanne C. Chee-Sanford, Lynn Connor, Rachel Van Allen, Angela D. Kent, Wendy H. Yang","doi":"10.1016/j.soilbio.2024.109683","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109683","url":null,"abstract":"Climate change is increasing the frequency and intensity of large precipitation events that flood soils and establish anoxic conditions that promote microbial denitrification, a predominant source of atmospheric nitrous oxide (N<sub>2</sub>O, a strong greenhouse gas). Denitrification may be favored within topographic depressions in otherwise flat fields that are prone to ponding, establishing “hotspots” of N<sub>2</sub>O emissions. The location of N<sub>2</sub>O hotspots may also depend on the distribution of soil microbial communities that are responsible for the production and consumption of N<sub>2</sub>O in soils. Yet, relating soil microbial community composition to N<sub>2</sub>O emissions remains challenging. To assess how spatial variation in soil microbial communities affects N<sub>2</sub>O emissions, we measured the community composition of active microorganisms using amplicon-based sequencing of cDNA generated from mRNA transcripts associated with N-cycling processes in response to experimentally flooding and draining soils in the lab. We also used stable isotope tracers to relate microbial communities to process rates. Consistent with the hypothesis that denitrifying microbial communities are not functionally redundant, we found that the diversity of microbial taxa expressing nitrite reduction genes (<em>nirK</em>) and N<sub>2</sub>O reduction genes (Clade I <em>nosZ)</em> were correlated with denitrifier-derived N<sub>2</sub>O emissions. Depressional soils had more diverse active N<sub>2</sub>O consuming communities (assessed using Clade I <em>nosZ</em>) under flooded conditions, limiting net N<sub>2</sub>O emissions compared to upslope soils. Our results show that depressional soils maintain distinct microbial communities that likely promote higher rates of N<sub>2</sub>O reduction compared to upslope soils. Soil microtopography can, therefore, select for distinct microbial communities that emit different amount of N<sub>2</sub>O in response to large precipitation events.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"16 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142782731","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 : 2024-12-05DOI: 10.1016/j.soilbio.2024.109675
Zhiyang Zhang, Yi Jiao, Steffen Kolb
Yak dung is an input to the carbon (C) and nutrient cycles that maintain ecosystem functions on the Tibetan Plateau. Yak dung is C and nutrient-rich excreta that is conducive to the growth and metabolic activities of bacterial communities, thus predicting that more bacterial than fungal processes are responsible for the degradation of yak dung. A three-year yak dung degradation experiment in a yak-grazing alpine rangeland was designed to investigate the changes in dung moisture content, chemical and enzymatic properties, and bacterial and fungal communities during degradation, as well as to explore how these parameters may regulate the degradation of yak dung. After three years of decomposition, yak dung had a 79 % reduction in mass, and most of the mass loss occurred within the first 2 years. Cellulosic polymers, especially cellulose and hemicellulose, determined the rate of yak dung degradation. The main changes in dung bacterial communities occurred during the first 2 years of degradation, largely related to changes in moisture and available substrates (e.g., dissolved organic C, dissolved organic nitrogen (N), ammonium, nitrate, and available phosphorus). In contrast, dung fungal communities did not change until 1.5–3 years of degradation, in response to the total substrates (e.g., total C and N). The relative abundances of Proteobacteria, Bacteroidota, Firmicutes, Basidiomycota, and Ascomycota, and the activities of endo-cellulases, exo-cellulases, β-1,4-glucosidase, and β-1,4-xylosidase, which were associated with cellulose and hemicellulose degradation, decreased during decomposition. The relative abundances of Actinobacteria, and activities of peroxidases and polyphenol oxidase were positively correlated with dung lignin content. Structural equation modeling suggested that degradation of lignocellulose in dung was mainly the consequence of bacterial community activities. Additionally, moisture was the most important abiotic factor influencing lignocellulose degradation, as it can directly affect dung substrate availability, and ultimately bacterial communities and associated enzyme activities. As the microbial degradation of lignocellulose in yak dung is strongly related to moisture, any change to the rainfall pattern in the future is expected to influence yak dung degradation in this alpine region.
{"title":"Degradation dynamics and microbial processes in yak dung on the Tibetan Plateau","authors":"Zhiyang Zhang, Yi Jiao, Steffen Kolb","doi":"10.1016/j.soilbio.2024.109675","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109675","url":null,"abstract":"Yak dung is an input to the carbon (C) and nutrient cycles that maintain ecosystem functions on the Tibetan Plateau. Yak dung is C and nutrient-rich excreta that is conducive to the growth and metabolic activities of bacterial communities, thus predicting that more bacterial than fungal processes are responsible for the degradation of yak dung. A three-year yak dung degradation experiment in a yak-grazing alpine rangeland was designed to investigate the changes in dung moisture content, chemical and enzymatic properties, and bacterial and fungal communities during degradation, as well as to explore how these parameters may regulate the degradation of yak dung. After three years of decomposition, yak dung had a 79 % reduction in mass, and most of the mass loss occurred within the first 2 years. Cellulosic polymers, especially cellulose and hemicellulose, determined the rate of yak dung degradation. The main changes in dung bacterial communities occurred during the first 2 years of degradation, largely related to changes in moisture and available substrates (e.g., dissolved organic C, dissolved organic nitrogen (N), ammonium, nitrate, and available phosphorus). In contrast, dung fungal communities did not change until 1.5–3 years of degradation, in response to the total substrates (e.g., total C and N). The relative abundances of <em>Proteobacteria</em>, <em>Bacteroidota</em>, <em>Firmicutes</em>, <em>Basidiomycota</em>, and <em>Ascomycota</em>, and the activities of endo-cellulases, exo-cellulases, β-1,4-glucosidase, and β-1,4-xylosidase, which were associated with cellulose and hemicellulose degradation, decreased during decomposition. The relative abundances of <em>Actinobacteria</em>, and activities of peroxidases and polyphenol oxidase were positively correlated with dung lignin content. Structural equation modeling suggested that degradation of lignocellulose in dung was mainly the consequence of bacterial community activities. Additionally, moisture was the most important abiotic factor influencing lignocellulose degradation, as it can directly affect dung substrate availability, and ultimately bacterial communities and associated enzyme activities. As the microbial degradation of lignocellulose in yak dung is strongly related to moisture, any change to the rainfall pattern in the future is expected to influence yak dung degradation in this alpine region.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"28 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142782655","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 : 2024-12-04DOI: 10.1016/j.soilbio.2024.109674
Ran Wu, Hua Wang, Hanche Xia, Haoyi Zheng, Yaxin Zhu, Lijuan Liu, Shaoting Du
In China, heavy metal (HM) contamination of farmland soil is severe. However, the differential effects of herbicides, particularly their chiral configurations, on the bioavailability of soil HMs and their underlying mechanisms remain unclear. Therefore, in this study, we applied different configurations of the typical herbicide Napropamide (NAP) to various types of soils contaminated with composite HMs, including cadmium (Cd), nickel (Ni), lead (Pb), and zinc (Zn), to demonstrate enantiomeric differences in the influence of herbicide isomers on HM bioavailability. Interestingly, we noticed notable enantiomeric variations in the dissolved organic carbon (DOC) levels within these systems. These differences vanished once the systems underwent γ-irradiation sterilization. This suggests a deep-rooted connection between DOC and HMs, facilitated by soil carbon (C)-related bacterial functional groups such as cellulolysis, aromatic compound degradation, and chitinolysis. These functional groups, which are influenced by NAP, play a role in differentially regulating the availability of soil HMs. When NAP isomers coexisted, the soil DOC content increased, as did iron reducing bacteria, leading to the formation of iron (Fe) oxides. The Mantel test results suggested that the DOC-driven C-Fe coupling was a crucial factor in the impact of NAP on soil HM bioavailability. The enantiomeric differences in soil Zn and Ni bioavailability induced by R- and S-NAP were associated with variations in the complexity of soil C- and Fe-related bacterial networks and key species such as Mesorhizobium silamurunense. This study is the first to reveal the underlying mechanism by which herbicide isomers affect soil HMs from a microbially-driven C-Fe coupling perspective, providing a more comprehensive theoretical basis for the scientific application of herbicides and the mitigation of soil HM contamination.
{"title":"Bacterially mediated carbon-iron coupling drives differential effects of herbicide enantiomers on soil heavy metal bioavailability","authors":"Ran Wu, Hua Wang, Hanche Xia, Haoyi Zheng, Yaxin Zhu, Lijuan Liu, Shaoting Du","doi":"10.1016/j.soilbio.2024.109674","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109674","url":null,"abstract":"In China, heavy metal (HM) contamination of farmland soil is severe. However, the differential effects of herbicides, particularly their chiral configurations, on the bioavailability of soil HMs and their underlying mechanisms remain unclear. Therefore, in this study, we applied different configurations of the typical herbicide Napropamide (NAP) to various types of soils contaminated with composite HMs, including cadmium (Cd), nickel (Ni), lead (Pb), and zinc (Zn), to demonstrate enantiomeric differences in the influence of herbicide isomers on HM bioavailability. Interestingly, we noticed notable enantiomeric variations in the dissolved organic carbon (DOC) levels within these systems. These differences vanished once the systems underwent γ-irradiation sterilization. This suggests a deep-rooted connection between DOC and HMs, facilitated by soil carbon (C)-related bacterial functional groups such as cellulolysis, aromatic compound degradation, and chitinolysis. These functional groups, which are influenced by NAP, play a role in differentially regulating the availability of soil HMs. When NAP isomers coexisted, the soil DOC content increased, as did iron reducing bacteria, leading to the formation of iron (Fe) oxides. The Mantel test results suggested that the DOC-driven C-Fe coupling was a crucial factor in the impact of NAP on soil HM bioavailability. The enantiomeric differences in soil Zn and Ni bioavailability induced by <em>R</em>- and <em>S</em>-NAP were associated with variations in the complexity of soil C- and Fe-related bacterial networks and key species such as <em>Mesorhizobium silamurunense</em>. This study is the first to reveal the underlying mechanism by which herbicide isomers affect soil HMs from a microbially-driven C-Fe coupling perspective, providing a more comprehensive theoretical basis for the scientific application of herbicides and the mitigation of soil HM contamination.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"117 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142776514","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 : 2024-12-02DOI: 10.1016/j.soilbio.2024.109652
Shiting Li, Maokui Lyu, Cui Deng, Wei Deng, Xiaohong Wang, Anne Cao, Yongmeng Jiang, Jueling Liu, Yuming Lu, Jinsheng Xie
The authors regret to inform that there were errors in the originally published article. The corrections are as follows:
1.On page 2, the geographical coordinates were incorrectly formatted as "25°38 ′25 ′N, 116° 25′29′E". The correct formatting should be "25°38′25″N, 116°25′29″E".
2.On page 4, there is an error in Eqn (7). The correct equation should be: 13C-PLFA = [(13Catom%)PLFA, treatment - (13Catom%)PLFA, control]/100 × PLFA
{"title":"Corrigendum to “Input of high-quality litter reduces soil carbon losses due to priming in a subtropical pine forest” [Soil Biology and Biochemistry 194 (2024) 109444]","authors":"Shiting Li, Maokui Lyu, Cui Deng, Wei Deng, Xiaohong Wang, Anne Cao, Yongmeng Jiang, Jueling Liu, Yuming Lu, Jinsheng Xie","doi":"10.1016/j.soilbio.2024.109652","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109652","url":null,"abstract":"The authors regret to inform that there were errors in the originally published article. The corrections are as follows:<ul><li><span>1.</span><span>On page 2, the geographical coordinates were incorrectly formatted as \"25°38 ′25 ′N, 116° 25′29′E\". The correct formatting should be \"25°38′25″N, 116°25′29″E\".</span></li><li><span>2.</span><span>On page 4, there is an error in Eqn (7). The correct equation should be: <sup>13</sup>C-PLFA = [(<sup>13</sup>Catom%)<sub>PLFA, treatment</sub> - (<sup>13</sup>Catom%)<sub>PLFA, control</sub>]/100 × PLFA</span></li></ul>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"22 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758588","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}
Storing soils at low temperatures, a common practice in microbial research, substantially impacts microbial community composition and microbial-mediated processes, leading to potential inaccuracies in conclusions. However, there is a dearth of guidance on the best practices for storing soil microbiomes, especially in regard to preserving microbial viability for future use. Here, we stored samples of four types of soil at 4 °C and -20 °C for durations of 0, 5, 40, and 210 days. For soils stored at -20 °C, we adopted two thawing methods: direct thawing at room temperature and gentle thawing at 4 °C. We investigated trends and influencing factors of microbial viability during storage and variations in microbial-mediated respiration during incubation. Our findings revealed that microbial viability was more robust at 4 ºC compared to -20 ºC, and wetland soils were not conducive to the maintenance of microbial viability during storage. For soils stored at -20 ºC, gentle thawing at 4 ºC for 3 days resulted in maximum cells viability, and was 26.2% higher than direct thawing at room temperature. In addition, the days of incubation required for respiration rates and cumulative respiration to re-equilibrate are strongly dependent on soil types. Overall, this study provides empirical evidence to guide the development of optimal soil storage and pre-incubation practices tailored to preserve living soil microorganisms' purposes and ensure accurate respiration measurements.
{"title":"Temperature-dependent soil storage: changes in microbial viability and respiration in semiarid grasslands","authors":"Chen Tian, Dongqing Cui, Yue Cao, Sheng Luo, Huimin Song, Peizhi Yang, Yongfei Bai, Jianqing Tian","doi":"10.1016/j.soilbio.2024.109673","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109673","url":null,"abstract":"Storing soils at low temperatures, a common practice in microbial research, substantially impacts microbial community composition and microbial-mediated processes, leading to potential inaccuracies in conclusions. However, there is a dearth of guidance on the best practices for storing soil microbiomes, especially in regard to preserving microbial viability for future use. Here, we stored samples of four types of soil at 4 °C and -20 °C for durations of 0, 5, 40, and 210 days. For soils stored at -20 °C, we adopted two thawing methods: direct thawing at room temperature and gentle thawing at 4 °C. We investigated trends and influencing factors of microbial viability during storage and variations in microbial-mediated respiration during incubation. Our findings revealed that microbial viability was more robust at 4 ºC compared to -20 ºC, and wetland soils were not conducive to the maintenance of microbial viability during storage. For soils stored at -20 ºC, gentle thawing at 4 ºC for 3 days resulted in maximum cells viability, and was 26.2% higher than direct thawing at room temperature. In addition, the days of incubation required for respiration rates and cumulative respiration to re-equilibrate are strongly dependent on soil types. Overall, this study provides empirical evidence to guide the development of optimal soil storage and pre-incubation practices tailored to preserve living soil microorganisms' purposes and ensure accurate respiration measurements.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"30 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760670","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}
Mineral-associated organic matter (MAOM) is an important carbon reservoir in relation to soil organic carbon sequestration over long timescales, and its saturation status is pertinent to the judicious formulation of agricultural management practices and global climate mitigation strategies. However, the existence of MAOM saturation is controversial due to the ambiguity of the MAOM concept and the variability of the underlying model. Based on this, we update and extend the concept of MAOM saturation into theoretical and apparent components, and propose the hypothesis that clay minerals, microbial communities, and input organic matter regulate the apparent saturation of MAOM. The theoretical saturation of MAOM represents the maximum sequestration potential of MAOM in natural soil ecosystems, which may require update of many current models of global carbon sequestration. In contrast, apparent saturation of MAOM capacity can be derived by comparing natural ecosystems with ecosystems subject to anthropogenic disturbances, and by monitoring single ecosystems on annual time scales over many years. Future research therefore needs to consider some new indicators and models to study MAOM saturation.
{"title":"The need to update and refine concepts relating to mineral-associated organic matter saturation in soil","authors":"Xiaojun Song, Huijun Wu, Shengping Li, Ping He, Xueping Wu","doi":"10.1016/j.soilbio.2024.109672","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109672","url":null,"abstract":"Mineral-associated organic matter (MAOM) is an important carbon reservoir in relation to soil organic carbon sequestration over long timescales, and its saturation status is pertinent to the judicious formulation of agricultural management practices and global climate mitigation strategies. However, the existence of MAOM saturation is controversial due to the ambiguity of the MAOM concept and the variability of the underlying model. Based on this, we update and extend the concept of MAOM saturation into theoretical and apparent components, and propose the hypothesis that clay minerals, microbial communities, and input organic matter regulate the apparent saturation of MAOM. The theoretical saturation of MAOM represents the maximum sequestration potential of MAOM in natural soil ecosystems, which may require update of many current models of global carbon sequestration. In contrast, apparent saturation of MAOM capacity can be derived by comparing natural ecosystems with ecosystems subject to anthropogenic disturbances, and by monitoring single ecosystems on annual time scales over many years. Future research therefore needs to consider some new indicators and models to study MAOM saturation.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"260 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756360","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 : 2024-11-26DOI: 10.1016/j.soilbio.2024.109662
Thomas Dussarrat , Claudio Latorre , Millena C. Barros Santos , Constanza Aguado-Norese , Sylvain Prigent , Francisca P. Díaz , Dominique Rolin , Mauricio González , Caroline Müller , Rodrigo A. Gutiérrez , Pierre Pétriacq
Plants modulate their rhizochemistry, which affects soil bacterial communities and, ultimately, plant performance. Although our understanding of rhizochemistry is growing, knowledge of its responses to abiotic constraints is limited, especially in realistic ecological contexts. Here, we combined predictive metabolomics with soil metagenomics to investigate how rhizochemistry responded to environmental constraints and how it in turn shaped soil bacterial communities across stress gradients in the Atacama Desert. We found that rhizochemical adjustments predicted the environment (i.e. elevation, R2 between 96% and 74%) of two plant species, identifying rhizochemical markers for plant resilience to harsh edaphic conditions. These metabolites (e.g. glutamic and succinic acid, catechins) were consistent across years and could predict the elevation of two independent plant species, suggesting biochemical convergence. Next, convergent patterns in the dynamics of bacterial communities were also observed across the elevation gradient. Finally, rhizosphere predictors were associated with variation in composition and abundance of bacterial species. Biochemical markers and convergences as well as potential roles of associated predictive bacterial families reflected the requirements for plant life under extreme conditions. This included biological processes such as nitrogen and water starvation (e.g. glutamic and organic acids, Bradyrhizobiaceae), metal pollution (e.g. Caulobacteraceae) and plant development and defence (e.g. flavonoids, lipids, Chitinophagaceae). Overall, findings highlighted convergent patterns belowground, which represent exciting insights in the context of evolutionary biology, and may indicate unique metabolic sets also relevant for crop engineering and soil quality diagnostics. Besides, the results emphasise the need to integrate ecology with omics approaches to explore plant-soil interactions and better predict their responses to climate change.
{"title":"Rhizochemistry and soil bacterial community are tailored to natural stress gradients","authors":"Thomas Dussarrat , Claudio Latorre , Millena C. Barros Santos , Constanza Aguado-Norese , Sylvain Prigent , Francisca P. Díaz , Dominique Rolin , Mauricio González , Caroline Müller , Rodrigo A. Gutiérrez , Pierre Pétriacq","doi":"10.1016/j.soilbio.2024.109662","DOIUrl":"10.1016/j.soilbio.2024.109662","url":null,"abstract":"<div><div>Plants modulate their rhizochemistry, which affects soil bacterial communities and, ultimately, plant performance. Although our understanding of rhizochemistry is growing, knowledge of its responses to abiotic constraints is limited, especially in realistic ecological contexts. Here, we combined predictive metabolomics with soil metagenomics to investigate how rhizochemistry responded to environmental constraints and how it in turn shaped soil bacterial communities across stress gradients in the Atacama Desert. We found that rhizochemical adjustments predicted the environment (<em>i.e.</em> elevation, R<sup>2</sup> between 96% and 74%) of two plant species, identifying rhizochemical markers for plant resilience to harsh edaphic conditions. These metabolites (<em>e.g.</em> glutamic and succinic acid, catechins) were consistent across years and could predict the elevation of two independent plant species, suggesting biochemical convergence. Next, convergent patterns in the dynamics of bacterial communities were also observed across the elevation gradient. Finally, rhizosphere predictors were associated with variation in composition and abundance of bacterial species. Biochemical markers and convergences as well as potential roles of associated predictive bacterial families reflected the requirements for plant life under extreme conditions. This included biological processes such as nitrogen and water starvation (<em>e.g.</em> glutamic and organic acids, Bradyrhizobiaceae), metal pollution (<em>e.g.</em> Caulobacteraceae) and plant development and defence (<em>e.g.</em> flavonoids, lipids, Chitinophagaceae). Overall, findings highlighted convergent patterns belowground, which represent exciting insights in the context of evolutionary biology, and may indicate unique metabolic sets also relevant for crop engineering and soil quality diagnostics. Besides, the results emphasise the need to integrate ecology with omics approaches to explore plant-soil interactions and better predict their responses to climate change.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"202 ","pages":"Article 109662"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Soil organic matter (SOM) is partitioned among structurally and functionally distinct pools. Information on these different SOM fractions in mangrove environments are emerging and the three-pool classification of SOM into particulate organic matter (POM), mineral-associated organic matter (MAOM) and dissolved organic matter (DOM) has become the operational framework of most mangrove studies. The differences in degree of protection provided by physical and chemical mechanisms against microbial decomposition of these fractions lay a strong foundation for empirical SOM studies in mangroves. In this review, we discuss the formation and transformation pathways and stabilization mechanisms of these SOM fractions in mangroves under different environmental conditions. We also show that further studies on lesser-known forms of SOM such as FeS-MAOM, pyrite-MAOM, and Al-MAOM could set a path better understanding long-term stabilization of mangrove SOM. The binding capacity of sediments with DOM points to a hidden potential of mangroves to store soil carbon, which is not accounted in traditional sediment and carbon accumulation models. In addition, incorporating the feedback from SOM fractions to different physiochemical and climatic conditions can improve carbon dynamic projections in mangrove ecosystems using carbon models.
土壤有机质（SOM）在结构上和功能上分为不同的池。有关红树林环境中这些不同 SOM 部分的信息不断涌现，SOM 的三池分类法已成为大多数红树林研究的操作框架，即颗粒有机物（POM）、矿物相关有机物（MAOM）和溶解有机物（DOM）。物理和化学机制对这些部分微生物分解提供的保护程度不同，这为红树林 SOM 的实证研究奠定了坚实的基础。在本综述中，我们讨论了不同环境条件下红树林中这些 SOM 部分的形成和转化途径以及稳定机制。我们还表明，进一步研究鲜为人知的 SOM 形式，如 FeS-MAOM、黄铁矿-MAOM 和 Al-MAOM，可以更好地了解红树林 SOM 的长期稳定机制。沉积物与 DOM 的结合能力表明，红树林具有储存土壤碳的隐藏潜力，而传统的沉积物和碳累积模型并未考虑到这一点。此外，将 SOM 部分对不同物理化学和气候条件的反馈纳入碳模型，可以改善红树林生态系统的碳动态预测。
{"title":"A review of properties of organic matter fractions in soils of mangrove wetlands: Implications for carbon storage","authors":"Pestheruwe Liyanaralalage Iroshaka Gregory Marcelus Cooray , Gareth Chalmers , David Chittleborough","doi":"10.1016/j.soilbio.2024.109660","DOIUrl":"10.1016/j.soilbio.2024.109660","url":null,"abstract":"<div><div>Soil organic matter (SOM) is partitioned among structurally and functionally distinct pools. Information on these different SOM fractions in mangrove environments are emerging and the three-pool classification of SOM into particulate organic matter (POM), mineral-associated organic matter (MAOM) and dissolved organic matter (DOM) has become the operational framework of most mangrove studies. The differences in degree of protection provided by physical and chemical mechanisms against microbial decomposition of these fractions lay a strong foundation for empirical SOM studies in mangroves. In this review, we discuss the formation and transformation pathways and stabilization mechanisms of these SOM fractions in mangroves under different environmental conditions. We also show that further studies on lesser-known forms of SOM such as FeS-MAOM, pyrite-MAOM, and Al-MAOM could set a path better understanding long-term stabilization of mangrove SOM. The binding capacity of sediments with DOM points to a hidden potential of mangroves to store soil carbon, which is not accounted in traditional sediment and carbon accumulation models. In addition, incorporating the feedback from SOM fractions to different physiochemical and climatic conditions can improve carbon dynamic projections in mangrove ecosystems using carbon models.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"201 ","pages":"Article 109660"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-26DOI: 10.1016/j.soilbio.2024.109656
Minghui Liu, Hanyang Lin, Junmin Li
Microbial carbon (C) use efficiency (CUE) is a comprehensive parameter to measure the accumulation and loss of soil C caused by microbial growth and respiration, which is considered to determine the fate of soil organic C (SOC). Microbial CUE is sensitive to the changes in soil nutrients, such as nitrogen (N) and phosphorus, making it crucial to assess the response of microbial CUE to nutrient inputs caused by climate change and human activities, as well as its contribution to SOC accumulation. Here, we curated a dataset from 58 studies (389 paired observations) to examine the effects of nutrient inputs on global soil microbial CUE and the relationship between microbial CUE and SOC. The meta-analysis showed that nutrient inputs increased soil microbial CUE by 11.5%. The response of microbial CUE to nutrient inputs varied among different treatments (i.e., nutrient form, application rates in N, and experiment duration), ecosystems, and climatic factors. The variable response of microbial CUE to nutrient inputs was mainly affected by the changes of soil N availability and C-, N-related hydrolase activity, showing significant positive and negative relationships, respectively. There was no significant statistic correlation between microbial CUE and SOC under the condition of nutrient inputs. While a significant positive correlation was observed between microbial CUE and SOC under both inorganic and short-term nutrient inputs. The present study sheds light on a comprehensive understanding of microbial CUE in the global range of nutrient inputs, and highlights the need for more studies paying more attention to the role of microbial CUE in SOC sequestration.
{"title":"Are there links between nutrient inputs and the response of microbial carbon use efficiency or soil organic carbon? A meta-analysis","authors":"Minghui Liu, Hanyang Lin, Junmin Li","doi":"10.1016/j.soilbio.2024.109656","DOIUrl":"10.1016/j.soilbio.2024.109656","url":null,"abstract":"<div><div>Microbial carbon (C) use efficiency (CUE) is a comprehensive parameter to measure the accumulation and loss of soil C caused by microbial growth and respiration, which is considered to determine the fate of soil organic C (SOC). Microbial CUE is sensitive to the changes in soil nutrients, such as nitrogen (N) and phosphorus, making it crucial to assess the response of microbial CUE to nutrient inputs caused by climate change and human activities, as well as its contribution to SOC accumulation. Here, we curated a dataset from 58 studies (389 paired observations) to examine the effects of nutrient inputs on global soil microbial CUE and the relationship between microbial CUE and SOC. The meta-analysis showed that nutrient inputs increased soil microbial CUE by 11.5%. The response of microbial CUE to nutrient inputs varied among different treatments (i.e., nutrient form, application rates in N, and experiment duration), ecosystems, and climatic factors. The variable response of microbial CUE to nutrient inputs was mainly affected by the changes of soil N availability and <em>C</em>-, <em>N</em>-related hydrolase activity, showing significant positive and negative relationships, respectively. There was no significant statistic correlation between microbial CUE and SOC under the condition of nutrient inputs. While a significant positive correlation was observed between microbial CUE and SOC under both inorganic and short-term nutrient inputs. The present study sheds light on a comprehensive understanding of microbial CUE in the global range of nutrient inputs, and highlights the need for more studies paying more attention to the role of microbial CUE in SOC sequestration.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"201 ","pages":"Article 109656"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142713012","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 : 2024-11-25DOI: 10.1016/j.soilbio.2024.109661
Yanchun Liu , Hui Wang , Andreas Schindlbacher , Shirong Liu , Yujing Yang , Huimin Tian , Lin Chen , Angang Ming , Jian Wang , Jiachen Li , Zuwei Tian
The chemical composition and degradability of soil organic matter (SOM) are among the most important factors influencing the feedback between soil CO2 emissions and climate warming. We hypothesized that the response of soil respiration to long-term warming in various forest ecosystems depends on how soil warming alters the chemical composition of SOM. Therefore, we compared the effects of long-term soil warming on soil respiration, SOM molecular structure, and bacterial and fungal diversity in two forest ecosystems in the southern subtropical and warm temperate zones of China. In the subtropical forest, soil warming did not affect soil respiration in the short term (2–3 years) but decreased it in the longer term (10 years, −10%). The decline in soil respiration was associated with an increased aliphaticity of SOM and lower O-alkyl C content, along with an increased abundance of microbial K-strategists over time. In the warm temperate forest, soil warming significantly stimulated soil respiration by 35% in the short term and 30% in the long term. The sustained positive response to warming was likely related to the increased decomposability of SOM owing to increased root C input. Our results suggest that the molecular composition of SOM is affected by warming and in turn feeds back to longer-term soil respiration responses. The different responses at the two study sites suggest considerable variation in the feedback within different forest ecosystems.
土壤有机质（SOM）的化学成分和降解性是影响土壤二氧化碳排放与气候变暖之间反馈的最重要因素之一。我们假设，在各种森林生态系统中，土壤呼吸对长期变暖的响应取决于土壤变暖如何改变 SOM 的化学组成。因此，我们比较了中国南亚热带和暖温带两个不同森林生态系统中长期土壤变暖对土壤呼吸、SOM分子结构以及细菌和真菌多样性的影响。在亚热带森林中，土壤变暖在短期内（2-3 年）不影响土壤呼吸作用，但在长期内（10 年，-10.3%）会降低土壤呼吸作用。土壤呼吸作用的下降与 SOM 脂肪族含量的增加和 O- 烷基 C 含量的减少有关，同时随着时间的推移，微生物 K-策略分子的数量也在增加。在暖温带森林中，土壤变暖显著促进了土壤呼吸作用，短期为 35.3%，长期为 29.8%。对气候变暖的持续积极反应可能与根部 C 输入量增加导致 SOM 可分解性提高有关。我们的研究结果表明，SOM 的分子组成受气候变暖的影响，进而反馈到长期的土壤呼吸反应中。两个研究地点的不同反应表明，不同森林生态系统之间的反馈存在很大差异。
{"title":"Soil respiration related to the molecular composition of soil organic matter in subtropical and temperate forests under soil warming","authors":"Yanchun Liu , Hui Wang , Andreas Schindlbacher , Shirong Liu , Yujing Yang , Huimin Tian , Lin Chen , Angang Ming , Jian Wang , Jiachen Li , Zuwei Tian","doi":"10.1016/j.soilbio.2024.109661","DOIUrl":"10.1016/j.soilbio.2024.109661","url":null,"abstract":"<div><div>The chemical composition and degradability of soil organic matter (SOM) are among the most important factors influencing the feedback between soil CO<sub>2</sub> emissions and climate warming. We hypothesized that the response of soil respiration to long-term warming in various forest ecosystems depends on how soil warming alters the chemical composition of SOM. Therefore, we compared the effects of long-term soil warming on soil respiration, SOM molecular structure, and bacterial and fungal diversity in two forest ecosystems in the southern subtropical and warm temperate zones of China. In the subtropical forest, soil warming did not affect soil respiration in the short term (2–3 years) but decreased it in the longer term (10 years, −10%). The decline in soil respiration was associated with an increased aliphaticity of SOM and lower O-alkyl C content, along with an increased abundance of microbial K-strategists over time. In the warm temperate forest, soil warming significantly stimulated soil respiration by 35% in the short term and 30% in the long term. The sustained positive response to warming was likely related to the increased decomposability of SOM owing to increased root C input. Our results suggest that the molecular composition of SOM is affected by warming and in turn feeds back to longer-term soil respiration responses. The different responses at the two study sites suggest considerable variation in the feedback within different forest ecosystems.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"201 ","pages":"Article 109661"},"PeriodicalIF":9.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696629","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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